// debugging alerts through # 2 //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeWireframeAllCheckbox() { var ckscv = ""; var ckaw = ""; var ckhv = ""; if (!sidechainsVisible) ckscv = " checked"; if (allWireframe) ckaw = " checked"; if (!hydrogensVisible) ckhv = " checked"; var allw = "
\ \ \ Hide sidechains. \ \
\ More detail: Show all non-water atoms colored by element. \ \
\ Hide hydrogens. \
"; return allw; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeSmallWaterCheckbox() { // This is called whenever the checkbox is offered. It always starts // with big water. waterIsSmall= false; var smallw = "
\ \ Smaller Water. \
"; return smallw; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeSmallLigandCheckbox() { // This is called whenever the checkbox is offered. It always starts // with big ligand. top.ligandIsSmall= false; var smalll = "
\ \ Smaller Ligands+. \
"; return smalll; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeNonStandardCheckbox() { var nsc = "
\ Show " + makeNotesLink("Non-Standard", "nsr") + " amino acids and nucleotides as: \
    "; return nsc; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHideRadios(cck, gck, ack) { var hr = "Chain†     \ Residue/Group     \ Atom \ "; return hr; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHelpPrefix(helpname) { var hp = ""; var hhp = makeHiddenHelpPrefix(helpname); var fhp = makeFoundHelpPrefix(helpname); var chp = makeContactsHelpPrefix(helpname); if ((hhp.length + fhp.length + chp.length) > 0) { hp += "
\n" + hhp; if (hhp.length > 0 && fhp.length > 0) hp += "   "; hp += fhp; if ((hhp.length + fhp.length) > 0 && chp.length > 0) hp += "   "; hp += chp; hp += "
"; } // alert("help.js #2: makeHelpPrefix():\n" + hp); return hp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHiddenHelpPrefix(helpname) { if (match(helpname, "makehidehelp")) return ""; var hhp = ""; var hiddenTot = getHiddenTot(); if (hiddenTot > 0) { hhp = "Portions Hidden (\ Re-Display..<\/a>)\ "; } return hhp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeFoundHelpPrefix(helpname) { // if (match(helpname, "precontacts")) // return ""; var fhp = ""; if (toFind != "") { var tf = toFind.replace(/ /g, " "); fhp = "Halos around: " + tf + "."; if (!match(helpname, "makefindhelp")) fhp += " (Change<\/a>)"; } return fhp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeContactsHelpPrefix(helpname) { if (!contactsShowing) return ""; if (match(helpname, "contactsshown")) return ""; var chp = "Return " + "to Contacts<\/a>"; return chp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHideHelp() { if (hideMode == "") hideMode = "c"; var cck = gck = ack = ""; var hidden; var hiddenTot = getHiddenTot(); var toHide; var lastHidden; if (hideMode == "c") { cck = " checked "; hidden = top.hiddenChains.length; toHide = "Chain"; lastHidden = top.hiddenChains[hidden - 1]; } else if (hideMode == "g") { gck = " checked "; hidden = top.hiddenGroups.length; toHide = "Residue/Group"; lastHidden = top.hiddenGroups[hidden - 1]; } else if (hideMode == "a") { ack = " checked "; hidden = top.hiddenAtoms.length; toHide = "Atom"; lastHidden = top.hiddenAtoms[hidden - 1]; } // alert("help.js #1: hidden = " + hidden); var hh = " \ \ \ \ Hide: Click on any \
" + makeHideRadios(cck, gck, ack) + "
to hide<\/b> it, or hide " + makeHideCheckboxes() + "<\/center> \ Currently hidden:" + listHidden(hiddenTot); // hc + "<\/b> Chains, " + // hg + "<\/b>† Residues/Groups, " + // ha + "<\/b>‡ Atoms.\ hh += "
These will remain hidden in all views, \ until re-displayed: \ <\/form>"; if (hidden > 0) hh += "Re-Display<\/a> \ the most recently hidden " + toHide + "<\/b>. \ "; else hh += "(No " + toHide + " hidden to re-display.)<\/font>"; if (hiddenTot > 0) hh += "
\ Re-Display Everything.<\/a> "; hh += "

\ Center Visible Chains<\/a> \       \ Center by Clicking<\/a> " + //
\ //Hide Nothing Else<\/a> \ "

\ † Ligands+ are not hidden when you hide a chain, even if they \ belong to that chain. Use the Residue/Group option, or the \ Ligands+ button to hide them. \
\ Nonstandard residues are not always hidden with the chain, \ but can be hidden as Residues. \
\ * "Protein", "DNA", or "RNA", \ as the terms are used here, exclude amino acids or nucleotides that are not \ part of a polymer chain. \ <\/small>"; //† Count of hidden Residues/Groups excludes those in entire hidden chains. \ //
\ //‡ Count of hidden Atoms excludes those in entire hidden residues/groups/chains. \ //§ squiggle return hh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHideCheckboxes() { var hp = hd = hr = hc = hh = ""; if (hideProtein) hp = " checked"; if (hideDNA) hd = " checked"; if (hideRNA) hr = " checked"; if (hideCarbohydrate) hc = " checked"; if (hideHydrogen) hh = " checked"; var cbs = " \ <\/table> \ "; return cbs; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function listHidden(hiddenTot) { var is; var curhid = ""; if (hiddenTot > 0) curhid += ""; else return("
   Nothing"); var allhid = ""; if (hideProtein) allhid += "Protein*\n"; if (hideDNA) { if (allhid.length > 0) allhid += ", \n"; allhid += "DNA*\n"; } if (hideRNA) { if (allhid.length > 0) allhid += ", \n"; allhid += "RNA*\n"; } if (hideCarbohydrate) { if (allhid.length > 0) allhid += ", \n"; allhid += "Carbohydrate " + makeNotesLink("[?]", "predef"); } if (hideHydrogen) { if (allhid.length > 0) allhid += ", \n"; allhid += "Hydrogen\n"; } if (allhid.length > 0) allhid = "
   All " + allhid; curhid += allhid; for (is = 0; is < hiddenChains.length; is++) { if (is == 0) // @@ { if (hiddenChains[0].length > 1) // unnamed Protein or Nucleic chain { curhid += "
   The Unnamed "; } else { curhid += "
   Chain" if (hiddenChains.length > 1) curhid += "s" curhid += " "; } } else curhid += ", " curhid += hiddenChains[is]; if (is == 0 && hiddenChains[0].length > 1) // unnamed Protein or Nucleic chain { if (hiddenChains[0].charAt(0) == "N") curhid += " Acid"; curhid += " Chain"; } } for (is = 0; is < hiddenGroups.length; is++) { if (is == 0) { curhid += "
   " if (hiddenGroups.length == 1) curhid += "Residue/Group "; else curhid += "Residues/Groups "; } else curhid += ", " curhid += hiddenGroups[is]; } for (is = 0; is < hiddenAtoms.length; is++) { curhid += "
  " + hiddenAtoms[is].substring( hiddenAtoms[is].indexOf(" ")); // This made a one-line list, before the element name was included // if (is == 0) // { // curhid += "
   Atom Serial" // if (hiddenAtoms.length > 1) // curhid += "s" // curhid += " "; // } // else // curhid += ", " // // curhid += "#" + hiddenAtoms[is]; } if (hiddenTot > 0) curhid += "<\/b><\/font>"; return curhid; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeHideNoMoreHelp() { // Prior to call, lastHideMode is set to hideMode, then hideMode is blanked. // In this implementation, lastHideMode is not used. // (See abandoned unnecessarly complicated idea in 0.98/obsolete/unhideh.js) var uhh = "Hiding Exited: \ Clicked atoms will be identified. \
"; if (getHiddenTot() > 0) uhh += "To re-display hidden moieties, at any time, click Re-Display.. above. \ "; else uhh += "(Nothing is hidden.)"; return uhh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeSelectRadios(cck, gck, ack, rck, fck) { var hr = "
\ Chains     \ Residues/Groups     \ Atoms \
\ Range of residues in one chain (2 clicks) \
\ or Atoms with Halos. " + makeNotesLink("FAQ", "contactsFAQ", "", "Target Selection: Frequently Asked Questions") + "<\/center> "; return hr; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makePreContactsHelp() { if (selectMode == "") { clearSelectedArrays(); selectMode = "c"; } // SET CHECKBOXES var cck = gck = ack = rck = fck = ""; if (selectMode == "c") cck = " checked "; else if (selectMode == "g") gck = " checked "; else if (selectMode == "a") ack = " checked "; else if (selectMode == "r") rck = " checked "; if (selectedFound != "") fck = " checked"; var sfck = ctck = wtck = ""; if (preContactsView == "sf") sfck = " checked"; else ctck = " checked"; if (selectedWater) wtck = " checked"; var swck = ""; if (preContactsWater) swck = " checked"; var hh = "
"; if (selectedRangeStart != "") hh += "Range starts at " + selectedRangeStart.replace(/:/, " in chain ") + "
Click on End of range, or " + "Cancel" + "
"; hh += "View: \ Spacefill   or   \ Cartoon \
\ \ Select Targets for Contacts: \ \
\ Whose contacts do you want to see? \ Click on the molecule to select, as the target, one or more:
" + makeSelectRadios(cck, gck, ack, rck, fck) + "then
\ Show \ Atoms Contacting Target. \
\
Click again to deselect. \
Hide.. or Find.. (above) \ can be used to make target selection easier. \
Show Water. \     \ Target All Water."; //What you select will be decorated with only the atoms within \ //
\ //  \ //3.5 Å (out to weak hydrogen bonds) \ //
\ //  \ //4.0 Å (out to weak salt bridges) \ //
\ //  \ //4.5 Å (out to weak van der Waals interactions) \ //
\ //  \ //7 Å (out to weak cation-pi interactions) \ hh += "

\ Currently selected: \
" + listSelected() + "
Start Over (Deselect All) \ \ <\/form>"; if (preContactsView == "sf") hh += "In this view, all atoms are spacefilling."; hh += "Protein and nucleic acid \ chains are each given a distinct pastel color, while \ Ligands+ \ and \ Water are colored \ as in Composition. \ "; if (preContactsView != "sf") hh += "For further description of this cartoon view, click on \ Cartoon (top panel above)."; return hh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeContactsShownHelp() { var ck; // STOP SELECTING selectMode = ""; // STOP HIDING hideMode = ""; var hh = " "; hh += "
Contacts Shown:
"; hh += "The target you selected, \
" + listSelected() + "
is decorated with all* contacting atoms \ (" + makeNotesLink("Definitions", "contacts", ".)"); // CHECKBOXES, CENTERING // hh += "
    "; hh += "
Protein* \ \ DNA* \ \   Hydrogen \
\ " + makeNotesLink("Carbohydrate", "predef") + "   \ \ RNA* \
"; if (!labelContacts) { ck = ""; if (markContactsTargets) ck = " checked"; hh += "
Mark target
"; } else hh += "
\ Mark target
"; ck = ""; if (backboneContacts) ck = " checked"; hh += //"
    \ " Backbones"; hh += "		     "; ck = ""; if (labelContacts) ck = " checked"; hh += //"
    \ "
Labels (" + makeNotesLink("?", "contactsLabels", ")", "Explanation of Labeling") + "
"; hh += //"
    \ "Center Contacts \ " + "

"; // VIEW RADIO BUTTONS var cktSF, cktBS, cktCHN, cktCPK; var ckcSF, ckcBS, ckcCHN, ckcCPK; cktSF = cktBS = cktCHN = cktCPK = ""; ckcSF = ckcBS = ckcCHN = ckcCPK = ""; ck = " checked"; if (targetSF) cktSF = ck; else cktBS = ck; if (targetCPK) cktCPK = ck; else cktCHN = ck; if (contactingSF) ckcSF = ck; else ckcBS = ck; if (contactingCPK) ckcCPK = ck; else ckcCHN = ck; var dag, Dag; dag = Dag = ""; // if (targetCPK || contactingCPK) // Dag = "‡"; // if (!targetCPK || !contactingCPK) // CHAIN // dag = "†"; var starstar = ""; // if (!targetSF || !contactingSF) // starstar = "**"; // BEGIN SNAPSHOTS TABLE if (!contactsRadioViews) hh += "
\
Contacts Views† -- Click Snapshots:
\
\ \   \ \   \ \   \ \ \
"; // END SNAPSHOTS TABLE // BEGIN RADIO BUTTONS TABLE else hh += "
\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \
\ View 1§ \
\ View 2 \
\ View 3 \
\ View 4 \ 		  Target  Contacts  View†
\ \
\ \
Spacefilled
\ \
\ \
Balls" + starstar + " & Sticks
\ \
\ \
Colored by Chain" + dag + "
\ \
\ \
Colored by Element" + Dag + "
"; // END RADIO BUTTONS TABLE ck = ""; if (contactsRadioViews) ck = " checked"; hh += "
\ Distances: " + makeNotesLink("How?", "distances", "", "How to Measure Distances and Angles") + "  \ Hide. \     \ More views. \
\   \ Uncheck / \ Check \ all.
\ "; // SHOW WATER BRIDGES var watcol = "#" + colorSolvent; if (contactingCPK) watcol = "magenta"; ck = ""; if (showWaterBridges) ck = " checked"; hh += " Show putative " + makeNotesLink("water bridges", "waterbridges", "") + " (target to non-target).
"; // SHOW WATER ck = ""; if (showContactsWater) ck = " checked"; hh += " Show \ water \ putatively " + makeNotesLink("hydrogen bonded", "hbonds", "") + " to target.
\ "; // SHOW HBONDS ck = ""; if (showContactsHBonds) ck = " checked"; hh += " Show putatively " + makeNotesLink("hydrogen bonded", "hbonds", "") + " non-water.
\ "; // SHOW HYDROPHOBIC ck = ""; if (showContactsHphob) ck = " checked"; hh += " Show " + makeNotesLink("hydrophobic (apolar van der Waals)", "hphob") + " interactions.
\ "; // SHOW SALT BRIDGES ck = ""; if (showContactsSB) ck = " checked"; hh += " Show putative " + makeNotesLink("salt bridges", "saltbr", ".") + "
\ "; // SHOW CATION PI ck = ""; if (showContactsCatPi) ck = " checked"; hh += " Show possible " + makeNotesLink("cation-pi", "catpi", "") + " interactions.
\ "; // SHOW METALS & MISC ck = ""; if (showContactsMeMi) ck = " checked"; hh += " Show possible " + makeNotesLink("metal and misc", "memi", ".") + " bonds.
\ "; //- - - - - - - - - - - - - - - // SHOW STICKS? if (!contactingSF) // need to make form reading, or use hidden input? { ck = ""; if (showContactsSticks) ck = " checked"; hh += "    Show sticks.
\ "; } // HYDROGENS ck = ""; if (hydrogensContacts) ck = " checked"; hh += "    Show " + makeNotesLink("hydrogens (if present in model)", "hydrogen", "."); // NOTES hh += "
    \
  • Find.. or Hide.. \ (above) can be used on the Contacts display. \
  • Any other view clears the contacts display. \
\ "; // "ALL" CONTACTING ATOMS hh += "*All contacting atoms in the model are shown, regardless of whether they were \ hidden during target selection. NOT SHOWN, however, are \ crystal contacts\ ."; // PRESET VIEWS if (contactsRadioViews) hh += "
§ Views 1-4 are the most useful of the 16 possible \ settings of the radio buttons." hh += "
†"; // BALLS if (!targetSF || !contactingSF) { hh += //"
** \ "
Small balls signify atoms likely noncovalently-bonded \ to the target (" + makeNotesLink("Definitions", "contacts", ").") + " Slightly larger and darker balls are target atoms likely \ non-covalently bonded to the target-contacting atoms.\n"; if (showContactsSticks) hh += "Optionally, residues containing balls are shown as sticks, \ solely for context.\n"; hh += "
Use Center Atom.., Zoom and \ Slab (above) to see details with less clutter. "; } // CHAIN COLORS if (!targetCPK || !contactingCPK) hh += //"
† "
Colors: \ Protein and nucleic acid chains are each given a distinct \ pastel color. \ Ligands+ \ and \ Water are colored \ as in Composition."; // ELEMENT COLORS if (targetCPK || contactingCPK) hh += //"
‡ \ "
Colors:\ Atoms are colored by element, except that \ water oxygens are colored magenta. \ Target atom colors are darker. " + colorByElement; hh += "<\/form>"; return hh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function listSelected() { var is; var cursel = ""; for (is = 0; is < selectedChains.length; is++) { if (cursel.length > 0) cursel += "
" if (selectedChains[is].length > 1) { if (selectedChains[is] == "Protein") cursel += "  The Unnamed Protein Chain"; else cursel += "  The Unnamed Nucleic Acid Chain"; } else cursel += "  Chain " + selectedChains[is]; } for (is = 0; is < selectedGroups.length; is++) { if (cursel.length > 0) cursel += "
" cursel += "  Residue/Group " + selectedGroups[is]; } for (is = 0; is < selectedAtoms.length; is++) { if (cursel.length > 0) cursel += "
" cursel += "  " + selectedAtoms[is].substring(selectedAtoms[is].indexOf(" ")); } if (selectedFound != "") { if (cursel.length > 0) cursel += "
" cursel += "  Halos: " + selectedFound; } for (is = 0; is < selectedRanges.length; is++) { if (cursel.length > 0) cursel += "
" cursel += "  " + "Range: " + selectedRanges[is]; } if (selectedWater) { if (cursel.length > 0) cursel += "
" cursel += "  All Water"; } if (cursel.length == 0) cursel = "  Nothing"; else cursel = "" + cursel + ""; return cursel; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeFindHelp() // mfh { var pfh = " \ Find: \ \ Clear Halos \
\
\ \ \ See All Halos Easily \     \ Undo \

\ In the slot above, enter one or more (separated by commas): \
    \
  • " + makeNotesLink("Sequence", "seq", "") + " number(s) (such as 10,51). \
  • Range of " + makeNotesLink("sequence", "seq", "") + " numbers (such as 18-23). \
  • Amino acid " + makeNotesLink("3-letter names", "aanames", "") + " (such as PRO,HIS). \
  • Nucleotide 1-letter names (A,C,G,T,U). \
  • Name-sequence combinations (SER41, C9). \
  • To restrict one of the above to a specific \ chain, add colon plus the chain letter \ (such as 41:A, C9:D). \
  • Full name(s) of elements (zinc, selenium). \
  • " + makeNotesLink("Advanced uses", "advancedFind", ".") + "
\ After pressing Enter, yellow dot-halos will appear \ around the atoms in the residues listed in the slot above (even if \ the atoms themselves are not visible). \ If no halos appear, either the listed residues don't exist \ in this molecule, or your list is not formatted correctly \ following the above examples. \

\ The halos will remain present in all views until you click Clear Halos \ or Reset above. \ \ "; return pfh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeBePatientHelp() { var bph = "
\
FirstGlance in Jmol
\ Please Be Patient! It may take several minutes \ for the Jmol applet to arrive the first time you use \ FirstGlance in Jmol. Subsequent sessions will \ show the molecule much faster. \ (Please don't reload/refresh* until you see the molecule.) \ "; if (top.usingSignedApplet) bph += "
If you did not trust the signed Jmol applet, \ close this window because the molecule will never appear. \ "; bph += "
\ Please click the button above to go to the Introduction. \

" + makeProteopediaTeaser() + "\

\ (Large molecules or multiple-model NMR data may need \ extra time to arrive.) \
\ *Reloading/refreshing before you see the molecule sometimes prevents the \ molecule from ever appearing. To fix this, just close/quit \ your browser, and restart it. \
\ "; return bph; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var noClick = ""; /* " (Currently, this does not work for nucleic acids with the \ Cartoon or Secondary Structure displays, but works with the \ N->C Rainbow display or on nucleotide bases as Vines. \ A future version will fix this.) <\/small>"; */ //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var macHover = "(On Macintosh OSX, click on blank background near the molecule \ first.)"; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var identifySubhelp = "Identify any atom by clicking on it. Its identity will be \ displayed to the lower left of the molecule (and in the browser status bar). " + makeNotesLink("More..", "ident", "") + " If you don't recognize the abbreviation, click on the PDB \ icon above, and there, the Biology & Chemistry tab, and look under \ Ligands and Prosthetic Groups; or click the \ OCA icon above, and look under ligand. \ "; //After about two seconds of touching an atom, a message will appear its //identity will be displayed. This works best \ //with spinning toggled off. \ //" + macHover; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var inspectSubhelp = "

Click the Slab button (above) for instructions on how to \ zoom in and see a region of interest, without clutter."; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var addHeteroSubhelp = "Clicking the Ligands+ or Water buttons adds \ these components to the display, if they are not already visible,\ or hides them if they are."; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var hideHeteroSubhelp = "

Clicking the Ligands+ or Water buttons hides \ these components."; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var drumsSubhelp = "

This color scheme is adapted from the \ \ Drums Standardized \ Color Schemes for Macromolecules. \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var colorByElement = "
\
\ \ " + coloredElements + " \
\ (more elements..) \
\ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeSlabHelp() { var ck10 = ck6 = ck3 = ""; if (slabThickness == "10") ck10 = " checked"; else if (slabThickness == "6") ck6 = " checked"; else if (slabThickness == "3") ck3 = " checked"; var slh = "
" + //
\ //
Molecule disappeared?   \ // Fix!  " + //  (" + // + makeNotesLink("More..", "zoombugs", ")") + //
\ "Slab \ mode hides the front and rear of the \ molecule, leaving visible only a thin central slab, \ parallel to the screen. \ This is best appreciated when spinning is toggled off. \
\ Slab thickness: \ 10% \   \ 6% \   \ 3% \
\ \
\ With slab mode off (so you can see the entire molecule), \ use Center Atom.. (above) to center a region \ of interest. " + noClick + "Centering ensures that the region \ of interest will be visible after you turn slab mode on. Next, Zooming \ in may help see details, and also pushes more of the front and back \ out of the visible slab zone, producing a less obstructed view of the \ centered moiety. \ \

Click Center Atom.. (above) to re-center the entire molecule, and \ click Slab again to toggle slab mode off.

\ "; // + identifySubhelp; NOT IN SLAB! return slh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeWaterHelp() { var wath = "Water \ oxygens are displayed as \ \ red spheres of van der Waals radii, \ as shown at left. \ \ (If the Water button does not show any red \ spheres, no water was included in the model.) \ \ " + makeSmallWaterCheckbox() + " \ \ Typically, only 10-20% of the water in protein crystals is tightly-enough \ bound to be resolved, so 80-90% of the water present is invisible \ (due to disorder). \ \

\ \ Hydrogen atoms are not resolved in most \ protein crystallographic results, \ so often the water oxygens lack hydrogens. When hydrogen atoms are \ modeled, they appear as two white atoms \ attached to the red water oxygens, as shown at left. \ "; return wath; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeLigandsHelp() { var ligh = "Ligands+ \ displays the "ligands+" subset of atoms as spheres of van der Waals \ radii, colored by element: " + colorByElement + ""Ligands+" includes all components of the model that are not \ water, and not " + makeNotesLink("chains", "lig", "") + " of protein, DNA, or RNA. \ Thus, it includes substrate or inhibitors, prosthetic groups such as \ heme, cofactors such as NAD, \ carbohydrate, metal ions, \ and so forth, \ regardless of whether these are covalently \ or non-covalently bound to the protein or nucleic acid chains. \ It also includes isolated standard amino acids or nucleotides \ that are not members of a " + makeNotesLink("standard protein or nucleic acid chain", "lig", "") + " (Caution: Rare ligands may fail to be displayed, but will be displayed \ when you check non-standard residues below. " + makeNotesLink("More..", "lig", ")") + "

\ Clicking Ligands+ a second time hides the ligands+. " + makeSmallLigandCheckbox() + makeNonStandardCheckbox() + identifySubhelp; return ligh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var centerAtomHelp = " \ \ \ Center Atom (or Entire Molecule) \ \
\ Click on any atom \ to center it. \
\ Mac OSX Firefox: two clicks may be needed. See " + makeNotesLink("Notes", "macff", ".") + "

" + // \ //2. Centering mode remains on until you \ //
\ // \ //Turn Off or Cancel Centering. \ // \ //
\ //
\ "At any time, you may
\ Re-Center the \ Entire Molecule
. \ " + inspectSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var centeringCancelledHelp = "Centering Exited. \ \

\ At any time, you may \ Re-Center the Entire Molecule. \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var centerAllHelp = "Center All \ centers the entire molecule. This is useful after you have clicked \ on the molecule, which centers the clicked atom. \ \

\ To inspect details in a region of interest, click on an atom \ in the region to center that region, Then zoom in. Turning on \ Slab will hide portions of the molecule distant from the \ centered region, simplifying the view. \ \

\ When finished, click Center All and zoom out if you wish to restore \ an overview of the entire molecule. \ \

\ \ Protein Explorer (see link above) can be used to capture any view of a \ molecule in a slide with a rotating molecular view, called a MolSlide. \ Please see MolSlides.Org for \ examples and details. \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var allModelsHelp = "All Models \ enables you to see whether there is more than one model. \ It displays a very thin backbone trace for each model. \ In most cases, you will see the chain(s) for a single model. \ Sometimes, however, you will see multiple models -- \ and in these cases, clicking on the molecule will report \ Model=n, where n is the model number. \

\ Use the links above to PDB or OCA to find out \ the experimental method. \ About 85% of \ 3D macromolecular structure data files (PDB files) result from \ X-ray crystallography, which produces a single model. \ \ Most of the remaining data files come from solution nuclear magnetic \ resonance spectroscopy (NMR), which typically produces \ multiple models. \ An example \ (2BBN) \ is shown at left. \ In such cases, all the other options in FirstGlance \ show only the first model. \

\ In NMR results, the discrepancies between models can result either from \ thermal motion in solution, or from regionally insufficient data. \ Nothing in the published data file distinguishes these two sources \ of the discrepancies. \

\ For more information about the currently loaded data file, \ click the links above to the PDB, \ OCA, or More Views... \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeVinesHelp() { vh = "Vines: All atoms "; var closeparen = ""; if (!toggleIsDown[waterIndex] || !sidechainsVisible || !hydrogensVisible) { vh += "(except "; closeparen = ")"; } var except = ""; if (!toggleIsDown[waterIndex]) except += "water"; if (!sidechainsVisible) { if (except.length > 0) except += " and "; except += "sidechains"; } if (!hydrogensVisible) { if (except.length > 0) except += " and "; except += "hydrogen"; } if (!allWireframe) { if (except.length > 0) except += " and "; except += "backbone"; } vh += except; vh += closeparen + " are displayed as sticks (or tiny balls, if not \ covalently bonded) colored by element: " + colorByElement; if (!allWireframe) vh += "
\ Backbone atoms are hidden, except for traces connecting protein alpha carbon \ atoms or nucleic acid phosphorus atoms. The backbone for each chain is given a distinct \ pastel color. "; vh += makeWireframeAllCheckbox() + addHeteroSubhelp + "

" + identifySubhelp + inspectSubhelp; return vh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var zoomHelp = "Zoom \

\ In addition to using the zoom-arrow buttons above, \ here are other ways to zoom: \
    \
  • Click on the background of the molecular rectangle, then use \ the wheel on your mouse. \
  • Hold down the Shift key, then drag up or down on the molecule. \
\ Fit molecule to window. \     \ Center entire molecule. \
\ "; //Zooming too large (close to the maximum) may distort the \ //molecule. " + //(More..). \ //"Zoom a bit smaller to correct these distortions. \ //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var chargeHelp = "Charge: \ Amino acids are colored \
    \
  • Hydrophobic \
  • Polar, uncharged \
  • Cationic + \
  • Anionic - \
  • Backbone atoms \ <\/big> (charged or uncharged) <\/ul> \ Nucleic acid is shown as \ Cartoons \ with each chain given a different color. \ Ligand and solvent are initially hidden. \

    " + addHeteroSubhelp + "

    " + identifySubhelp + drumsSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var polarityHelp = "Hydrophobic/Polar: \ Amino acids are colored either \
      \
    • Hydrophobic or \
    • Polar \ <\/big><\/big> (charged or uncharged) <\/ul> \ Nucleic acid is shown as \ Cartoons \ with each chain given a different color. \ Ligand and solvent are initially hidden. \

      " + addHeteroSubhelp + "

      " + identifySubhelp + drumsSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - // Before the black table, //
        \ //
      • Protein \ //
      • DNA \ //
      • RNA \ //
      • "Ligand"* \ //
      • Solvent** \ //<\/big><\/ul> \ // Black table with white for zombies. //
        \ // \ // Protein \ //
        DNA \ //
        RNA \ //
        "Ligand"* \ //
        Solvent** \ //         \ //
        ?*** \ //         \ //         \ //
        \ var compositionHelp = "Composition: \ All atoms are shown as spacefilling spheres of van der Waals radii, colored \ as follows: \
          \
        • Protein \
        • DNA \
        • RNA \
        • "Ligand"* \
        • Solvent** \ <\/big><\/ul> \ \ * Here, \ "Ligand" includes everything that is not protein, \ DNA, RNA, or solvent. \ \
          \ **Solvent is water plus inorganic sulfate or phosphate ions. \           \ " + hideHeteroSubhelp + "

          " + identifySubhelp + drumsSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var rainbowHelp = "NC Rainbow \

          \ Protein and nucleic acid chains are shown as smooth backbone traces, \ with nucleic acids thicker. \ Amino (N) termini \ of proteins and \ 5' termini \ of nucleic acids are \ blue. \ Carboxy (C) termini \ of proteins and \ 3' termini \ of nucleic acids are \ red. \ Between termini, colors follow a spectral rainbow sequence. \
          \ \ \ \ \ \ \ \ \
          N, 5'      C, 3'
          \
          " + addHeteroSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var rocketHelp = "Secondary Structure \

          \ This display affects only protein chains; the previous display of non-protein \ moieties remains unchanged. \ Alpha helices \ are shown as \ "rockets". \ Beta strands \ are shown as \ planks. \ \

          \ Arroheads point towards the carboxy termini. \ \

          \ The entire protein chain is shown as a smoothed backbone trace. \ Random coils are white. \ Make the background black \ with the Background button to make the backbone trace \ easier to see. \ Turns may (or may not) be colored \ blue. \ \

          \ If secondary structure was specified by the authors of the published \ model (PDB file), secondary structure is shown accordingly. \ Otherwise, Jmol determines secondary \ structure objectively using a modified Kabsch-Sander algorithm. \ Authors who specify helices and strands often do not specify turns, \ which is why turns are often not colored blue. \

          " + addHeteroSubhelp + drumsSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var cartoonHelp = "Cartoon \

          \ Each chain is a different pastel color. \ Protein alpha helices and beta strands are shown as ribbons, with arrowheads \ pointing towards the carboxy termini. \ Random coil is shown as smoothed backbone traces. \ Nucleic acids are shown as schematic bases extending from smoothed \ backbone traces. \ This display affects only protein and nucleic acid; the previous display \ of other moieties remains unchanged.

          " + addHeteroSubhelp; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeTroubleHelp() { var trh = "Troubleshooting \

          \ Please be patient! \ The first time you use FirstGlance, it might take up to several \ minutes before the molecule appears. This time is required to transfer \ and initialize the Jmol java applet. After the first use, loading \ will be faster. \ \

          \ Please don't reload/refresh until after you see the molecule. \ Reloading prematurely may prevent the molecule from ever appearing! \ To fix this, just close (quit) your browser, and restart it. \ \

          \ If the white rectangle at right turns completely blank \ ("Jmol" disappears \ from the lower right corner), this means that the PDB file was not \ available. Often, this means that the Protein Data Bank has not released \ the data file yet. You can check this by "; if (top.validPDBId.length > 0) trh += "searching for " + top.validPDBId + " at RCSB. "; else trh += "searching for the PDB code at RCSB. "; trh += ""Status HPUB" means the entry is supposed to be released \ upon publication of the journal article describing it. \ If it was not, contact info@rcsb.org. \

          \ FirstGlance requires " + makeNotesLink("java", "java", ".") + " Some installations of Windows or \ linux may have \ no java. You can install or update free java by going to \ java.com. Updating java is always \ a good idea, especially if FirstGlance does not seem to be working \ properly. " + makeNotesLink("More..", "java", "") + "

          \ Not all browsers work well with FirstGlance. \ Recommended browsers \ are the current versions of: \
            \
          • Windows \ (get/update java from \ java.com) \ \
              \
            • Internet Explorer 6 or 7\
            • Netscape 7 or 8 \
            • Firefox 1.5 or later \
            • Mozilla \
            \ \
          • Mac OSX \ (Apple Software Upgrades include java. Keeping your \ software upgrades up to date is recommended.) \
              \
            • Safari (see important " + makeNotesLink("Notes", "safari", ")") + "
            • Firefox 1.5 (imperfect; see " + makeNotesLink("Notes", "macff", ")") + "
            \ \
          • linux \
            • Mozilla Firefox
             \
          \ \ FirstGlance in Jmol may not work properly in any browser \ not listed above. It \ does not work in these browsers: \ \
          • Netscape Communicator 4.x \
          • Konqueror \
          • Opera \
          \ "; return trh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeIntroHelp() { var introHelp = "
          Introduction<\/center> \ \ \ FirstGlance in Jmol \ is a simple, free tool for macromolecular visualization. \ The initial display is \ Cartoon \ plus \ Ligands+. " + "(Unusual moieties, when present, are " + makeNotesLink("crosses", "nsr") + "* or " + makeNotesLink("dots", "anomalous") + "†.) " + "Click on the links and buttons above to see different \ aspects of the molecular structure. \ \
            \
          • Rotate the molecule by dragging near it with the mouse. \
          • " + identifySubhelp + //"
          • Center a region of interest by clicking on it. " "
          • Center a region of interest using Center Atom above. " + noClick + "You can then inspect details by zooming in. \ Regions distant from the centered moiety can be hidden by \ toggling Slab on. (When finished, \ Center Atom offers the option to re-center the entire molecule.) \ \

            \ \
          • Click the PQS button above to visualize specific oligomers or \ single molecules. \ \
          • Click More Views.. above \ for advanced techniques, and views that go beyond those offered above. \ \
          • For more information about the molecule (name, species, \ sequence, etc.), click on the PDB or OCA links above. \ \

            \ \
          • For a quick tour of what FirstGlance can do, \ visit the Snapshot Gallery. \ \
          • Snapshots of your work can easily be \ pasted \ into a Powerpoint presentation. \ \
          • About FirstGlance in Jmol \ has instructions on setting up links to display molecules, \ troubleshooting, copyright, acknowledgements, version history, and more. \ \
          • " + makeProteopediaTeaser() + "\
          \ * Crosses represent " + makeNotesLink("non-standard residues", "nsr") + ". To hide or highlight them, click on More Views in \ the upper left panel. \
          \ † Dots represent " + makeNotesLink("anomalous atoms", "anomalous") + ". To hide or highlight them, click on More Views in \ "; return introHelp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeMoreViewsHelp() { var ack = ucck = bbck = aack = aadots = aass = ""; if (axesOn) ack = "checked "; if (unitcellOn) ucck = "checked "; if (boundboxOn) bbck = "checked "; if (showAnomalous) aack = " checked"; if (anomalousDots) aadots = " checked"; else aass = " checked"; var moreHelp = "
          More Views<\/b><\/center> \ \
            \
          • " + makeNonStandardCheckbox() + "
          • Show \ All Protein Cation-Pi Interactions \ and Salt Bridges throughout the molecule. " + "
          • \ Show " + makeNotesLink("Anomalous atoms", "anomalous") + " as
            \ dots, or
            \ dots with spacefilled atoms. \
            " + "
          • " + makeNotesLink("Sequences", "seq") + " are available. \
          • To evaluate the Quality of the Molecular Model \ (More..): \
              \
            • Color \ by Uncertainty \ ("temperature", "disorder", "B factor"). \ More.. \ \
            • All-Atom Contact Analysis \ with the MolProbity Server \ (More..) corrects \ ASN, GLN and HIS rotamers, detects atomic clashes and compares the overall \ "clash score" with those for similar-resolution models, \ performs Ramachandran analysis, and more. \ \
              • <\/ul> \
            • You can " + makeNotesLink("measure distances or angles", "distances", "") + " between atoms. " + //click \ //"Jmol" \ //(to lower right of molecule) \ //and on the menu that pops up, select About Jmol, Mouse Manual. \ "
              \ Hide distances and angles. \

              \ \
              • \
            • Show Atomic Coordinate Axes. \
            • Show Crystallographic Unit Cell. \   (Shows nothing for NMR models.) \
            • Show Bound Box. \
              • \ \
            • Jmol's extensive menu \ (click "Jmol" to the lower right of the molecule) \ enables you to select subsets of atoms, then apply custom \ displays or colors, and much more. \ \
            • Jmol has a \ powerful \ command language. To send commands to the Jmol applet (in \ FirstGlance), \ click Jmol (to lower right of molecule) \ and on the menu that pops up, select Console, Open. \ \
            "; moreHelp += "For more depth than FirstGlance offers, use the links above \ to PDB or OCA, \ or try out the resources linked below. \ \ \ \ Click About \ FirstGlance in Jmol<\/a> \ for full documentation, including troubleshooting, \ linking to or installing, license and copyright, \ contributors, and versions. \ "; //
          • \ // showSptInWindow(moreHelp.replace(/\/g, ">")); return moreHelp; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var helpFooter = "

            \
            \ Copy this view and paste it into a presentation. \ \ How? \

            " + makeProteopediaTeaser() + "\

            \ Return to \ Introduction \ (atom identification, centering, related resources, \ troubleshooting, license, etc.). \ To reset to the default view, click Reset (above). \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var nohelp = "To Be Written ..."; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - var licenseHelp = "Copyright, Licenses & Acknowledgements \

            \ \ FirstGlance in Jmol is copyright © 2005, 2006 by \ Eric \ Martz. FirstGlance in Jmol is freely available, \ including its source code*. \ No restrictions are placed on its use or redistribution, except that \ all derivatives must display a prominent link to the home website \ of FirstGlance in Jmol (bioinformatics.org/firstglance) stating \ "Portions adapted from \ FirstGlance \ in Jmol". Specifically, proprietary, commercial derivatives of \ FirstGlance in Jmol are permitted provided they meet the \ above requirement. \ \

            \ \ \ Creative Commons License \ This work is licensed under a Creative Commons Attribution 2.5 License. \ \ \

            \ *Source Code is available from the project home website, \ bioinformatics.org/firstglance. \ \

            \ FirstGlance in Jmol would not be possible without the \ free, open-source java applet \ Jmol. Thanks \ are due many people who have selflessly contributed their time \ and expertise to creating Jmol. Special thanks are due Miguel \ Howard for the quality and quantity of his programming contributions \ to the Jmol project, and to \ Robert Hanson for his contributions \ to Jmol, and for creating and maintaining \ the indispensible Jmol reference manual. \ Jmol \ is licensed under the \ GNU \ "Library" or Lesser General Public License. \ Briefly, this means that Jmol is free, that its source code is openly \ available, and that all derivatives of Jmol itself (the "library") \ must also be free and have open source code. However, proprietary \ commercial products may utilize Jmol, so long as Jmol itself is unmodified, \ and is redistributed in accord with the terms of the license. \ \

            \ Special thanks to Frieda Reichsman \ (moleculesinmotion.com) \ for a large number of insightful suggestions that improved FirstGlance \ substantially. \ \

            \ Thanks to Jeff Bizzaro and \ bioinformatics.org for providing a home for this project. \ Thanks to Phil Bourne \ and the San \ Diego Supercomputer Center for providing a very fast \ server, and to Andy Sanderson for configuring it. \ \

            \ Thanks to \ Jaime Prilusky for contributing the " + makeNotesLink("CGI program", "uploads", "") + " and server that accepts an uploaded \ PDB file, and displays it in FirstGlance. Also for determining most of \ the carbohydrates present in the Protein Data Bank. Also for developing \ and maintaining the OCA browser, which provides mirror sites for \ FirstGlance in Jmol. \ \

            \ Thanks to Guoli Wang and Roland L. Dunbrack for their \ S2C \ server, linked to " + makeNotesLink("Sequence Notes", "seq") + ". Thanks to Jaime Prilusky for providing an installation of S2C \ that responds quickly, and is updated routinely. \ \

            \ Thanks, for good ideas and technical help, to Miguel Howard, Bob Hanson, \ Cris Necocea, Jaime Prilusky, \ Frieda Reichsman, Tim Driscoll, Michael Maroney, Andreas Bohne, Thomas \ Luetteke, and Joel Sussman. \ Thanks to Miguel Howard for enhancements \ to Jmol requested for the FirstGlance project. \ \

            \ Development of FirstGlance in Jmol was supported by a grant from the \ Division of Undergraduate Education of the \ US National Science Foundation \ (Award 9980909), and by the \ University of Massachusetts. \ "; //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function checkAll(result) { document.contactsForm.contactsWater.checked = result; document.contactsForm.waterBridges.checked = result; document.contactsForm.contactsHBonds.checked = result; document.contactsForm.contactsHphob.checked = result; document.contactsForm.contactsSB.checked = result; document.contactsForm.contactsCatPi.checked = result; document.contactsForm.contactsMeMi.checked = result; // if (!contactingSF) // document.contactsForm.contactsSticks.checked = result; // document.contactsForm.contactsHydrogens.checked = result; changeContactsView(); } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeCatPiSBHelp() { // STOP SELECTING selectMode = ""; // STOP HIDING hideMode = ""; var ckcp, cksb, ckcoe, ckcoc, ckbb; ckcp = cksb = ckcoe = ckcoc = ckbb = ""; var cpsb; if (showCatPi) { ckcp = " checked "; cpsb = "Cation-Pi Interactions" } else { cksb = " checked "; cpsb = "Salt Bridges" } if (colorCatPiSBChain) ckcoc = " checked"; else ckcoe = " checked"; if (showCatPiSBBackbones) ckbb = " checked"; var hh = "
            "; hh += "
            Salt Bridges / Cation-Pi Orbital Interactions
            \
            \ \ Show Protein " + makeNotesLink("Salt Bridges", "saltbr", "") + "
            \ Show Protein " + makeNotesLink("Cation-Pi Interactions", "catpi", "*") + "
            Color Protein " + cpsb + "
              by Element \ \
              by Chain \ \
            Show Backbones \ \

            \ These interactions are shown for protein chains only. FirstGlance \ does not show interactions involving ligands or nucleic acids. \

            \ *Caution: Some cation-pi interactions shown may not be \ energetically significant, while some energetically signficant \ interactions may fail to be shown. Consult \ CaPTURE \ for a definitive list. " + makeNotesLink("More..", "catpi", "."); hh += "
            "; return hh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeBadPDBFileHelp() { var bfh = 'We are sorry, but '; if (usePDBId) bfh += validPDBId; else bfh += pdbToLoad; bfh += ' is not available'; if (usePDBId) bfh += ' from the Protein Data Bank.\n\ If the PDB identification code above is correct, then most likely \n\ the atomic coordinates (PDB file) have not yet been released \n\ to the public. Often there is a delay of up to a week between publication \n\ and release of the coordinates. To find out, please \n\ check the \n\ status of ' + validPDBId + ' at the Protein Data Bank.'; else bfh += '. There may be an error in the filename or URL.' bfh += ' FirstGlance in Jmol is unable to display the molecule\n\ as specified. (You may close this window.)'; return bfh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeProteopediaTeaser() { var ppt = "\ \ Share \ custom molecular views linked to explanations \ -- with ease -- at Proteopedia.Org! \ "; return ppt; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeProteopediaHelp() { var pph = "\ \ Proteopedia.Org, \ is a \ wiki \ with easy tools for authoring and sharing customized interactive molecular scenes in \ Jmol. \ Like \ Wikipedia.Org, \ the Proteopedia wiki enables anyone to create or add to articles \ and molecular scenes. Molecular scenes (views) obtained in FirstGlance \ in Jmol can be \ saved and installed in Proteopedia. \

            \ There is an automatically-generated page for every entry in the \ PDB. \ "; if (top.validPDBId.length > 0) pph += 'See ' + top.validPDBId.toLowerCase() + ' at Proteopedia.Org.' + ' You are invited to add molecular scenes and text to this page.'; pph += "

            Green links in the text of Proteopedia articles display new molecular scenes, \ connecting them to their descriptions. \ Unlike in Wikipedia, articles in Proteopedia can be protected from editing \ by others, and are signed by the real names of their authors. Articles in \ Proteopedia can be used as supplementary materials for journal articles, \ educational tutorials, or as reference material. \ Take a look at \ Proteopedia.Org. \ "; return pph; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -