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: \ "; 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> \
\
| \ Previously hidden moieties are displayed, and vice versa. \ |
Everything else will remain hidden in all views, \ until re-displayed. To change what is displayed (and hidden), \ you must first uncheck Invert Hiding (below). \ "; hh += "
\ Center Visible Chains<\/a> \ \ Center by Clicking<\/a> \
\ 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 = "
| Protein* \ | \ DNA* \ | \ Hydrogen \ | |||||
| \ " + makeNotesLink("Carbohydrate", "predef") + " \ | \ RNA* \ |
\
Most of the remaining data files come from \
| \
// \
// Protein \
// DNA \ // RNA \ // "Ligand"* \ // Solvent** \ // \ // ?*** \ // \ // \ // |
- \
- Protein \
- DNA \
- RNA \
- "Ligand"* \
- Solvent** \ <\/big><\/ul> \ \ * Here, \ "Ligand" includes everything that is not protein, \ DNA, RNA, or solvent. \ \
- "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 citing the publication.\ \
- "No results were found matching your query" usually means \ that the PDB code above is incorrect. \
- Windows \
(get/update java from \
java.com) \
\
- \
- Internet Explorer 6 or later\
- Firefox 1.5 or later\
- Chrome 3 or later\
- Opera 10.10 (Windows only!) or later\
- Safari-Windows 4.0 or later \
- Mac OS X \
(Apple Software Upgrades include java. Keeping your \
software upgrades up to date is recommended.) \
- \
- Safari (see important " + makeNotesLink("Notes", "safari", ")") + "
- Firefox 1.5 or later (imperfect; see " + makeNotesLink("Notes", "macff", ")") + "
- linux \
- Mozilla Firefox
- Opera 10.10 for Mac OS X \
- Netscape Communicator 4.x \
- Konqueror \
- Mac PPC OS9
Classic
(any browser: current java is unavailable for OS9)\
\ **Solvent is water plus inorganic sulfate or phosphate ions. \ \ " + hideHeteroSubhelp + "
" + identifySubhelp(); // in makeCompositionHelp() comph += drumsSubhelp; return comph; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeRainbowHelp() { var bowh = "N
C 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; return bowh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeRocketHelp() { var rockh = "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; return rockh; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeCartoonHelp() { var carth = "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; return carth; } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - function makeCheckAtRCSB() { var ckrcsb = "You can check this by "; if (top.validPDBId.length > 0) ckrcsb += "searching for " + top.validPDBId + " at RCSB. "; else ckrcsb += "searching for the PDB code at RCSB."; ckrcsb += "
\ 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. "; trh += makeCheckAtRCSB(); trh += "
\ 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 \ (see browser popularity) \ are the current versions of: \
- \
| \ | Introduction | \español | \
![](nsf4c_50bt.gif "Supported by the Division of Undergraduate Education of the \
US National Science Foundation")
\
FirstGlance in Jmol \
is a simple, free tool for macromolecular visualization. \
The initial display is \
Cartoon \
plus \
Ligands+. "
+
"\
(Unusual moieties, when present, are labeled "
+ makeNotesLink("X, S-, or ?", "labels") + ".) " +
"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(); // in makeIntroHelp() introHelp += "
- 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.) \
\
\ \ - Specific oligomers or single molecules can be visualized using \ Key \ External Resources. \ \
- See Salt Bridges, Cation-Pi Interactions, evaluate model \ quality (e.g. color by Temperature), etc. by clicking on \ More Views.. above. \ \
- For more information about the molecule (name, species, \
sequence, etc.), use the \
Key \
External Resources. \
\
\ \ - Snapshots of your work can easily be \ pasted \ into a Powerpoint presentation. \ \
- For a quick tour of what FirstGlance can do, \ visit the Snapshot Gallery \ and see \ What Is FirstGlance?. \ \
- About FirstGlance in Jmol \ has instructions on setting up links to display molecules, \ troubleshooting, copyright/license, acknowledgements, version history, and \ extensive technical information. \
- \
- Show \ All Protein \ Cation-Pi Interactions \ and Salt Bridges throughout the molecule. " + "
- " + 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> \
- " + makeNonStandardCheckbox() + "
- " + "
- 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. \
\ \
- 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 type commands and send them to the Jmol applet, \ click Jmol (to lower right of molecule), \ then on the menu that pops up, select Console, Open. \ \
\ For more depth than FirstGlance offers, use the \ Key \ External Resources, \ or try out the resources linked below. \ \
- \
";
var hpdbid = getPDBId();
//------DIPOLES--------
moreHelp +=
"
- Visualize dipole moments ";
if (hpdbid.length > 0)
moreHelp +=
"of " + hpdbid.toUpperCase() + " with the \
Dipole Moment Server<\/a>.";
else
moreHelp +=
" with the Dipole Moment Server<\/a>.";
//------MOLVISINDEX--------
moreHelp +=
"
- World Index of Molecular Visualization Resources: \ MolVisIndex.Org. \ "; //------MOLVIZ-------- moreHelp += "
- MolviZ.Org \ (tutorials on DNA, \ hemoglobin, lipid bilayers, etc.; links to many molecular visualization \ resources) \ \
"; var ppl = ""; if (pdbid.length == 0) // can't get PDB ID { ppl += " "; keyHelp += ppl + "
\
Proteopedia" +
upidFull +
": \
Full name of molecule and publication abstract; full names of ligands, sites, non-standard residues; \
evolutionary conservation; custom scenes immediately online to share, \
structural terminology. \
Proteopedia is the best place to start exploring a PDB code; \
then use its \
link to FirstGlance in Jmol. \
\
" + makeNotesLink( "
\
Probable Quaternary Structure"
+ upidFull, "pqs", "")
+ ': Visualize specific oligomers, the \
functional biological unit, or monomers, \
regardless of the contents of the \
crystallographic asymmetric unit \
in the published PDB file. \
More.. \
\
'; keyHelp += ppl + "
\
Evolutionary Conservation " + upidFull +
' is available at Proteopedia. Consider doing a ConSurf run that \
limits the analysis to proteins of a single function. \
\
'; keyHelp += makeNotesLink( "
\
Missing pieces"
+ upidFull, "seq", "")
+ ': Often, parts of the protein or nucleic acid chains are disordered \
in the crystal, and are missing from the model. Find out what parts \
are missing! \
\
'; keyHelp += '
\
See atomic clashes' + upidFull +
', get the overall clash score, and flip sidechains \
into energetically more favorable positions using \
MolProbity, \
a key tool for assessing \
model quality. \
\
'; keyHelp += "" + "
\
Protein Data Bank" + upidFull +
': Get \
R \
and \
Rfree \
to assess \
model quality. \
Get details on biology & chemistry; etc. etc. \
About the PDB. \
\
' + '' + "
\
OCA Browser" + upidFull + ": \
Key information conveniently summarized on one page, with links to unique \
resources. \
";
}
return keyHelp;
}
//- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var helpFooter =
"\
\ Copy this view and paste it into a presentation. \ \ How? \
\ 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 & License \
\
\
FirstGlance in Jmol is copyright © 2005-2010 by \
Eric \
Martz. FirstGlance in Jmol is freely available, \
including its source code*. \
It may be used and redistributed for non-commercial purposes. \
Use in a commercial context, such as a link to FirstGlance in Jmol \
from the website of a for-profit scientific journal, is permitted \
provided that no payment is required for the use of FirstGlance in Jmol. \
All modified derivitives or copies must obey the same license. \
\
\
\
\
 Version " +
fgijVersion +
" of FirstGlance in Jmol by \
Eric Martz is licensed under a \
Creative \ Commons Attribution-Noncommercial-Share Alike 3.0 United States License. \ \ \ \ (Versions 1.42 and earlier used a less restrictive license.) \ |
\ *Source Code is available from the project home website, \ bioinformatics.org/firstglance. \ \
\ Acknowledgements and Credits \
\ 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. \ \
\ Thanks to Evelyn Jabri for her encouragement while at Nature Publishing \ Group. \ 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, inspiration, or technical help, \ to Miguel Howard, Bob Hanson, \ Cris Necocea, Jaime Prilusky, \ Frieda Reichsman, Tim Driscoll, Michael Maroney, Andreas Bohne, Thomas \ Luetteke, Joel Sussman, Evelyn Jabri, and Boyana Konforti. \ 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 = ""; 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. Sometimes there is a delay of a week or more between journal publication \n\ and release of the coordinates. '; bfh += makeCheckAtRCSB(); } 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/tab.)'; return (bfh); } //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - //- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -