From: SourceForge.net <no...@so...> - 2010-09-20 08:34:48
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Bugs item #3066682, was opened at 2010-09-15 10:48 Message generated for change (Comment added) made by lili35 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3066682&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Applet Group: v11 Status: Open Resolution: None Priority: 5 Private: No Submitted By: lili35 (lili35) Assigned to: Miguel (migueljmol) Summary: Bug in secondary prediction Initial Comment: Jmol seems to have a problem with some secondary structure prediction. Some amino acids represented in turn in some molecular graphic software (Pymol, Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol. You can see it in attachment. I think it is a bug. How can I fix it ? ---------------------------------------------------------------------- >Comment By: lili35 (lili35) Date: 2010-09-20 10:34 Message: Hello, I download last version available : 12.1.12 not 12.1.13. When I try 'set structure SHEET[-180, -10, 70, 180]', it don't recognize command : Script compiler ERROR: unrecognised SET parameter: : structure I also try 'set SHEET [-180, -10, 70, 180]', same error. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-19 03:09 Message: OK, this is available now on SVN. Jmol 12.1.13. It came out "set structure" not "structure set" Really we weren't intending anything too complicated here, but if you think this would be useful, that would be fine; if not, that's fine, too. Nice to have it out there and customizable anyway. -- Bob set structure HELIX|SHEET|TURN [phi-psi ranges] Ideally, PDB files will contain header information relating to helix, sheet, or turn locations. When this information is not present, or when the calculate structure command is given, Jmol uses an admittedly crude Ramachandran angle range check to determine structure type. The set STRUCTURE command allows setting those Ramachandran angle ranges for helix, sheet, and turn. [phi-psi range] is a set of angles in groups of four. Each group of four numbers includes the minimum and maximum phi values followed by the minimum and maximum psi values that would be valid for this structure type. For example, set structure HELIX [-160, 0, -100, 45] sets "helix" to be defined as phi >= -160 and phi <= 0 and psi >= -100 and psi <= 45 (the Jmol default). The default setting for sheet (really just a strand, since we are not requiring cross-strand hydrogen bonding) and turn are set SHEET [-180, -10, 70, 180, -180, -45, -180, -130, 140, 180, 90, 180]; set TURN [30, 90, -15, 95]. It is recommended that this command be followed immediately with calculate structure;cartoons only. (Jmol 12.1.13) ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-17 19:58 Message: should be "<= 80" there.... ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-17 19:57 Message: 12.1.15 -- I've added structure SHEET set [-180,-40, 50, 80, -160, -30, 60, 90] # nonsense numbers here. meaning "define SHEET to be phi>=-180 and phi <=-40 and psi >= 50 and psi < 80 OR phi >=-160 and phi <=-30 and psi >=60 and psi <= 90" similar --- structure HELIX... structure TURN.... I realize this does not solve the issue that strands are not sheets, but it is what I propose for now. Ages ago Jmol did attempt to use hydrogen bonding to identify sheets, but this was only for intra-strand sheets, which was not very satisfactory. We could still do something along those lines, but really it is so rarely the issue -- mostly we use PDB files that have all this defined already -- and the calculation is fairly involved to get all the hydrogen bonds. Bob Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-17 18:02 Message: I do hate to see you create an all new applet just for this. Why don't we make it adjustable? ---------------------------------------------------------------------- Comment By: lili35 (lili35) Date: 2010-09-17 16:42 Message: Thanks for your help. On my website, I will use Jmol to visualize hundred of models like this. So manually disable structure is not easier. I prefer reduce phi / psi angle allowed in the function 'isSheet' and create my own JmolApplet. I do this, it works but I can't build the Applet with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6). I have this error message : Buildfile: ~/Documents/workspace/Jmol/build.xml [taskdef] Could not load definitions from resource net/sf/antcontrib/antlib.xml. It could not be found. BUILD FAILED ~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml imported from ~/Documents/workspace/Jmol/build.xml Can you help me again ? ;-) ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2010-09-16 17:02 Message: It may not be a bug - as you point out, the torsions are 'strand like' - but isolated segments like this are definitely not sheets. A sheet has at least two strands, hbonded to each other. In fact, this stretch of chain is something like a poly-proline helix conformation, I think. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-16 16:58 Message: This is not a bug. Usually Jmol uses the HELIX and SHEET designations in the PDB file, but this file has no header, so Jmol is doing the calculation itself. That calculation is simply: private static boolean isSheet(float psi, float phi) { return ( (phi >= -180) && (phi <= -10) && (psi >= 70) && (psi <= 180) ) || ( (phi >= -180) && (phi <= -45) && (psi >= -180) && (psi <= -130) ) || ( (phi >= 140) && (phi <= 180) && (psi >= 90) && (psi <= 180) ); } In this case we have for phi/psi: GLU29 -75.46 -41.95 ASN30 -111.74 70.29 * ILE31 -94.93 109.93 * PRO32 -52.12 166.21 * so 30-32 are being tagged as sheet. I'm sure the other programs are using hydrogen bonding. If you don't like it, use in this case structure none {30-32} cartoons on Bob ---------------------------------------------------------------------- Comment By: lili35 (lili35) Date: 2010-09-15 22:15 Message: It's done ! ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-09-15 17:28 Message: please upload the PDB file. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3066682&group_id=23629 |