Bugs item #1959402, was opened at 2008-05-07 05:39 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&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: None Group: None Status: Closed Resolution: Fixed Priority: 1 Private: No Submitted By: bob morane (bobmorane84) Assigned to: Bob Hanson (hansonr) Summary: Select chain Command does not work anymore Initial Comment: With "select :A" or "select *:A" it should be possible to select Chain A in a PDB File. It's not working but it works with older versions (11.4.0). Tested with PDB files 1qsf and 1hla. Also tested JMol Applet on PDB website. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-05-07 15:38 Message: Logged In: YES user_id=1082841 Originator: NO PLEASE let's get the word to RCSB that they need to update Jmol to 11.4. Bob ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2008-05-07 15:05 Message: Logged In: YES user_id=1065324 Originator: NO I don't think it is a bug in Jmol. PDB is using 10.2.0. I tested locally the 10.2.0 app and chain selection works. The problem seems to be that 1qsf has its 2 chains identified as "0", except for a single amino acid, THR113, which has chain "A". The whole 1HLA has chain "0". A randomly-chosen hemoglobin, 1O1J, has also all "0" But if you look at the PDB file contents, the "A" etc. are there indeed. So this seems like Jmol 10.2.0 is misreading the chain IDs in the whole PDB database! Maybe a consequence of remediated PDB? Can't see the reason Wait! I'm looking at the PDB contents, but Jmol is displaying the CIF.gz. Maybe the difference is there... Downloaded 1qsf.cif.gz has the same problem when opened locally in 10.2.0, but not in 11.4.2. Downloaded 1qsf.pdb.gz and "original" pdb1qsf.ent.Z are OK even in 10.2.0. So it seems a problem in 10.2.0 reading (mm)CIF files. In any case, there must be other problems with remediated PDB running on 10.2, don't you think so? Compatibility has been added more recently. ---------------------------------------------------------------------- Comment By: bob morane (bobmorane84) Date: 2008-05-07 12:34 Message: Logged In: YES user_id=1996704 Originator: YES Ok your right it works with the newest version stable and prerelease. It's only a problem with the RSCB PDB website so I wrote to them. They are using a old version of Jmol 10.2.0. We were only shocked and thought that the bug is in the current version of jmol. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2008-05-07 07:30 Message: Logged In: YES user_id=1082841 Originator: NO I cannot reproduce this problem. Certainly with 11.5.35 I get: $ load =1qsf $ select *:A 2179 atoms selected $ select *:B 837 atoms selected $ select :A 2179 atoms selected Nothing has been done in the chain selection area for some time. Please try the latest 11.5.x version and let us know if the problem persists. If it does, please send a state file (from WRITE STATE "chainselect.spt") to [EMAIL PROTECTED] illustrating the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1959402&group_id=23629 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
