Menu
▾
▴
jmol-developers
|
From: SourceForge.net <no...@so...> - 2008-02-07 14:21:46
|
Bugs item #1888804, was opened at 2008-02-07 14:21 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&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: Open Resolution: None Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Nobody/Anonymous (nobody) Summary: 11.4.RC2 - Secondary structure of 3BKD Initial Comment: Jmol 11.4.RC2 (and also Revision 8973 retrieved from SVN a few minutes ago) doesn't display the annotated secondary structure of the asymmetric unit of PDB entry 3BKD correctly. The asymmetric unit PDB file (attached together with the file of biological unit 1 in a ZIP file) contains several "HELIX" records. After loading it Jmol displays the whole protein as unstructured. If the PDB file of the biological unit 1 is loaded instead, the helices are displayed as annotated. Since the PDB just copies (some) of the header lines from the asymmetric unit files to the biological unit files the 'HELIX' records are identical in both files. I havn't found other cases yet. There are at least cases where it works correctly like entry 1DEH. The problem was introduced somewhere between 11.3.47 and 11.3.60 because the display is correct with 11.3.47. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&group_id=23629 |
|
From: SourceForge.net <no...@so...> - 2008-02-07 17:56:01
|
Bugs item #1888804, was opened at 2008-02-07 08:21 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&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: Open Resolution: None Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) >Assigned to: Bob Hanson (hansonr) Summary: 11.4.RC2 - Secondary structure of 3BKD Initial Comment: Jmol 11.4.RC2 (and also Revision 8973 retrieved from SVN a few minutes ago) doesn't display the annotated secondary structure of the asymmetric unit of PDB entry 3BKD correctly. The asymmetric unit PDB file (attached together with the file of biological unit 1 in a ZIP file) contains several "HELIX" records. After loading it Jmol displays the whole protein as unstructured. If the PDB file of the biological unit 1 is loaded instead, the helices are displayed as annotated. Since the PDB just copies (some) of the header lines from the asymmetric unit files to the biological unit files the 'HELIX' records are identical in both files. I havn't found other cases yet. There are at least cases where it works correctly like entry 1DEH. The problem was introduced somewhere between 11.3.47 and 11.3.60 because the display is correct with 11.3.47. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-02-07 11:56 Message: Logged In: YES user_id=1082841 Originator: NO The issue is the CONECT records. In the file that has CONECT records, Jmol is not attempting to make any further connections to the HETATM atoms. The problem before was that Jmol was not respecting CONECT records within/to HETATM groups. Newer versions of Jmol correct this flaw, but the effect in this case is to disqualify that HELIX definition, because the helix polymer "breaks" at group 34 into three separate unconnected polymers. Apparently HETATM conect records fail to provide connections to ATOM records. Jmol COULD be encouraged to bond ATOM to HETATM atoms with a bit of modifications. First, though, I would want to know if this is really what is desired. Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&group_id=23629 |
|
From: SourceForge.net <no...@so...> - 2008-02-07 18:21:06
|
Bugs item #1888804, was opened at 2008-02-07 08:21 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&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: Open Resolution: None Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Bob Hanson (hansonr) Summary: 11.4.RC2 - Secondary structure of 3BKD Initial Comment: Jmol 11.4.RC2 (and also Revision 8973 retrieved from SVN a few minutes ago) doesn't display the annotated secondary structure of the asymmetric unit of PDB entry 3BKD correctly. The asymmetric unit PDB file (attached together with the file of biological unit 1 in a ZIP file) contains several "HELIX" records. After loading it Jmol displays the whole protein as unstructured. If the PDB file of the biological unit 1 is loaded instead, the helices are displayed as annotated. Since the PDB just copies (some) of the header lines from the asymmetric unit files to the biological unit files the 'HELIX' records are identical in both files. I havn't found other cases yet. There are at least cases where it works correctly like entry 1DEH. The problem was introduced somewhere between 11.3.47 and 11.3.60 because the display is correct with 11.3.47. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-02-07 12:20 Message: Logged In: YES user_id=1082841 Originator: NO fixed for 11.5.6 and 11.4.RC4 PDB atom sets are automatically connected between ATOM and HETATM records while still preserving CONECT bonding between any two HETATM atoms. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2008-02-07 11:56 Message: Logged In: YES user_id=1082841 Originator: NO The issue is the CONECT records. In the file that has CONECT records, Jmol is not attempting to make any further connections to the HETATM atoms. The problem before was that Jmol was not respecting CONECT records within/to HETATM groups. Newer versions of Jmol correct this flaw, but the effect in this case is to disqualify that HELIX definition, because the helix polymer "breaks" at group 34 into three separate unconnected polymers. Apparently HETATM conect records fail to provide connections to ATOM records. Jmol COULD be encouraged to bond ATOM to HETATM atoms with a bit of modifications. First, though, I would want to know if this is really what is desired. Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&group_id=23629 |
|
From: SourceForge.net <no...@so...> - 2008-03-12 02:32:46
|
Bugs item #1888804, was opened at 2008-02-07 08:21 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&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: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Bob Hanson (hansonr) Summary: 11.4.RC2 - Secondary structure of 3BKD Initial Comment: Jmol 11.4.RC2 (and also Revision 8973 retrieved from SVN a few minutes ago) doesn't display the annotated secondary structure of the asymmetric unit of PDB entry 3BKD correctly. The asymmetric unit PDB file (attached together with the file of biological unit 1 in a ZIP file) contains several "HELIX" records. After loading it Jmol displays the whole protein as unstructured. If the PDB file of the biological unit 1 is loaded instead, the helices are displayed as annotated. Since the PDB just copies (some) of the header lines from the asymmetric unit files to the biological unit files the 'HELIX' records are identical in both files. I havn't found other cases yet. There are at least cases where it works correctly like entry 1DEH. The problem was introduced somewhere between 11.3.47 and 11.3.60 because the display is correct with 11.3.47. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2008-02-07 12:20 Message: Logged In: YES user_id=1082841 Originator: NO fixed for 11.5.6 and 11.4.RC4 PDB atom sets are automatically connected between ATOM and HETATM records while still preserving CONECT bonding between any two HETATM atoms. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2008-02-07 11:56 Message: Logged In: YES user_id=1082841 Originator: NO The issue is the CONECT records. In the file that has CONECT records, Jmol is not attempting to make any further connections to the HETATM atoms. The problem before was that Jmol was not respecting CONECT records within/to HETATM groups. Newer versions of Jmol correct this flaw, but the effect in this case is to disqualify that HELIX definition, because the helix polymer "breaks" at group 34 into three separate unconnected polymers. Apparently HETATM conect records fail to provide connections to ATOM records. Jmol COULD be encouraged to bond ATOM to HETATM atoms with a bit of modifications. First, though, I would want to know if this is really what is desired. Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1888804&group_id=23629 |
Thanks for helping keep SourceForge clean.
X