Bugs item #1470262, was opened at 2006-04-14 02:57 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1470262&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 Submitted By: Egon Willighagen (egonw) >Assigned to: Bob Hanson (hansonr) Summary: group3 to groupID translation failure for 1D66.cif Initial Comment: While parsing of the 1D66.cif seems to work fine (atom.group3 is set to HOH), when doing a selection 'select [HOH]' zero atoms are found. The groupID, at the command evaluation, indeed is incorrect. Email content: =========================================== On Friday 14 April 2006 03:11, Eric Martz wrote: > I added an option to use mmCIF files instead of PDB format files (click > Advanced Options on the main page). Jmol appears to have significant > problems reading mmCIF correctly, and PDB files are working fine, so use of > mmCIF remains something to work towards in the future. (Some problems I > noticed: http://bioinformatics.org/firstglance/fgij/cif.htm) 1D66: the select water problem: confirmed. This problem is not in the CIF reader: I checked and made sure that it reads and sets the group3 variable ('HOH' for the problem HETATM's) is done properly. When doing the select, however, the groupID is 'CD' instead of the wanted 'HOH', but was not able to figure out where the problem source is. =========================================== ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-04-14 09:01 Message: Logged In: YES user_id=1082841 This was not really a Jmol bug, but because of the mmCIF file error, Jmol was returning improper information; so that is fixed. Please notify the creators of this mmCIF file of the error below: Consider the PDB file 1d66.pdb: HETATM 1715 CD CD 42 33.200 64.497 45.835 1.00 39.60 1D661802 HETATM 1716 O HOH 301 40.594 60.277 53.968 1.00 16.15 1D661803 Now consider the mmCIF file 1d66.cif: HETATM 1711 CD CD . CD H 4 . ? 33.200 64.497 45.835 1.00 39.60 ? ? ? ? ? 42 CD ? CD 1 HETATM 1712 O O . HOH I 5 . ? 40.594 60.277 53.968 1.00 16.15 ? ? ? ? ? 301 HOH ? O 1 Note the "?" in that last line on each record. That "?" is supposed to be the group sequence number, 42 in the case of CD, 301 in the case of HOH. The program that generates these CIF files is ignoring the group sequence number for HETATM records. Jmol could not distinguish beteen the two numbers because they are not there in the mmCIF file. So it was not considering HOH to be different from CD, and was assigning it that group name. (Instead of a group sequence number, Jmol was assigning to both CD and HOH "Integer.MIN_VALUE".) This is now fixed by having Jmol assign unique sequence numbers to faulty records of this type. select [HOH] now works. Bob Hanson ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2006-04-14 04:03 Message: Logged In: YES user_id=25678 I've looked at it a bit more. HOH is in the predefined set of group names, so not registered. 'CD' is registered, but the ID gets assigned to the 'HOH' atoms too. But can't figure out where it goes wrong :( ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1470262&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
