Bugs item #1470262, was opened at 2006-04-14 09:57 Message generated for change (Comment added) made by egonw 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: Open Resolution: None Priority: 5 Submitted By: Egon Willighagen (egonw) Assigned to: Nobody/Anonymous (nobody) 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: Egon Willighagen (egonw) Date: 2006-04-14 11:03 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
