Bugs item #946848, was opened at 2004-05-03 11:44 Message generated for change (Settings changed) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=946848&group_id=23629
>Category: Graphics Group: None Status: Open Resolution: None Priority: 5 Submitted By: Miguel (michaelthoward) >Assigned to: Miguel (michaelthoward) Summary: alpha carbon only structures Initial Comment: Jmol currently requires all 4 NCCO atoms in order to draw protein backbone shapes. Jan is working with 1alm ... with alpha carbons only. Backbone & trace do not work. ---------------------------- Original Message ---------------------------- Subject: backbone with *.CA only structures From: "Jan Reichert" <[EMAIL PROTECTED]> Date: Mon, May 3, 2004 9:38 To: "Miguel" <[EMAIL PROTECTED]> -------------------------------------------------------------------------- Hi Miguel, with 1alm which is a *.CA only model structure no backbone (and no trace) is drawn http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1alm but at least for backbone *.CA positions should be sufficient. Regards, Jan ---------------------------- Original Message ---------------------------- Subject: Re: backbone with *.CA only structures From: "Miguel" <[EMAIL PROTECTED]> Date: Mon, May 3, 2004 11:41 To: "Jan Reichert" <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] -------------------------------------------------------------------------- > for me, the source of the major quantity of PDB formated files is the RCSB/PDB, therefore if a *.ca is recognized as being part of a protein, and this is the case with > 1alm > select *.ca & protein > 2989 atoms selected > (or > select backbone & protein > ) > I expected that the *.ca trace or backbone (all what is only dependent on the *.ca of amino acids / or *.p of nucleic) could be rendered. Furthermore, this is RasMol/Chime compatible. Good points. Particularly since you can say select *.ca & protein Q: What does RasMol do if you try to do a trace or a cartoon? I think another problem may be that I have a number of assumptions in the code that all 4 atoms of the backbone are present. I will file a bug report and take another look at this when I work on nucleotide chain backbones & secondary structure graphical representations. Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=946848&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
