Angel Herraez wrote: >On 6 May 2007 at 17:35, David Leader wrote: > > > >>2. The edited pdb files with Hydrogens added screw up the parsing of >>certain atoms in Jmol 11 and give them a clubfoot appearance. >> >> > >I don't know what you mean by that, but likely improper column alignment of >text in the PDB; Jmol follows strictly the PDB standard, and many >programas don't do so. I've had, for example, H atoms labeled HG seen as >mercury and hence with bonds drawn to all 8 neighbours around them. > > > > If the PDB file has the element symbol field filled, then there is no problem. 11.1.32 fixes this issue with Hg as mercury when the file does not contain this information by assigning H to any atom name starting with H (He, Hf, Hg) in ATOM records. -- Mercury could only appear in HETATM records, I think. But, yes, earlier versions of Jmol did not properly assign H in just this situation.
>>As regards the jmol.js bug, check All Motifs and then uncheck any of >>the ones below. All remains checked. >> >> > >That is so by design, David; quoting the doc: >"Whenever one of the followers is checked or unchecked, its siblings are >examined; if all have the same state, the leader will be checked or >unchecked accordingly." > >I know that's debatable, but since there is no "grey" state for a checkbox, >one choice or the other must be taken. Bob took this. If you uncheck all >siblings individually, the master wll automatically unckeck. > > >A separate problem is that when loading for the first time, I checked "All >motifs" and the children did not get checked and there was a javascript >error; but now this is not happenning again, so it must be hace been a delay >in the applet getting ready. > > > > >>As regards the bad display, select single motif display and then >>Catmat: 48,48,50 . Glu 50 is screwed up. >> >> > >That looks that an alternate position (Alt) problem; there are e.g. >[Glu]50:A.CD%A and [Glu]50:A.CD%B, and Jmol is drawing both. >I have not used Alt locations, but I know it's been dealt with; make sure to >read the doc for that. > >Yes! Using the pop-up menu: "Configurations", you have A, B and C; check >"A" and your funny Glu is gone. > > > > ah, so glad "configuration" is of some use. See also http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/altloc.htm >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
