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. > 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. ------------------------------------------------------------------------- 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
