Hello! I am developing the web site that allows to see interactively macromolecular structures. I use Jmol/JmolApplet for this purpose and I'm very impressed by the program.
But I have noted one drawback in the 'monitor' command. If my PDB file looks as in the example below: >HEADER >ATOM 9 N VAL L 2 48.846 46.436 69.577 1.00 15.18 >ATOM 10 CA VAL L 2 49.050 45.060 69.985 1.00 12.92 >ATOM 11 C VAL L 2 47.789 44.490 69.366 1.00 11.92 >ATOM 12 O VAL L 2 46.695 44.982 69.583 1.00 3.87 >ATOM 13 CB VAL L 2 49.051 44.935 71.545 1.00 13.90 >ATOM 14 CG1 VAL L 2 49.184 43.485 71.940 1.00 14.02 >ATOM 15 CG2 VAL L 2 50.215 45.714 72.150 1.00 11.16 >END When I click on any, let's say, of CG atoms I see in console: $ Atom: CG1 14 VAL 2 Chain:L Atom: CG2 15 VAL 2 Chain:L and this is expected. When I try to use command 'monitor' to draw a distance line: $ monitor 14 15 ScriptException: bad atom number ScriptLine: monitor 14 15 I receive an error (see above). 1). I believe Jmol renumbers consequently all atoms in the PDB file starting from 1. But it makes very difficult the use of the 'monitor' command. A lot of PDB files do not start from 1, some other ones have gaps, etc . The user has to renumber atoms in PDB file in order to able to use 'monitor'. 2). The Jmol command "color monitor" select only one color, if there are different types of atom contacts in protein, I need to have many colors for connecting atoms with lines and labels in one image. 3). Chime remove the monitor line and distance by giving the command "monitor" with selecting pair of atoms a second time, how to make it in Jmol. Could you advise me if there is any way to fix this problems? Thank you in advance. Regards, Sergey Gerzon -- Gerzon Sergey Department of Plant Sciences Weizmann Institute of Science Rehovot 76100 ISRAEL [EMAIL PROTECTED] Tel: +972-8-9344434 Fax: +972-8-9469124 Tel: +972-55-306815 ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
