Sergey, I added you to both jmol-developers and jmol-users
This is probably a better question for the jmol-users mailing list. > 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. Good. > 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'. You are correct. That is a bug in the current implemenation of 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. I believe that RasMol/Chime only allow one color for all the monitors. Therefore, it was implemented this way to be compatible with existing scripts. (The same goes for the _label_ command ... all the same color) I agree that this should probably be changed. But we have an issue in how one chooses which monitors are colored differently. I believe that this would need to be a function of the selected atoms. A monitor would only change colors if all of its atoms were currently selected. If Chime allows one to make the monitor lines be different colors then please let me know ... we need to do it in a backwards-compatible manner. > 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. I think I understand you to say that saying *monitor* a second time will turn the monitor off. This may not be implemented in Jmol. > Could you advise me if there is any way to fix this problems? The monitor code has not had a lot of work because only a few people have asked for it. But it is a good thing for me to work on. I suspect that we can get these issues resolved within a week. Note that Jmol provides extended monitor commands to support angles and torsion angles. monitor 1 2 # distance monitor 1 2 3 # angle monitor 1 2 3 4 # torsion angle Miguel ------------------------------------------------------- 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
