I have been working on the 'monitor' code this weekend. Things are going to change this week.
I have to go ... Miguel > Miguel, > > > 1. In Chime - If I select a pair of atoms and run 'monitor', I get > the line between these two atoms and distance. - The same in Jmol > > > 2. In Chime - If I than select a next pair of atoms and run 'monitor', > I get line between these two new atoms and distance. The previos > line and distance still on the screen. - The same in Jmol. > > 3. In chime - I cann to remove all previous lines and distances. > with command 'monitor off'. > > How remove the lines and distances in Jmol?. > ( all previous lines and distances or one previous line and distance) > > > Best regards > > > >>===== Original Message From "Miguel Howard" <[EMAIL PROTECTED]> ===== >>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 > > -- 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 -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Peņa Primera 11-13 esc dcha 6B 37002 Salamanca Espaņa Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. 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