Re: [Jmol-users] contact

2014-08-06 Thread Pshemak Maslak
Thank you for clarification and the fix of the problem. PM On 8/5/2014 8:37 AM, Robert Hanson wrote: It's a bug. Three issues there. First, the CONTACT command has a bug that makes it only work on the first model. Second, you probably should be issuing mySet1={1.6 & _H}; mySet2={1.6 &

Re: [Jmol-users] contact

2014-08-05 Thread Robert Hanson
It's a bug. Three issues there. First, the CONTACT command has a bug that makes it only work on the first model. Second, you probably should be issuing mySet1={1.6 & _H}; mySet2={1.6 & _H}; contact* model 1.6 *150% {mySet1} {mySet2} to display the contact in the proper model. Third, CONTACT wa

Re: [Jmol-users] contact

2014-08-04 Thread Pshemak Maslak
I still have problems with "contact" when using butane file containing 20 models (rotamers around the central C-C bond). Separately, one frame (say gauche) shows contacts fine: contact 100% {_H} {_H}, (net volume 0.14 A^3), but when that frame is a part (frame 6) of the collection, something l

Re: [Jmol-users] contact

2014-05-06 Thread Robert Hanson
Oh, sure. But it's generally designed to ignore intramolecular contacts. contact {atomset1} {atomset2} and if {atomset2} is not present, then "same model and not atomset1" is the default. You can do intramolecular clashes by specifying two distinct intramolecular atom sets. For example: $ load

[Jmol-users] contact

2014-05-06 Thread Pshemak Maslak
Can "contact" command be used to visualize "clashes" in small molecules (such as eclipsed CH3/CH3 in butane, for example)? What would the full command look like? Thanks, PM -- Is your legacy SCM system holding you

Re: [Jmol-users] contact command

2012-07-02 Thread Robert Hanson
You mean so that you see only non-clash contacts? You can do this: contact HBOND Those aren't clashes. On Fri, Jun 29, 2012 at 6:49 AM, Pascal Auffinger < p.auffin...@ibmc-cnrs.unistra.fr> wrote: > Hi, > > Is there a way to set contact clash ON or OFF though set contact ON; set > contact

[Jmol-users] contact command

2012-06-29 Thread Pascal Auffinger
Hi, Is there a way to set contact clash ON or OFF though set contact ON; set contact OFF ? Thanks for your reply, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -

Re: [Jmol-users] Contact command

2012-06-28 Thread Robert Hanson
: *Robert Hanson > *Objet : **Rép : [Jmol-users] contact command* > *Date : *26 juin 2012 19:33:26 HAEC > *À : *jmol-users@lists.sourceforge.net > *Répondre à : *jmol-users@lists.sourceforge.net > > > Great! > > What version of Jmol are you using? > > > O

[Jmol-users] Contact command

2012-06-28 Thread Pascal Auffinger
Well its Jmol 12.2.22 Pascal --- De : Robert Hanson Objet : Rép : [Jmol-users] contact command Date : 26 juin 2012 19:33:26 HAEC À : jmol-users@lists.sourceforge.net Répondre à : jmol-users@lists.sourceforge.net Great! What version of Jmol are you using? On Tue, Jun 26, 2012 at 10:41 AM

Re: [Jmol-users] contact command

2012-06-26 Thread Robert Hanson
Great! What version of Jmol are you using? On Tue, Jun 26, 2012 at 10:41 AM, Pascal Auffinger < p.auffin...@ibmc-cnrs.unistra.fr> wrote: > Dear All, > > I would like to draw contacts between a residue and what is shown in the > applet. This command does not seem to work for me. Anything wrong ?

[Jmol-users] contact command

2012-06-26 Thread Pascal Auffinger
Dear All, I would like to draw contacts between a residue and what is shown in the applet. This command does not seem to work for me. Anything wrong ? jmolCheckbox('contact {~res} {visible} clash','','Clashes ','','miniApplet_clashes','Show/hide clashes'); Thanks for help, Pascal - Pasca