[Chimera-users] Chimera comands

Michał Kadlof m.kadlof at cent.uw.edu.pl
Thu Nov 16 04:19:26 PST 2017

Thank you for your answer, it almost covers my needs.

Maybe I was not precise. When I was asking about rotation I mean the same
effect when I modify field angle in Volume Viewer -> Features ->
Cooridnates. Is it possible in command line?

pozdrawiam serdecznie
Michał Kadlof <m.kadlof at cent.uw.edu.pl>

2017-11-14 22:17 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Michał,
> Yes, it’s a little tricky finding commands for some of those things.
> (1) open trajectory would just be done with “open” but you have to use a
> metafile, which is a text file listing the input file(s) as well as any
> other parameters that would be required inputs if you were using the MD
> Movie GUI.  Examples and explanation:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/
> movie.html#metafile>
> (2) there is no command to open a generic pseudobond file, just the
> PseudoBond Reader tool (in menu under Tools… Depiction).  However, you can
> either have python to open it, or instead use a bunch of “distance”
> commands to add distance monitor pseudobonds.  You can control their colors
> etc. with “setattr,” for example:
> distance :53.a at ca :58.a at ca
> setattr p label ''
> setattr p color dodger blue
> setattr g lineType 1
> setattr g lineWidth 3
> If you select any pseudobond and then show the Selection Inspector by
> clicking the green magnifying glass, you can see in the dialog which
> attributes are of the pseudobond (“p” in setattr) or pseudobond group (“g”)
> and (by mouseover in the dialog) its name and values that could be used in
> the setattr command.  You can put atomspecs at the ends of those setattr
> commands to only affect certain pseudobonds instead of all pseudobonds.
> The label command has two single quotation marks (not a single double
> quotation mark). You could also use two double quotation marks, but be sure
> to type in the plain ones… my e-mail app insists on changing them to fancy
> open and close quotation marks, which won’t work.
> (3) The “volume” command includes options to change origin and voxel size.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/
> volume.html#dimensions>
> (4) You can rotate a model with “turn” or “roll”.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Nov 14, 2017, at 1:41 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl>
> wrote:
> >
> > Hello,
> > I have some troubles with finding in documentation suitable commands.
> >
> > How do I should write script which:
> > - open a trajectory in saved PDB or PSF/DCD in MD movie tool.
> > - read pseudobonds from file, and change the color of all of them at once
> > - change origin, voxel size and rotation angle of opened volumetric data
> >
> > Can you help me?
> > --
> > ​best wishes,
> > Michał Kadlof <m.kadlof at cent.uw.edu.pl>
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