<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">There is not a command equivalent of Volume Viewer / Features / Coordinates / Rotation axis + angle. But that is not the usual way of moving a map (e.g. for fitting). That changes the mapping of map grid indices (i,j,k) into physical space (x,y,z). But there is another positioning matrix that every Chimera model has that transforms its physical space coordinates into the world coordinates. Almost always you change this second transform, and that is done with move and turn commands using the "models" option of those commands to specify which model you want to shift or rotate.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 16, 2017, at 4:19 AM, Michał Kadlof wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:monospace,monospace">Thank you for your answer, it almost covers my needs.</div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">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?<br class=""></div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="font-family:monospace,monospace" class="">--<br class="">pozdrawiam serdecznie<br class="">Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" target="_blank" class="">m.kadlof@cent.uw.edu.pl</a>></span><br class=""></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">2017-11-14 22:17 GMT+01:00 Elaine Meng <span dir="ltr" class=""><<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Michał,<br class="">
Yes, it’s a little tricky finding commands for some of those things.<br class="">
<br class="">
(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:<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/<wbr class="">ContributedSoftware/movie/<wbr class="">movie.html#metafile</a>><br class="">
<br class="">
(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:<br class="">
<br class="">
distance :53.a@ca :58.a@ca<br class="">
setattr p label ''<br class="">
setattr p color dodger blue<br class="">
setattr g lineType 1<br class="">
setattr g lineWidth 3<br class="">
<br class="">
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.<br class="">
<br class="">
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.<br class="">
<br class="">
(3) The “volume” command includes options to change origin and voxel size.<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/UsersGuide/midas/<wbr class="">volume.html#dimensions</a>><br class="">
<br class="">
(4) You can rotate a model with “turn” or “roll”.<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/UsersGuide/midas/<wbr class="">turn.html</a>><br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D.<br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<div class="HOEnZb"><div class="h5"><br class="">
> On Nov 14, 2017, at 1:41 AM, Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" class="">m.kadlof@cent.uw.edu.pl</a>> wrote:<br class="">
><br class="">
> Hello,<br class="">
> I have some troubles with finding in documentation suitable commands.<br class="">
><br class="">
> How do I should write script which:<br class="">
> - open a trajectory in saved PDB or PSF/DCD in MD movie tool.<br class="">
> - read pseudobonds from file, and change the color of all of them at once<br class="">
> - change origin, voxel size and rotation angle of opened volumetric data<br class="">
><br class="">
> Can you help me?<br class="">
> --<br class="">
> best wishes,<br class="">
> Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" class="">m.kadlof@cent.uw.edu.pl</a>><br class="">
<br class="">
</div></div></blockquote></div><br class=""></div>
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