[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Wed Sep 6 00:49:03 PDT 2017


Thank you, Elaine!

Regarding presets
Is it possible to define step-by-step some commands to obtain
something like preset 2 visualization state?

Gleb

2017-09-05 18:54 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi Gleb,
> Maybe that makes sense, because the “pub” presets use some fancier display settings (compared to the interactive presets) that may be more likely to reveal graphics driver problems.
>
> If you already know the degrees of rotation that you want, you can just use the “turn” command in your script.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
>
> If you have a whole bunch of different proteins and you don’t know ahead of time how much rotation will make a better image of each one, it becomes more difficult.  You might be able to devise something more general by defining the protein long axis (“define axis” command), “align” command to align it along the line of sight, “turn” to rotate 90 degrees (and then perhaps ~define to get rid of the axis).
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.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 Sep 4, 2017, at 1:09 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>
>> Hi Greg,
>>
>> I am using Ubuntu with Nvidia driver.
>>
>> I have updated all those packages and copy files to chimera_batch lib
>> dir but it was the same effect.
>>
>> then I found that the problem was hidden in my batch script!
>> "preset apply pub 2" produced that crash !
>> but if I change it to "preset app int all" everything is fine.
>>
>> P.S. as I found in the resulted images on the default the protein is
>> aligned along its Z vector. Is it possible to turn it via some command
>> to display in-front or in the pseudo-isometrical projection?
>>
>> Thanks!!
>>
>> Gleb
>



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