2011-10-20 14:01, Jason Vertrees skrev:
> Hi Daniel,
> If you need a scripted solution but not using grid mode, how about
> something like this from a freshly loaded PyMOL:
> # get the view matrix for the origin
> o = cmd.get_view()
> # fetch a protein
> fetch 1rx1, async=0
> # get the position
> x = cmd.get_position()
> # restore the camera to the original coordinates
> # move the loaded protein to the origin
> cmd.translate( [-x, -x, -x], "1rx1")
> You could easily make this into a loop over your set of structures.
> This is nice because you can still rotate the camera and it will not
> change how far away (and thus change the scale) of the view.
The above looks promising. What I'm missing, because of my lack of
experience with Pymol, is how to move the camera away (i.e. zoom out) a
defined distance. From the documentation of set_view it appears I should
fiddle with the 15th and/or 16th floating point number, while keeping
the other but 18 parameters is a bit dauting.
> -- Jason
> On Thu, Oct 20, 2011 at 10:51 AM, Daniel Lundin
> <daniel.lundin@...> wrote:
>> I'm quite new to Pymol, but have searched and found nothing on how to
>> visualise and draw a molecule to a certain scale. The reason I want to
>> do this is to be able to output figures of several molecules separately
>> in a format that displays their relative sizes. I can of course do this
>> manually but it's error prone and laborious, so I'd prefer to be able to
>> say I want a certain number of angstroms per pixel or so. I will ray
>> trace the images.
>> Daniel Lundin, Postdoc
>> SciLifeLab, School of biotechnology,
>> KTH Royal institute of technology,
>> Stockholm, Sweden
>> Postal address:
>> Box 1031
>> 171 21 Solna
>> Visiting address:
>> Tomtebodavägen 23 A
>> Mobile: +46 (0)708 123 922
>> Email: daniel.lundin@...
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Daniel Lundin, Postdoc
SciLifeLab, School of biotechnology,
KTH Royal institute of technology,
171 21 Solna
Tomtebodavägen 23 A
Mobile: +46 (0)708 123 922