Thanks Jason, 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 > cmd.set_view(o) > > # move the loaded protein to the origin > cmd.translate( [-x[0], -x[1], -x[2]], "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.
> Cheers, > > -- Jason > /Daniel > On Thu, Oct 20, 2011 at 10:51 AM, Daniel Lundin > <daniel.lun...@scilifelab.se> wrote: >> Hi, >> >> 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 >> >> -- >> Daniel Lundin, Postdoc >> SciLifeLab, School of biotechnology, >> KTH Royal institute of technology, >> Stockholm, Sweden >> >> Postal address: >> Box 1031 >> 171 21 Solna >> Sweden >> >> Visiting address: >> Tomtebodavägen 23 A >> >> Mobile: +46 (0)708 123 922 >> Email: daniel.lun...@scilifelab.se >> >> ------------------------------------------------------------------------------ >> The demand for IT networking professionals continues to grow, and the >> demand for specialized networking skills is growing even more rapidly. >> Take a complimentary Learning@Ciosco Self-Assessment and learn >> about Cisco certifications, training, and career opportunities. >> http://p.sf.net/sfu/cisco-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > -- Daniel Lundin, Postdoc SciLifeLab, School of biotechnology, KTH Royal institute of technology, Stockholm, Sweden Postal address: Box 1031 171 21 Solna Sweden Visiting address: Tomtebodavägen 23 A Mobile: +46 (0)708 123 922 Email: daniel.lun...@scilifelab.se ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Ciosco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
