Re: [PyMOL] Sessions and Scope
Tsjerk, Great question with a crummy answer: you can't! But this seems like a really good idea, at least for primitives stored in ordinary built-in Python containers. Saving class instances would be problematic, since session files wouldn't necessarily be restorable in the absence of accompanying class definitions [we do rely upon Python pickling machinery, and are thus subject to its limitations]. Cheers, Warren > -Original Message- > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > Sent: Friday, October 02, 2009 6:04 AM > To: pymol-users > Subject: [PyMOL] Sessions and Scope > > Hi, > > At present I'm setting some variables in the globals() > dictionary/global scope, but when I save the session, these variables > are lost. What would be the best way to preserve them? (This question > may also be interpreted as: what does Pymol write to a session file?). > > Cheers, > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > > -- > > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > ___ > 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 > > -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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
Re: [PyMOL] rmsd for multiple snaphosts
>Dear all,
>
>i have multiple conformations files (multi pdb) and would like to
>compute for each one, the rmsd for each snapshot against the first
>snapshot.
>Is it possible with pymol to do such a task ?
>
>thank you in advance for the gain of time ... :-)
>
>nicolas floquet
Yes, using a short Python loop:
# .pml example PyMOL script
# load structure into "input" object
fetch 1nmr, input, async=0
# choose the reference state
create ref, input, 1, 1
# now iterate using Python
python
for i in range(cmd.count_states("input")):
cmd.create("tmp", "input", i+1, 1)
print 1, i+1, cmd.fit("tmp", "ref")
cmd.delete("tmp")
python end
# end example
Cheers,
Warren
--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf
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[PyMOL] Sessions and Scope
Hi, At present I'm setting some variables in the globals() dictionary/global scope, but when I save the session, these variables are lost. What would be the best way to preserve them? (This question may also be interpreted as: what does Pymol write to a session file?). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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
