[PyMOL] How to get the coordinates of the center of a group of atoms?
hi,
I have a pdb file with serveral frames, I hope to get the trajectory
of the center of a selected group of atoms.
I use the following commands, but return the same coord.
cmd.load(a.pdb)
coord=[]
for i in range(cmd.count_frames()):
cmd.frame(i+1)
cmd.center('id 1-24')
coord.append(cmd.get_position())
What should I do?
Thank you!
Zhang Cun
--
Blog: http://www.edwardpku.com/cun
--
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Re: [PyMOL] How to get the coordinates of the center of a group of atoms?
Hi Cun,
That's a good start. Just a couple things needs to be changed.
First, frames don't track coordinates, states do. Frames are for
movies; states are for coordinates. Next, instead of using center,
use the origin command with the state parameter specified. Here's
example code for 1NMR a multi-state protein, adjust his for your
application:
python
cmd.fetch(1nmr, async=0)
coord=[]
for i in range(1,cmd.count_states()+1):
cmd.origin(i. 1-24, state=i)
coord.append(cmd.get_position())
print coord
python end
Cheers,
-- Jason
On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang apzc2...@gmail.com wrote:
hi,
I have a pdb file with serveral frames, I hope to get the trajectory
of the center of a selected group of atoms.
I use the following commands, but return the same coord.
cmd.load(a.pdb)
coord=[]
for i in range(cmd.count_frames()):
cmd.frame(i+1)
cmd.center('id 1-24')
coord.append(cmd.get_position())
What should I do?
Thank you!
Zhang Cun
--
Blog: http://www.edwardpku.com/cun
--
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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Re: [PyMOL] How to get the coordinates of the center of a group of atoms?
Dear Jason,
Thank you for you quick reply!
And This problem is solved!
Yours,
Zhang Cun
On Thu, Apr 29, 2010 at 9:31 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Cun,
That's a good start. Just a couple things needs to be changed.
First, frames don't track coordinates, states do. Frames are for
movies; states are for coordinates. Next, instead of using center,
use the origin command with the state parameter specified. Here's
example code for 1NMR a multi-state protein, adjust his for your
application:
python
cmd.fetch(1nmr, async=0)
coord=[]
for i in range(1,cmd.count_states()+1):
cmd.origin(i. 1-24, state=i)
coord.append(cmd.get_position())
print coord
python end
Cheers,
-- Jason
On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang apzc2...@gmail.com wrote:
hi,
I have a pdb file with serveral frames, I hope to get the trajectory
of the center of a selected group of atoms.
I use the following commands, but return the same coord.
cmd.load(a.pdb)
coord=[]
for i in range(cmd.count_frames()):
cmd.frame(i+1)
cmd.center('id 1-24')
coord.append(cmd.get_position())
What should I do?
Thank you!
Zhang Cun
--
Blog: http://www.edwardpku.com/cun
--
___
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
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Blog: http://blog.4message.net
--
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[PyMOL] for evaluation only
hi all, i am an academic using pymol and the new build places a for evaluation only graphic on top of the rendered structure. not very helpful for presentations, publications and the like. how do i circumvent this without using chimera to generate my images for pubs. thanks. victor -- ___ 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] for evaluation only
On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon vicken...@gmail.com wrote: i am an academic using pymol and the new build places a for evaluation only graphic on top of the rendered structure. not very helpful for presentations, publications and the like. how do i circumvent this without using chimera to generate my images for pubs. Use the open-source version, I would be very surprised if that overlays anything. Or download one of the builds of version 0.99, which is missing some nifty features but still more than adequate for publication graphics as long as you don't need to show anisotropic Bs. http://www.pymol.org/rel/099/ -- ___ 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] for evaluation only
hi victor, if you are on windows and need the latest pymol version, please take a look at christoph's pymol builds (thanks christoph!): http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol best, shiven On Thu, Apr 29, 2010 at 6:32 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon vicken...@gmail.comwrote: i am an academic using pymol and the new build places a for evaluation only graphic on top of the rendered structure. not very helpful for presentations, publications and the like. how do i circumvent this without using chimera to generate my images for pubs. Use the open-source version, I would be very surprised if that overlays anything. Or download one of the builds of version 0.99, which is missing some nifty features but still more than adequate for publication graphics as long as you don't need to show anisotropic Bs. http://www.pymol.org/rel/099/ -- ___ 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 -- ___ 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] for evaluation only
The quick answer is Don't use an evaluation build. You have 3 main options: 1) become a sponsor and get builds of the latest code http://pymol.org/funding.html 2) use the free builds that are several years old http://pymol.org/rel/099/ 3) build pymol from source. There are instructions on http://www.pymolwiki.org/ for building on windows, mac, and linux, and solutions to many common problems you might face can be found by searching the archives of the list (linked to at the bottom of each message). If you run into any problems not discussed in the wiki or archives, people around here are nice and will likely help you out. -David On Thu, Apr 29, 2010 at 6:03 PM, victor kenyon vicken...@gmail.com wrote: hi all, i am an academic using pymol and the new build places a for evaluation only graphic on top of the rendered structure. not very helpful for presentations, publications and the like. how do i circumvent this without using chimera to generate my images for pubs. thanks. victor -- ___ 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 -- ___ 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
