[PyMOL] movie in pymol
Dear all, I am trying to make a movie in pymol with two structure of the same protein.one is crystal structure and one is NMR structure.The N-terminal part of crystal structure is in open conformation whereas that of NMR is closed.What command should I use.Is it possible to make the movie with the commands given in pymol manual or I should use Slerpy from PyMOL wiki.Any suggestions are welcome.Thanx in advance to all. Shivesh shivesh - Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
Re: [PyMOL] error on debian w/ pymol -c foo.pml
Hi Xavier,
we also stumbled over this error and resolved it in a similar fasion.
Also we have sent a bug report to debian:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=409188
The problem is that $* sends all command line arguments
as a single combined string to pymol's __init__.py.
The bug was introduced in the new debian package,
before there were no quotes.
Best.
Christof Andreas
xavier siebert wrote:
Hi,
I am using the pymol package provided with Debian testing (0.98+0.99r).
When I am trying to run a script without the gui, i.e. pymol -c
foo.pml, I get the following error :
Traceback (most recent call last):
File /var/lib/python-support/python2.4/pymol//__init__.py, line 364, in ?
invocation.parse_args(pymol_argv)
File /var/lib/python-support/python2.4/pymol/invocation.py, line
270, in parse_args
options.deferred.append(_do_spawn %s%av.pop())
IndexError: pop from empty list
I think I solved it by changing the last line of /usr/bin/pymol from
python2.4 ${PYMOL_PATH}/__init__.py $*
to
python2.4 ${PYMOL_PATH}/__init__.py $@
--X.
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Re: [PyMOL] movie in pymol
Shivesh, Given that this is your third post on the same topic, an important point needs to be made: It is not reasonable for one user to expect other PyMOL mailing list participants to teach them how to use the software, especially for involved tasks such as movie-making. Open source is largely about having the freedom and the opportunity to be self-sufficient. Indeed, the implicit expectation for free or open-source usage of PyMOL is that you will be strictly self-reliant, all the way down to compiling the current open-source code yourself, if necessary, since that is the one thing DeLano Scientific gives away without any expectation of reciprocity. With respect to obtaining assistance, the PyMOL user community will happily provide hints, exchange limited know-how, and point you at existing resources (such as Slerpy). However, it is unrealistic to expect one's peers to do more than that. They are busy folks, too! Thus, if one does not get an answer to his or her question, it is generally because one is asking for too much. Repeating such requests over and over again is poor list etiquette. Direct end-user assistance is something DeLano Scientific can provide, but only for Support-Level Subscribers (Power Users) who are effectively purchasing some help through high-level sponsorship of the project. We do try to assist Maintenance-Level Subscribers (Casual Users) on a workload-permitting basis, but right now we are swamped with 1.0, docs, and various Sponsor requests. Of course, when appropriate, we channel such assistance through the public mailing list so that others can benefit from some of the information we provide to PyMOL Sponsors. With respect to movie-making, this should eventually become easier to do thanks to improved software and documentation. But at the present time, it is not -- PyMOL is rather weak in this area. Generally speaking, you must first learn to write a PyMOL command script or a Python program, render and export a set of numbered PNG files, and then apply an external tool (such as QuickTime Pro) to assemble the raw images into a compressed movie. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of shivesh kumar Sent: Thursday, February 08, 2007 1:29 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] movie in pymol Dear all, I am trying to make a movie in pymol with two structure of the same protein.one is crystal structure and one is NMR structure.The N-terminal part of crystal structure is in open conformation whereas that of NMR is closed.What command should I use.Is it possible to make the movie with the commands given in pymol manual or I should use Slerpy from PyMOL wiki.Any suggestions are welcome.Thanx in advance to all. Shivesh shivesh _ Finding fabulous fares is fun. Let http://farechase.yahoo.com/promo-generic-14795097;_ylc=X3oDMTFtNW45amVpBF9T Azk3NDA3NTg5BF9zAzI3MTk0ODEEcG9zAzEEc2VjA21haWx0YWdsaW5lBHNsawNxMS0wNw-- Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
[PyMOL] trouble selecting residues with mouse
I have been trying to run the latest version of MacPyMOL on my new iMac with an Intel Core 2 Duo processor and the latest version of OSX. I have noticed problems trying to select residues with my mouse (either control-clicking to select or double clicking to get the menu). I can select some residues normally, but for others, when I control-click on them, a residue in another part of the protein gets selected. Still other residues cannot be selected at all using the mouse. This also happens with I try to pick atoms with the mouse. I've seen this happen with multiple PDB files and older versions of MacPyMOL as well.I don't have any problems selecting residues or atoms with the command line. This problem seems to be similar to the one that someone was having with the X11 version a couple of weeks ago. Does anyone have any suggestions? Thanks. Heidi ~~ Heidi K. Privett Graduate Student Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. MC 114-96 Pasadena, CA 91125 USA priv...@caltech.edu
Re: [PyMOL] function keys
Sorry for emailing you direct but I am having issues with
posting to the bulletin board. I think it is our end.
You're not the only one -- overzealous anti-spam measures at SourceForge are
causing problems for legitimate users.
Anyway I was wondering if there was a function key
(keystroke) shortcut for stereo?
Not built-in, but you can add such a key as follows:
cmd.set_key('F1',lambda:cmd.stereo({'on':0,'off':1}[cmd.get('stereo')]))
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Not yet a PyMOL Subscriber, but want to support the project? Email
sa...@delsci.com to quote your lab, school, or employer. Thank you for
sponsoring this open-source endeavor! -WLD
[PyMOL] caver plugin
Hi Has anyone successfully used Caver plugin using gromac trajectory files? Any suggestion is appreciated. Thanks Murali -- Dr. Ramachandran Murali Associate Professor 243 John Morgan Building Department of Pathology Lab. Medicine University of Pennsylvania Philadelphia, PA-19104-6082 Ph: 215-573-9256; Fax: 215-898-2401
[PyMOL] Using server CPU instead of client GPU?
Dear PyMOL users, We are using an old SGI (O2) classroom for teaching in a client/server setup in which compute-intensive modeling programs run on a few fast servers but display on slow SGI terminals. This works fine with some applications but PyMOL obviously recognizes SGI OpenGL setup and will use this for rendering, which makes things rather slow. Is there a way to redirect PyMOL to use server's CPU for some of the tasks, such as calculating the surfaces? Thanks in advance, Kalju ~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara
[PyMOL] caver plugin
Hi Has anyone successfully used Caver plugin using gromacs trajectory files? Any suggestion is appreciated. Thanks Murali -- Dr. Ramachandran Murali Associate Professor 243 John Morgan Building Department of Pathology Lab. Medicine University of Pennsylvania Philadelphia, PA-19104-6082 Ph: 215-573-9256; Fax: 215-898-2401
Re: [PyMOL] Using server CPU instead of client GPU?
Kalju, 1. Old SGIs have pitiful graphics performance when compared to modern PC graphics cards. You would likely get better results running PyMOL locally on a PC desktop or laptop than on an old SGI workstation. 2. Surfaces are calculated server-side, however, PyMOL was not optimized for client/server setups. set use_display_lists, 1 might help a bit when displaying surfaces and other complex geometries. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Kalju Kahn Sent: Thursday, February 08, 2007 1:38 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Using server CPU instead of client GPU? Dear PyMOL users, We are using an old SGI (O2) classroom for teaching in a client/server setup in which compute-intensive modeling programs run on a few fast servers but display on slow SGI terminals. This works fine with some applications but PyMOL obviously recognizes SGI OpenGL setup and will use this for rendering, which makes things rather slow. Is there a way to redirect PyMOL to use server's CPU for some of the tasks, such as calculating the surfaces? Thanks in advance, Kalju ~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara -- --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
