Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
Hi, > AFAIK, Debian's glibc uses tls/nptl only on Linux-2.6, not on Linux-2.4. > So using a 2.6 kernel should be fine. However, I do not have Nvidia > hardware to test this. Yes, I'm using the Nvidia driver 1.0-6111 on a Debain Sarge with the 2.6.7 kernel without any problems. Best regards, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
[PyMOL] re: Warning: Nvidia 6111 drivers for linux
There is one another solution. You can install Nvidia linux drivert with "-force-tls=classic" option. The command line loks like this : NVIDIA-Linux-x86-1.0-5336-pkg1.run -force-tls=classic cheers Vladimir Message: 7 Date: Wed, 13 Oct 2004 18:12:11 +0200 From: peter.du...@cellbio.unige.ch To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Warning: Nvidia 6111 drivers for linux Hello. I did a scan (albeit brief) of the mailing list for this issue, but didn't find it, so I decided to post it FYI. I wanted to mention a serious issue I just discovered after installing the new nvidia drivers for linux (specifically regarding the "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the same is true for all other 6111 drivers), on a 2.4.x kernel, as well as the solution. It may be important to make a note of this somewhere in the FAQ or installation instructions (or perhaps it would be easy to fix in one of the pymol scripts). PROBLEM: Running Pymol gives the following message: Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 90, in ? import pymol File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 306, in ? import _cmd ImportError: libnvidia-tls.so.1: cannot handle TLS data SOLUTIONS: == There are 2 solutions to this problem. (1) either rename /usr/lib/tls to something else, or delete it entirely. Pymol then works perfectly ok. However, since this is akin to "If it hurts, cut it off", it might break something down the line. Do note though, that the files contained within this dir are also in /usr/lib (not a symbolic link). (2) edit /etc/default/nvidia-glx (if it exists, for me it didn't), and set USE_TLS to 0. Reboot. Surely there must be another editable config file somewhere with this option, but I haven't found it. According to a thread on PyKDE, "The tls (thread local storage) stuff only works if you are running a tls-enabled glibc on a 2.6 kernel, and when installing nvidia-glx, you are normally asked by debconf on what to use." This suggests anyone running the new nvidia drivers on a 2.4.x kernel may encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, so I can't be sure the problem doesn't occur there either. Hope this helps someone. Cheers,
[PyMOL] Benchmarking of graphics cards - drivers with pymol
Hi all: I am trying to benchmark our graphics cards or more specifically different versions of the Linux NVidia drivers with pymol. I cobbled together a short python script, which I thought would do the trick but it did not. The intent was to rotate a representation a certain number of degrees in 1 degree increments and clock the time which had elapsed. That should give me a rough idea how well the drivers perform plus pymol/python overhead which should be constant. The problem is that I cannot figure out how to force pymol to redraw every frame of the animation on the screen. It just does the turns silently without actually displaying them. I also tried using the combination of mset, roll and mplay, but there the movie does not stop after specified number of frames, although in all fairness the docs did not indicate it should. Any ideas out there how to approach this in a better way are welcome. I attached the script, may be it is just something simple I am missing. Cheers, Carsten Carsten Schubert, Ph.D. Structural Biology J&J PRD (Exton) 665 Stockton Drive, Exton, PA, 19341, USA Tel:610-458-5264 Ext:6579 Fax:610-458-8249 eMail: cschu...@prdus.jnj.com bench.py Description: Binary data
Re: [PyMOL] pymol + gromacs trajectories
Hi Bruno,
Sure I'm aware of that, but for a bit of a system (as I usually have) and
a good bit of trajectory (as I usually have), that will ask for quite some
memory. Did it a few times, but prefer to use separate pdb's instead.
Though admitted that for small systems, a multistate pdb works great.
Cheers,
Tsjerk
On Thu, 14 Oct 2004, Bruno Afonso wrote:
> Hello,
>
> It's possible to convert to a single pdb file containing all the frames
> using:
>
> trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr
>
> You can then load it into pymol using:
>
> pymol trajout.pdb
>
> And it will load all the frames.
>
> If you render a movie into png you will have lots of *.png files, which
> you can convert into a movie using the following command:
>
> convert *.png ppm:- | ppmtoy4m | yuvscaler -O SVCD | mpeg2enc -f 3 -b
> 4500 -q7 -o mpegfile.m2v
>
> For this you need imagemagick (convert) and mjpeg-tools (rest)
>
> I've just started out doing some MD simulations and I was trying to use
> pymol to see the simulations (vmd is more widely used for this) and this
> is what I've came up so far. Next I will need to make a pymol script to
> automatically render the png files, preferably without running X as my
> number crunching box isn't even connected to a monitor.
>
> Best,
> BA
>
>
> Tsjerk Wassenaar wrote:
> >
> > Hi Yunfeng Hu,
> >
> > Frankly, with Pymol, people don't as far as I know. What I usually do is
> > determine for the first frame of the individual pdb files (obtained with
> > trjconv -sep) the orientation, viewing point and appearance. This I save
> > in a .pml script. Then with a bit of python code, looping over the
> > frames, calling them, processing the script, raytrace, write the image
> > and delete the object again. It's at present the best I can think of. It
> > appears that Dino is capable of processing a gromacs trajectory and
> > outputting raytraced frames, but I haven't felt like starting at the
> > bottom of that learning curve...
> >
> > To help out a bit, the loop code could look like this:
> >
> > for i in range(nr_of_frames):
> >cmd.load('frame_' + repr(i) '.pdb', 'prot')
> >cmd.do('@script.pml')
> >cmd.delete('prot')
> >
> > Everything to go in script.pml could ofcourse also be explicitly given
> > in the loop...
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > Yunfeng Hu wrote:
> >
> >> Hi, I wonder if people can give a summary of how pymol makes movies
> >> out of gromacs trr (or xtc) files without having to use all the
> >> individual frame pdb files. Thanks!
> >>
> >> Eric
> >>
> >>
> >>
> >> ---
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> >
> >
> >
> >
>
>
--
~
-- :)
-- :) Tsjerk A. Wassenaar, M.Sc.
-- :) Molecular Dynamics Group
-- :) Dept. of Biophysical Chemistry
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Re: [PyMOL] pymol + gromacs trajectories
Hello,
It's possible to convert to a single pdb file containing all the frames
using:
trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr
You can then load it into pymol using:
pymol trajout.pdb
And it will load all the frames.
If you render a movie into png you will have lots of *.png files, which
you can convert into a movie using the following command:
convert *.png ppm:- | ppmtoy4m | yuvscaler -O SVCD | mpeg2enc -f 3 -b
4500 -q7 -o mpegfile.m2v
For this you need imagemagick (convert) and mjpeg-tools (rest)
I've just started out doing some MD simulations and I was trying to use
pymol to see the simulations (vmd is more widely used for this) and this
is what I've came up so far. Next I will need to make a pymol script to
automatically render the png files, preferably without running X as my
number crunching box isn't even connected to a monitor.
Best,
BA
Tsjerk Wassenaar wrote:
Hi Yunfeng Hu,
Frankly, with Pymol, people don't as far as I know. What I usually do is
determine for the first frame of the individual pdb files (obtained with
trjconv -sep) the orientation, viewing point and appearance. This I save
in a .pml script. Then with a bit of python code, looping over the
frames, calling them, processing the script, raytrace, write the image
and delete the object again. It's at present the best I can think of. It
appears that Dino is capable of processing a gromacs trajectory and
outputting raytraced frames, but I haven't felt like starting at the
bottom of that learning curve...
To help out a bit, the loop code could look like this:
for i in range(nr_of_frames):
cmd.load('frame_' + repr(i) '.pdb', 'prot')
cmd.do('@script.pml')
cmd.delete('prot')
Everything to go in script.pml could ofcourse also be explicitly given
in the loop...
Hope it helps,
Tsjerk
Yunfeng Hu wrote:
Hi, I wonder if people can give a summary of how pymol makes movies
out of gromacs trr (or xtc) files without having to use all the
individual frame pdb files. Thanks!
Eric
---
This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
Use IT products in your business? Tell us what you think of them. Give us
Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out
more
http://productguide.itmanagersjournal.com/guidepromo.tmpl
___
PyMOL-users mailing list
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https://lists.sourceforge.net/lists/listinfo/pymol-users
--
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http://brunoafonso.net
http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs!
http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum
Re: [PyMOL] molecular Mechanics calculations
On Oct 13, 2004, at 14:40, Gabriel PAËS wrote: Is it possible to make some basic molecular mechanics calculations in PyMOL, in fact I would like to measure the binding energy between a protein and various ligands? Not with just PyMOL, as far as I know. However, you can use the MMTK release with PyMOL interface that I recently announced here to write PyMOL scripts and plugins that calculate energies and do other molecular mechanics operations. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hin...@llb.saclay.cea.fr -
Re: [PyMOL] using package Scientific from within pymol on OS X-X11 hybrid
On Oct 13, 2004, at 19:47, gilleain torrance wrote:
however, it turns out that if you copy the entire (python) source tree
of Scientific - IE:
"ScientificPython/Scientific/"
into
"/Applications/PyMolX11blahHybridetc/py23/lib/python2.3/site-packages"
Apparently you are using the X11 hybrid version for MacOS. This comes
with its own Python installation, but there doesn't seem to be a way to
use its Python interpreter separately, outside of PyMOL, so the
standard installation script for Scientific Python (or any other
package) cannot be used.
There are three solutions:
1) The one you used. Its main disadvantage is that you don't get the C
modules of Scientific Python, i.e. the netCDF interface.
2) Install Scientific Python with another Python 2.3 installation (i.e.
the one that comes with MacOS 10.3, or the one from fink) and copy
site-packages/Scientific from that installation to the the place you
already discovered.
3) [Hypothetical, I did not test this]. Modify the setup.py in such a
way that it does the buiild and install steps without requiring command
line parameters, then run it using the "run" command from inside PyMOL.
I used solution 1).
hopefully! Anyway, there might be a better way, but this works. One
tiny glitch is the change from Numeric to numarray. This can be
'fixed' ('hacked') by using *cough*perl*cough*:
perl -i -p -e 's/Numeric/numarray/g' *.py */*.py
which should substitiute all instances of 'Numeric' with 'numarray'.
But the PyMOL hybrid distribution comes with Numeric, not numarray. Or
has this changed recently? Mine is 0.95.
For daily use, I prefer to build PyMOL from source under the Python
that comes with fink. In that way, I have all my python packages
available for PyMOL scripts. In fact, I had almost forgotten that I
still had the X11 hybrid on my machine.
Konrad.
--
-
Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hin...@llb.saclay.cea.fr
-
[PyMOL] Re: PDB-Codes
Dear Christian,
Summary:
From within the same PyMOL instance, the command
pdb 1n1m
works, but the script
> from pymol import cmd
> time.sleep(1)
>
> list = ('1n1m')
>
> for strc in list:
> pdb strc
does not.
(IMO, the import is not necessary here).
Analysis:
You use the code above as a PyMOL .pml script. Thus, PyMOL will interpret each
command primarily as a PyMOL command. If no matching command is found, the
Python things will be tried.
Translation:
PyMOL probably thinks that 'strc' is the PDB-code rather than the variable. It
tries to download 'pdbstrc.ent' from the PDB server.
Question:
Does a script just containing
'pdb 1n1m' work? I guess yes.
Solution - Go Python:
script.py
---
from pymol import cmd
time.sleep(1)
list = ('1n1m')
for strc in list:
cmd.do('pdb %s'%(strc))
start it with:
run script.py
I hope that helps,
Kristian
Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
On Wed, Oct 13, 2004 at 06:12:11PM +0200, peter.du...@cellbio.unige.ch wrote: > According to a thread on PyKDE, "The tls (thread local storage) stuff only > works if you are running a tls-enabled glibc on a 2.6 kernel, and when > installing nvidia-glx, you are normally asked by debconf on what to use." > > This suggests anyone running the new nvidia drivers on a 2.4.x kernel may > encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, > so > I can't be sure the problem doesn't occur there either. AFAIK, Debian's glibc uses tls/nptl only on Linux-2.6, not on Linux-2.4. So using a 2.6 kernel should be fine. However, I do not have Nvidia hardware to test this. cheers, Michael
Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
Chen, Kernel: 2.4.26 (I observe the same with 2.4.25) Distribution: Debian (straight SARGE, and pymol was acquired with apt-get, so no funny compiling business here) Python: 2.3 (2.4 is also there, but only for testing purposes) I've noticed on other mailing lists, that people have reported similar error messages with other packages. This is how I found the original solutions. I just wanted to report that it also occurs with Pymol. Perhaps you are right, perhaps it's a python problem, but I'm not prepared to roll back to 2.2 to test it. > What Linux are you using? Seems it's not a problem on RedHat linux, I am > running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel respectively, > and the exact same NVIDIA version without any problem at all. > Although we are using python2.2, looks like you are using python2.3, maybe > that's the problem? > > Best > Chen Robert, According to what I've managed to learn from googling around a bit, this problem doesn't occur on 2.6.x kernels. > I'm running Fedora Core 2 with: > (II) Module glx: vendor="NVIDIA Corporation" > compiled for 4.0.2, module version = 1.0.6111 > > And: > 2.6.8-1.521 #1 Mon Aug 16 09:01:18 EDT 2004 i686 athlon i386 GNU/Linux > > With no problems whatsover... > > Robert Well, I'm glad to hear this problem isn't as endemic for Pymol users as I had feared. What surprised me was that it happened on a fresh Debian install. The solutions I had posted earlier *do* solve the problem (they did for me), so hopefully the information will be useful to some people who encounter it. Regards, Peter _.--'"`'--.__.--'"`'--.__.--'"`'--.__ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' ` Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Scinces III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@cellbio.unige.ch http://www.picard.ch/DP/DPhome.html _.--'"`'--.__.--'"`'--.__.--'"`'--.__ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' `
