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 simil
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
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
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 wit
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
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
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
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
T
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 u
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,
Di
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