Sebastien,
Yes, you can do with with a "p1m" file, which is like a "pml" file, but data can be
included as well. Also note that p1m files are intended for web publishing, so embedded Python is
disallowed. In p1m files, there is an "embed" command that enables this for PDB, MOL, MOL2, SDF,
an
Hi,
I need the rms values from pymol in an extra output file.
I tried to make it the same way like in the pymol / python example for
intra_rms.
rms = cmd.rms (selection1, selection2)
but it doesn't work.
Is this command line correct, or there are other possibilities to get access
to the vari
Hi,
I am trying to show different pdb files successively in a movie, loading the
first and displaying certain residue contacts, then dropping it and loading
the second, etc... Is this possible? If so, how do I drop a file?
Any advice would be greatly appreciated.
Thanks.
Nadine
___
Hi everybody,
I want to write a PCA script (.py) for use within PyMOL. Are there any matrix
operations or eigenvector calculations implemented by now, or do I have to
integrate other libraries? How do I do that in Linux?
Thanks for your help.
Yusuf
--
Yusuf Tanrikulu
Bioinformatics Diploma Stu
Hi Warren and PyMOL users,
It seems that a lot of the bigger protein molecules, when displayed, have
parts of them either clipped to thin threads or disappear when the rest of
the structures display perfectly in cartoon mode. (e.g. 1yce.pdb; 1dgj;
1s5l; 1wxr; 1p2y.) I thought it was a matter of
Yusuf,
You can use the Numeric Python or Numarray modules to perform such
tasks. The windows builds include a (somewhat dated) version of Numeric
by default that can be accessed as follows:
from Numeric import *
http://numeric.scipy.org/
Numeric's Linear algebra docs
http://numeric.scipy.org/
Nadine,
The way you'd do this PyMOL is by either loading multiple PDB files into
PyMOL as molecular states and then playing through them sequentially, or
by loading multiple objects and turning them on and off sequentially.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal
Libo,
This problem has been reported before with certain graphics card /
driver combinations. No solution is known, so my only suggestion is to
upgrade the drivers or consider replacing the graphics card.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLa
Daniel
> rms = cmd.rms (selection1, selection2)
will fail outright because "rms" is a PyMOL keyword. PyMOL only passes
input off to Python if it doesn't see a keyword following by a space as
the first word of the input line. Eliminating that first space, using a
different variable name, or addi
Hi Yusuf
The OpenSource statistics software "R" (http://www.r-project.org) has many
packages that can do PCA, PLS and other multivariate analyses, which we have
used with great success.
There are several Pyhton interfaces to R, eg.
http://www.omegahat.org/RSPython/
http://rpy.sourceforge.net
Hello,
Is there a way to use pymol to draw multiple copies of a structure. I want to
be able to specify the translation vectors and have pymol draw multiple copies
of a given structure.
thank you.
Sreekala.
Try, LAPACK packages. Available for most GNU/Linux
distributions
--
Message: 4
Date: Tue, 19 Jul 2005 14:53:47 +0200
From: tanri...@stud.uni-frankfurt.de
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Implementing PCA
Hi everybody,
I want to write a PCA script
Wan,
unset ignore_case
However note that doing this means that all atom selection will need to
be case-specific. For example
name ca
resn phe
glu/
must become
name CA
resn PHE
GLU/
etc.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific
Hello All-
From what I've read, the 'cartoon putty' command uses the PDB B-
factor value to determine the appearance of the sausage diagram. How
can I use the 'cartoon putty' command with NMR structures in a way
that represents the structure ensemble, similar to that as the MOLMOL
sausage
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