[PyMOL] depth cue and strand thcikness
Hi, Is there a way to change the depth cue rendering to go from light to dark rather than the dark to light as the default is? Also, is there a way to change the thickness of the strands in the cartoon representation? Sorry if it is in the archives, the sourceforge site seems to be down at the moment. Thanks balaji
[PyMOL] Alpha channel support gone?
What has happened to alpha channel support in PNG output? I could have sworn it used to be there. I'm now working in version 0.9. thanks Jean-Philippe Cartailler Vanderbilt University Medical Center S-3223 Medical Center North 1161 21st Avenue South Nashville, TN 37232-2372 Phone: 615.322.7729 FAX: 615.343.7156 email: jp.cartail...@vanderbilt.edu www: http://www.cartailler.com
RE: [PyMOL] Alpha channel support gone?
Jean, Did you set ray_opaque_background, 0 ? Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Cartailler, Jean-Philippe > Sent: Wednesday, October 08, 2003 7:46 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Alpha channel support gone? > > What has happened to alpha channel support in PNG output? I could have > sworn it used to be there. I'm now working in version 0.9. > > thanks > > Jean-Philippe Cartailler > > > Vanderbilt University Medical Center > S-3223 Medical Center North > 1161 21st Avenue South > Nashville, TN 37232-2372 > > Phone: 615.322.7729 > FAX: 615.343.7156 > email: jp.cartail...@vanderbilt.edu > www: http://www.cartailler.com > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Accessing PyMol's commands from outside (or without viewer)
Hi, This should be a trial question though I cannot find a way of doing it. I have a simple script that looks like this: (the original commands, rather than cmd.select..) select ligand, resn XYZ select protein, ! ligand select box, protein within 8 of ligand select box, box or byres box save box as box.pdb I don't need the viewer at all and would be even more efficient if I can call the PyMol API from the shell. Or, in a python script. For example, I would like to have something like: ./pymol select_box.py thanks!
RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
Shu-hsien
Sure, instead of cmd.select, use
cmd.do("select ligand, resn XYZ")
cmd.do("select protein, ! ligand ")
etc.
./pymol -qc select_box.py
Is the command line mode of PyMOL. "pymol -qc" can be used like
"python" in most cases.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu
> Sent: Saturday, November 08, 2003 10:58 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Accessing PyMol's commands from outside (or without
> viewer)
>
> Hi,
>
> This should be a trial question though I cannot find a way of doing
it.
> I have a simple script that looks like this:
> (the original commands, rather than cmd.select..)
> select ligand, resn XYZ
> select protein, ! ligand
> select box, protein within 8 of ligand
> select box, box or byres box
> save box as box.pdb
>
> I don't need the viewer at all and would be even more efficient if I
can
> call the PyMol API from the shell. Or, in a python script.
> For example, I would like to have something like:
> ./pymol select_box.py
>
> thanks!
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> SourceForge.net hosts over 70,000 Open Source Projects.
> See the people who have HELPED US provide better services:
> Click here: http://sourceforge.net/supporters.php
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Ribbon+cylinder representation of nucleic acids: now it can be done in PyMOL!
Dear PyMOLers, You might remember that some time ago I posted a message asking whether it was possible to make PyMOL display nucleic acids similarly to Ribbons (i.e. with backbone and bases represented by a ribbon and cylinders, respectively). At the time there was unfortunately no simple way of doing so, however, Kevin Weeks later on kindly suggested me a first way to display base cylinders within PyMOL. Based on Kevin's suggestion, I have now written a program - nuccyl - that allows to get the kind of representation we were looking for in a semi-automated way. As usual, pictures are much more meaningful than words, so you can see what I mean by having a look at some examples (static pictures and downloadable PyMOL session files) here: http://www.mssm.edu/students/jovinl02/research/nuccyl.html As explained much more throughly on the same page, which includes a step-by-step tutorial, you can either use RNAView to identify base pairs in your nucleic acid, or manually write a simple file containing this information. nuccyl will use this data to calculate coordinates for base cylinders which can be then displayed by PyMOL. If you are interested, you can download the program from the same link. I hope you will find nuccyl useful; please let me know of any problem you encounter, and of course suggestions and criticisms will always be welcome. Ciao, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell & Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com - luca.jov...@mssm.edu W3: http://www.mssm.edu/students/jovinl02
Re: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
Dear Dr.DeLano,
Thanks! That really helps!
Two more questions:
Does the 'pymol -qc' takes command line variables (os.argv in python)?
For example, the first line of my script would be:
cmd.do('load %s' %os.argv[1])
Second question might be off a little bit.
Is it possible to wrap PyMol as a module of Python? I know can be
installed as a Python module, but that doesn't seem to be able to let me
do things like:
# Sample Python script
import PyMol
PyMol.cmd.do('..')
distance = PyMol.cmd.do('distance ..')
Does it make any difference whether or not I installed PyMol independant
of Python?
I am a bit confused with cmd.do vs cmd.select.
So, if I am writing a script for running in PyMol(using @some_script.py),
I should use:
import PyMol
cmd.select('...')
If I am writing a script for running PyMol in command line,
I should use:
from PyMol import cmd
cmd.do('...')
Kind of confused...
-shuhsien
Shu-hsien
Sure, instead of cmd.select, use
cmd.do("select ligand, resn XYZ")
cmd.do("select protein, ! ligand ")
etc.
./pymol -qc select_box.py
Is the command line mode of PyMOL. "pymol -qc" can be used like
"python" in most cases.
Cheers,
Warren
RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
> Two more questions:
> Does the 'pymol -qc' takes command line variables (os.argv in python)?
> For example, the first line of my script would be:
> cmd.do('load %s' %os.argv[1])
That's not possible. In order to get this behavior (for now) you need
to treat PyMOL as a module (see below).
> Second question might be off a little bit.
> Is it possible to wrap PyMol as a module of Python?
Yes, but to do this (in most cases), you'll have to recompile and
install PyMOL as a standard "distutils" module. If you're not familiar
with compilation, then this isn't for you...
python setup.py build install
python setup2.py install
Then from python
import pymol
pymol.finish_launching()
can work
> I know can be
> installed as a Python module, but that doesn't seem to be able to let
me
> do things like:
>
> # Sample Python script
> import PyMol
> PyMol.cmd.do('..')
> distance = PyMol.cmd.do('distance ..')
Close.
from pymol import cmd
distance = cmd.distance('tmp',sele1,sele2)
> Does it make any difference whether or not I installed PyMol
independant
> of Python?
> I am a bit confused with cmd.do vs cmd.select.
cmd.do places string command to the PYMOL parser input queue and returns
nothing.
cmd.functionName calls the PyMOL API and returns the result (if any).
> So, if I am writing a script for running in PyMol(using
@some_script.py),
> I should use:
> import PyMol
> cmd.select('...')
>
> If I am writing a script for running PyMol in command line,
> I should use:
> from PyMol import cmd
> cmd.do('...')
The only time you'd use cmd.do is for convenience...
cmd.do("select cas, name ca")
will always be substantially slower than
cmd.select("cas","name ca")
because an extra parsing step in involved.
Cheers,
Warren
> Kind of confused...
>
> -shuhsien
>
> >Shu-hsien
> >
> >Sure, instead of cmd.select, use
> >
> >cmd.do("select ligand, resn XYZ")
> >cmd.do("select protein, ! ligand ")
> >
> >etc.
> >
> >./pymol -qc select_box.py
> >
> >Is the command line mode of PyMOL. "pymol -qc" can be used like
> >"python" in most cases.
> >
> >Cheers,
> >Warren
> >
> >
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> SourceForge.net hosts over 70,000 Open Source Projects.
> See the people who have HELPED US provide better services:
> Click here: http://sourceforge.net/supporters.php
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
