-mode-alist))
(global-font-lock-mode)
-- END .emacs excerpt
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
-Original Message-
From: DeLano, Warren
Charles,
.dat is a hopefully oversubscribed file extension, and the .dat
which PyMOL currently recognizes is for Macromodel. If you are have
some development skills, consider writing a Python-based CSD file parser
for the Chemical Python portion of PyMOL. Any ChemPy model can be
loaded
Danny,
I think your problem is one of two possibilities: either your
LD_LIBRARY_PATH is not being set correctly by pymol.com, or your
python1.5.so shared object isn't valid.
You might try using linking against a static Python library as described
in
Ricardo,
Yes, ray makes a huge difference in quality. You get true specular
reflections (not just OpenGL interpolations), you get perfectly round
spheres, you get shadows, you get clean transparent surfaces (without
artifacts), and you get better depth-cue fogging (although with light
Michael,
Try checking out a new copy of the source code from the current CVS
repository -- the Makefiles have been simplified somewhat, so
compilation under Linux may go easier. You should only need to change
the Python version in one place : )
Read INSTALL.linux-rh7x
Cheers,
Warren
--
NOTE: the following is unix-specific.
This is a common problem with PyMOL. Right now it is impossible (in
practice) to use PyMOL as merely an imported module within an external
interpreter (i.e. without using pymol.com instead of python to
invoke the interpreter). This will be fixed in a later
Busy day on the list : ) I'll take this one...
From: Albion Baucom [mailto:bau...@biology.ucsc.edu]
Nice to hear from you Albion, glad to see you're finally getting a
chance to try the package.
I want to make high resolution, smooth (high frame rate)
playing movies of
the Ribosome.
Great
From: Eckhart Guthöhrlein
I'm trying to use pymol for the display of pdb files
containing multiple
models using the MODEL card. Indeed, pymol reads in all
models in the file.
Currently, I'm able to switch between them using the frame
command. Is
there a different way to do this?
From: Mario Sanchez [mailto:sanc...@if.sc.usp.br]
I am drawing hydrogen bonds using command dist, but the rayied image
has a too thick line to these interactions. I was not able to find the
command to set the thickness of it, but I hope someone
(DeLano?) will be
able to help me.
You can
From: Byron DeLaBarre [mailto:by...@slac.stanford.edu]
Anyone out there know how to prevent bonding of adjacent but
chemically
unconnected atoms in pymol?
Two step process:
1. edit the PDB file and replace ATOM with HETATM
2. after the HETATM's add a single record CONECT following by
Gareth,
That is an unusual error. I suspect it has something to do with your
symbolic links, which isn't the most reliable way to solve the dependency
problem. Instead, delete those symlinks, and modify Rules.make to seek out the
system libraries in the usual location. Rules.linux-rh7x
From: Marc Saric [mailto:marc.sa...@mpi-dortmund.mpg.de]
2. Let's Introduce Your Company To China Government
(investcn2...@yahoo.com.cn)
^ ^ ^ ^
Shouldn't that have been filtered out?
Absolutely. After digging into the settings, I found that SourceForge doesn't
protect these
Michael,
A present, you can't simply import the PyMOL program as a module. You
need to use PyMOL as your Python interpreter.
You can use Run from the File menu or the run command from within PyMOL.
PyMOLcd c:\some_directory
PyMOLrun myscript.py
Since you are under windows, you can use the
My guess is that you may still be showing sticks in the original object,
instead of just cartoons. If you have the same overlapping representation in
two objects, it isn't predictable which will show up in the ray-tracer, and you
can get exactly this behavior, where you see one color in OpenGL
From: Kristian Rother [mailto:kristian.rot...@berlin.de]
As suggested by Warren, i have made some improvements to the
ScriptBox,
which should integrate better into PyMOL now,
Thanks Kristian!
On my page, there is also a 'quick and dirty' hack for PyMOL.
FilePipe.py allows to execute
From: Johan Leckner [mailto:jo...@pasteur.fr]
I'm having problems running PyMol from within another Python program.
This is not the recommended way to run PyMOL and may lead to problems. You can
run Python programs within PyMOL as follows:
from the command-line:
pymol example.py #
Jeff,
It would take a little Python programming, but modules/pymol/util.py
has the rainbow command which can be modified so as to give a more restricted
gradient than the current rainbow.
usage:
load prot.pdb
util.rainbow(prot)
(or just select the rainbow option on the color pop-up
Trissa,
I think that the line may have been wrapped in your copy of the input file. Try
making sure that entire Python in the script file appears on a single line --
then it should work.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis
So there is no way to run and control PyMol from within
another python program?
If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you
can launch PyMOL from an external Python program as shown in
examples/devel/start_pymol.py.
However, this is not recommended
Not right now...
In order to build PyMOL without linking to real GL libraries, you'd either need
a fake copy of the GL API, or #define out all of the gl calls in PyMOL (many
hours of work).
Sorry!
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis
Molecular sculpting works like a real-time energy minimizer, except that it
isn't minimizing the energy. Instead, its just trying to return local atomic
geometries (bonds, angles, chirality, planarity) to the configuration the
molecules possess when they were first loaded into PyMOL.
To
alter eys/,type='ATOM'
sort
The problem is that, by default, PyMOL doesn't create ribbons for HETATMs
(typically ligands and solvent). With the above command, you're converting
selenocysteine residues into regular atoms and sorting them into place so that
they can be included in the ribbon.
No, not a stupid question. PyMOL doesn't currently provide a means for doing
this -- I'll put it on the list...
Cheers,
Warren
-Original Message-
From: Luca Jovine [mailto:lucajov...@mac.com]
Sent: Thursday, August 08, 2002 4:41 PM
To: Mailing List PyMol
Subject: [PyMOL] How to
layer4/Selector.c
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/layer3/Selector.c
search for SELE_ARD_ and SELE_EXP_ in SelectorModulate1 in
and SELE_BYR1 in SelectorLogic1
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341
Yes, the Fink and GNU/Darwin versions of PyMOL are unaccelerated. As far as I
know, the only way to get access to hardware is to call Apple's
platform-specific OpenGL libraries from within a platform-specific window.
I am still working on the native OSX port, but with competition from all
Michael,
None of the official releases have Amber trajectory support (although
the mac 0.84 beta may have an early version of this code). I'm planning on
another release near the end of September.
If you can build from the CVS repository, then you can use the code today:
(1) make
Scott,
isomesh msh1, map1, 1.5, myobject, carve=2.1
The postfix carve=2.1 will trim density which is more than 2.1 A from
myobject.
You may want to play around with the exact cutoff...
Cheers,
Warren
-Original Message-
From: Scott Classen [mailto:clas...@uclink.berkeley.edu]
Hi Jeremy,
If the proteins have significant homology, then you can use the align command:
align prot1ca,prot2
which will perform a sequence alignment of prot1 against prot2, and then an
optimizing fit using the CA positions. I'm not sure if the help text for align
got into 0.82, but the
From: George Nicola
I've tried several settings and commands but cannot figure out how to make
a simple ball-and-stick representation of a molecule. Can it be done in
Pymol?
George,
Yes, but it is non-obvious:
hide lines
show sticks
show spheres
set stick_radius=0.1
set sphere_scale=0.25
Shohei,
The easiest way to do this is to split the objects and then use the rotate
command.
# save as a .pml file...
load 1FJ1.pdb
# split PDB file
create anti=(chain F)
create fab=(chain A,B)
# delete original object
delete 1FJ1
# color objects
color green,fab
color pink,anti
# color
Yep, we ran into the same problem with our ESGI emitters and FireGL2 cards --
we ended up having to buy new StereoGraphics (E-2) emitters for the Linux
machines (~$200).
http://www.qualixdirect.com/
part # SV-008-A-PC-E2
Cheers,
Warren
-Original Message-
From: Viktor Hornak
Thanks for the suggestion?
For now, why not just redefine the existing colors?
No need for a leading underscore...
set_color green= [0.00 , 0.53 , 0.22]
etc.
Note that there are default atom colors such as carbon, nitrogen, oxygen,
hydrogen, sulfur, etc. which should also be redefined.
From: Jules Jacobsen [mailto:jo...@hermes.cam.ac.uk]
you can change most of the parameters using set dash_n where
n= length,
width, gap, radius. Unfortunately dash_color doesn't exist.
...but you can change the color of a distance object
color red,dist01
Warren
Gordon,
I fully agree with your assessment that PyMOL is currently unable to reach
its potential due to a number of factors, including poor documentation.
Nevertheless, I do have a defined plan for eliminating these deficits. It
involves securing funding to hire people under contract
This is undocumented:
To get a list of settings:
from pymol import setting
print setting.get_name_list()
To get the current value of a setting:
print setting.get_setting_text(bg_rgb)
print setting.get_setting_text(gamma)
To get a list of names with values:
print map(lambda
mset 1 x360
movie.roll 1,180,1,axis=y
movie.roll 181,360,1,axis=x
-Original Message-
From: Craig Smith [mailto:boiler...@mac.com]
Sent: Wednesday, October 30, 2002 11:43 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] making a two step movie in pymol
How do I create a
Scott,
From: Scott Classen [mailto:clas...@uclink.berkeley.edu]
Hello fellow PyMOLers,
Is the surface in PyMOL a solvent accessible surface or
a molecular
surface? It looks like a solvent accessible surface to me. Is
there any
way to change the radius of the water probe that is
Bill,
There has been some discussion of this desirable feature, but it doesn't
currently exist.
Cheers,
Warren
-Original Message-
From: wgsc...@chemistry.ucsc.edu [mailto:wgsc...@chemistry.ucsc.edu]
Sent: Tuesday, November 12, 2002 1:27 PM
To: pymol-users@lists.sourceforge.net
Keith,
Thank you for bringing this issue to my attention.
I can confirm that PyMOL doesn't currently read SCALE records. In order
to generate correct crystal symmetry, it requires the input PDB coordinates to
be properly oriented and translated with respect to the crystal
Chris,
If you are talking about a controlled zoom into a specific active site
region, there isn't any automated way to do this. Peter's movie.zoom routine
can help with a general zoom. Try this:
fragment arg
mset 1 x100
movie.zoom 1,100,1,0
mappend 1:move z,-100
rewind
mplay
Cheers,
Stephen,
You're looking for the PyMOL API function extend:
from pymol import cmd
cmd.extend(ramp_colors,ramp_chain.ramp_colors)
Would then permit the following:
ramp_colors chain A
See help extend for more info...
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Tara,
Use Python (and the run command with .py files).
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write(%8.3f\n%dst)
f.close()
You could measure the whole protein this way by putting a loop around the
distance command:
from pymol
Jack,
What are all those extra Q atoms in the pdb file? They look to me like
compromise/placeholder coordinates for NMR-equivalent hydrogens...or something
like that.
To get a reasonable picture, you can get rid of the extra bonds with
unbond elem q*,all
or just nuke the Q atoms
From: Nukri Sanishvili [mailto:rsanishv...@anl.gov]
There is a new thing (I'm pretty sure it's a bug, not a
feature) in 0.86:
When I Tab for command completion, the command ends with a
comma when in
fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set
Jacob,
It look to me like you've found a bug in PyMOL with the manual
approach. What's happening is that the result of a subsequent ignore command
isn't updating the surface which was created before it. The scripted behavior
is correct, since all geometric objects should reflect the
Bartholomeus,
You have run into limitations in PyMOL's handling of single objects.
The answer to both these questions is to split your molecule into multiple
object and color/show independently. Use the create command to make copies,
and then use alter to reassign secondary structure codes
Anthony,
I agree that we need one, but it doesn't currently exist. The same can be said
for surface calculations, especially when you've loaded a 500 frame MD
trajectory and accidentally show surface (doh!).
My advice: save sessions often and make liberal use of PyMOL's logging
capability.
. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
-Original Message-
From: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br]
Sent: Thursday, February 06, 2003 7:41 AM
To: DeLano
internal raytracer isn't likely to support perspective any time
soon. Instead, I recommend using PovRay.
Cheers,
Warren
Subject: Re: [PyMOL] different transparencies
DeLano, Warren wrote:
Because of the way settings work in PyMOL, you will need to
split your spheres into different objects
Dear PyMOL Users and Friends,
It is with great excitement and anticipation that I announce a new
phase for PyMOL: Beginning April 3rd, 2003, I will be committed FULL-TIME to
the development, documentation, and support of this Open-Source package through
my limited liability company,
Kevin,
It looks to me like you are missing Numeric Python. Either you need to
remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy
installed. There is likely a Fink package which contains it, but I suspect
this dependency may have been missed in the creation of the
Fred,
Not currently. To the rest of the list: How important is this to
people? Please send me an email directly if you think it would be an important
feature to add.
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
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