[PyMOL] Learning Python for PyMOL
David Schuller asked about the best books for learning Python. There are two key resources: (1) Guido's online tutorial is a good starting point for learning the language. http://www.python.org/doc/current/tut/tut.html and (2) Python Essential Reference by David M. Beazley, (New Riders) is a must-have reference for writing Python code. These tare what got me going a couple years back along with the other documentation files on the Python web site. http://www.python.org/doc/current/ NOTE: In order to write Python effectively, you need an editor which supports its indentation scheme. The top choices are (1) emacs running python-mode, or (2) IDLE, the editor included with most Python distributions. Writing Python without a Python-aware editor is a thankless task due to Python's sensitive block structures which would be a chore to maintain. I recommend that you use spaces instead of tabs to indent Python code -- PyMOL's convention is 3 spaces per block. The relavent portions of my .emacs file are included below in case anyone is interested. I think most modern Linux distrubutions include a python mode in emacs by default. For simple tasks, the PyMOL command language (.pml files) is easier than Python because you can ignore the identation issue. However, .pml files are suited for real programming. Cheers, Warren -- BEGIN .emacs excerpt (setq-default visible-bell t) (setq-default backup-inhibited t) (setq-default auto-save-default nil) (global-set-key \C-c\C-w 'goto-line) (setq-default tab-stop-list '(3 6 9 12 15 18 21 24 27 30 33 36 39 42) ) (setq-default tab-width 3) (setq-default py-indent-offset 3) (setq-default indent-tabs-mode nil) (setq auto-save-default nil) (setq auto-save nil) (setq load-path (cons /usr/share/emacs/site-lisp/ load-path)) (autoload 'python-mode python-mode Python editing mode. t) (setq auto-mode-alist (cons '(\\.py$ . python-mode) auto-mode-alist)) (setq auto-mode-alist (cons '(\\.pym$ . python-mode) auto-mode-alist)) (setq interpreter-mode-alist (cons '(python . python-mode) interpreter-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 Sent: Monday, December 10, 2001 7:40 AM To: Glen L. Prosise Cc: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux) Gang, Last night I posted binaries of PyMOL 0.73 for Windows and Linux to the downloads page. Read more at http://www.pymol.org This is the first version to support fragment and residue-based molecular building. However, you may find the process challenging with the current rudimentary interface. Cheers, Warren ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] CSD .dat files
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 straight into PyMOL. This approach doesn't have quite the performance as native C reads but, it will suffice for moderate-throughput applications. Example Python code for reading MOL files can be found in modules/chempy/mol.py. The code is just over 105 lines and supports both reads and writes. One should be able to add a CSD reader with just an hour or two starting with a description of the CSD file format. Just focus on the atom symbols, coordinates, bonds, and bond orders...the rest can be dealt with later on. I propose using the extension .csd for csd structure files. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. From: Ross, Charles [mailto:charles.r...@stjude.org] I am running latest version (0.73) on an SGI Octane running IRIX 6.5.14m. Structures extracted from the Cambridge Structural Database have the extension .dat. This extension is recognized by PyMol, although perhaps not as a structure file - when I read it, I get no errors, but I get no structure either. Does PyMol recognize CSD structure files, and if so, what is the proper extension? thanks Charles Ross Department of Structural Biology St. Jude Children's Research Hospital ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] pymol on SGI
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 http://pymol.sourceforge.net/workarounds.html
Good luck!
Warren
--
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: Danny G Smith [mailto:d...@omega.omrf.ouhsc.edu]
Sent: Tuesday, December 18, 2001 12:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] pymol on SGI
I have complied pymol-0_73, with ext-0_51, useing the following
build.com in the ext subdirectory. When I try to run pymol.com I get
the following message:
omega[272]:/misc/local/src/pymol/pymol % ./pymol.com
Traceback (innermost last):
File /misc/local/src/pymol/pymol/modules/launch_pymol.py,
line 6, in
?
import pymol
File
/misc/local/src/pymol/pymol/modules/pymol/__init__.py, line 24,
in ?
import _cmd
ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
Fatal Error: Cannot Successfully map soname 'libpython1.5.so'
under any
of the filenames
/usr/local/lib/libpython1.5.so:/usr/lib32/libpython1.5.so:/usr
/lib32/internal/libpython1.5.so:/lib32/libpython1.5.so:/opt/li
b32/libpython1.5.so:
omega[273]:/misc/local/src/pymol/pymol %
Any help would be appreciated.
# build.com in ext directory
#!/bin/csh
#
#-
# Build script for making PyMOL External dependencies
#-
# (can't do this stuff in a makefile cause we need to define
# some important environmental variables)
#
#- Paths -
#
# --- Base
#setenv BASE /home/local/export/ext
setenv BASE /misc/local/src/pymol/pymol/ext
#
#- Targets
-
# -- Linux with just Tcl/Tk
# setenv PYMOL_TARGETS tcl tk zlib python distutils numpy
pmw png-linux
glut-linux
#
# -- Linux with Tcl/Tk and wxPython
# setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw
png-linux
glut-linux glib gtk wxgtk wxpython
#
# -- SGI/IRIX with just Tcl/Tk
# setenv PYMOL_TARGETS tcl tk zlib python distutils numpy
pmw png-irix
glut-irix
#
# -- SGI/IRIX with Tcl/Tk and wxPython
setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw png-irix
glut-irix glib gtk wxgtk wxpython
#-
#
#- For creation of a shared python library --
# --- Linux
#setenv LDALLFLAGS --whole-archive
# --- SGI/IRIX
setenv LDALLFLAGS -n32 -all
#-
#
#- Misc --
#
# --- SGI/IRIX
setenv SGI_ABI -n32
setenv MAKE gmake
setenv CXX CC
#
# --- Linux
#setenv MAKE make
#
#- Path pre-emption critical for building gtk/wx -
#
setenv PATH ${BASE}/bin:$PATH
setenv LD_LIBRARY_PATH ${BASE}/lib
#
#- Build
--
$MAKE -f Makefile.in $1
--
thanks,
Danny G Smith
UNIX Systems Administrator
Crystallography Dept Oklahoma Medical Research Foundation
phone 271-8954 fax 271-7953
=
UNIX air conditioned environment, keep the windows closed
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RE: [PyMOL] ray doubts
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 backgrounds you'll probably want to set ray_trace_fog to 0). It renders all objects in the scene except for labels (which it is incapable of handling at present). Yes, you need to render (ray-trace) again after the image is rotated. (If you rotate an object, the shadows move). Most of the figures you see in the top journals are generated using Molscript and Raster3D (or PovScript and PovRay) using a process very similar to the ray command. PyMOL simply makes creation of such figures much easier since you only need one program and you get to preview the exact image before-hand (set orthoscopic=0 to get a pixel-for-pixel match between OpenGL and the ray tracer). Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. From: Ricardo Aparicio [mailto:apari...@if.sc.usp.br] Dear PyMol users, as stated in the manual, command ray creates a ray traced image of the current frame. This can take some time (up to several minutes, depending on image complexity). My question is: - is it necessary? Does it make great difference in the final quality of figures published (in the case of a paper)? - does it renderize(?) all the active objects in the screen? - after finished ray process, if the image is rotated, is it necessary to renderize again (I think no, just to confirm) Many thanks, Ricardo Aparicio PhD Student - USP Sao Paulo - Brazil ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Installing from source on a linux box
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 -- 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: Michael George Lerner [mailto:mler...@umich.edu] Sent: Monday, January 28, 2002 1:44 PM To: pymol-us...@sourceforge.net Subject: [PyMOL] Installing from source on a linux box Hi, I have PyMol up and running on my windows partition .. the installation was super easy. Now, I want to set it up on my Linux partition. I have Mandrake 8.1 installed, which means that my default python version is 2.1. It also means that many things (Numeric, zlib, etc..) are pre-installed for me. So, I downloaded the PyMol sources and tried to install it. In the external packages bit, it looked like the only thing I need is glut. So, I changed the setenv BASE line in build.com to point to the right place (/home/mglerner/src/pymol/ext in my case) and changed the setenv PYMOL_TARGETS line to say glut-linux and did ./build.com. I also tried ./build.com glut-linux for variety .. both seemed to work. Then I went up a directory into the main pymol directory. I then moved Rules.linux to Rules.make and edited it. There were many instances of -lpython1.5 .. I changed all of them to -lpython2.1. It was still having some trouble finding libpython2.1, so I added -L/usr/lib/python2.1/config to the LIB_DIRS line. After typing make, things get pretty far, but it doesn't get far enough. I wasn't sure how many of the error messages to include, but I've tacked on the last screen or so of output at the end of this message. There were some things that made me think that various parts of this build process were really looking for python sources in the ext directory, so I placed a copy of the python 2.1 sources there just in case. It didn't seem to help. Sorry if this is a dumb question, -michael -- begin output from make -- make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules' rm -f *.o *~ rm -f *.a tags TAGS config.c Makefile.pre python sedscript rm -f *.so *.sl so_locations VERSION=`../../ext/bin/python -c import sys; print sys.version[:3]`; \ installdir=`../../ext/bin/python -c import sys; print sys.prefix`; \ exec_installdir=`../../ext/bin/python -c import sys; print sys.exec_prefix`; \make -f ./Makefile.pre.in VPATH=. srcdir=. \ VERSION=$VERSION \ installdir=$installdir \ exec_installdir=$exec_installdir \ Makefile /bin/sh: ../../ext/bin/python: No such file or directory /bin/sh: ../../ext/bin/python: No such file or directory /bin/sh: ../../ext/bin/python: No such file or directory make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules' make[3]: *** No rule to make target `/lib/python/config/Makefile', needed by `sedscript'. Stop. make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules' make[2]: *** [boot] Error 2 make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules' make[1]: *** [make-modules] Error 2 make[1]: Leaving directory `/home/mglerner/src/pymol/contrib' make: *** [.contrib] Error 2 -- end output from make -- -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] using external python interpreter to control pymol ??
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 version. For example: #!/bin/csh python END from pymol import cmd cmd.cls() END ...will fail. For now, you need to use the pymol.com script to launch your Python interpreter if you are going to use PyMOL. Normal commands are interpreted first by PyMOL and then passed to Python if PyMOL doesn't recognize the command. You can skip PyMOL evaluation with a preceeding /, which is almost equivalent to typing the same command (without a preceeding slash) in a Python interpreter: print hello /print hello However, you can run native Python script in external using the run command: run myscript.py ...which is almost equivalent to typing: python myscript.py ...on the unix or windows command shell, or by issuing execfile(myscript.py) ...from within an existing Python interpreter. IMPORTANT CONCEPT: The key difference between python myscript.py# on command line pymol.com myscript.py # on commmand line run myscript.py # in PyMOL is that default evaluation in PyMOL currently takes place in the pymol module, not __main__. Right now there is no easy way to start a process in the __main__ module. I will remedy this in the next public release, and probably make __main__ the default namespace for the run command (so long as that doesn't break anything). You can however, force evaluation of your script to occur in its own name-space: run myscript.py,module ...or in a local namespace: run myscript.py,local -- 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 From: Ingo Dramburg [mailto:dramb...@mailer.uni-marburg.de] Hi, I want to include my own modules into PyMOL for visualization purposes. If I try to use the pymol.cmd module to control a running PyMOL process from an external python interpreter I always get a segmentation fault. (SuSE 7.2, Python 2.0) Everything else works fine. Example: from pymol import cmd cmd.cls() segmentaion fault Is it possible to do such things in general or is it possible to switch to a 'native' python mode in the PyMOL window to enter python commands directly :-). The next question is how can I pass selections from PyMOL to external scripts to do calculations that are not supported by PyMOL and later back to PyMOL for visualization. Thanks you for any help, Ingo. -- Ingo Dramburg Institute of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, D 35032 Marburg, Germany Tel. + 49 6421 282 1313 Fax + 49 6421 282 8994 e-mail dramb...@mailer.uni-marburg.de http://www.agklebe.de/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] RNA and Pseudo-atom Models
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 -- PyMOL should be up to the task provided that you've got a fast machine with tons of RAM. Ideally I would like to move seperate objects in the view separeately, that is have things dock in the movies. I dont know if PyMol will do this yet ... Yes, it can do this using the translate, origin, and rotate commands. Unfortunately the docs are incomplete, so I recommend you take a look at the Python code in modules/pymol/editing.py (rotate, translate) and viewing.py (origin) for the specific calling conventions. def rotate(axis='x',angle=0.0,selection=all, state=0,camera=1,object=None): def translate(vector=[0.0,0.0,0.0],selection=all, state=0,camera=1,object=None): def origin(selection=(all),object=None,position=None): Here's a key bit of information for these commands: If you pass the object name using 'object=...', then you'll translate the entire object matrix. If instead you pass in a selection with object still equal to NULL, then you'll translate the atom coordinates within the object. This functionality is still primitive, but I think it will do the job...play around with them for a while, see if you can get them to do what you need. Now, the rRNA I have is phosphorus atom only, with some allatom proteins some CA-only proteins. Ugh -- this is something PyMOL doesn't yet handle well, and you're the third person to draw my attention to this in the last couple weeks! PyMol opens the psueudo-atom rRNA as a cloud of atoms, presumably because it does not know how to bond these files. That is my first question. How, and what do I modify (bond definition file) to make it bond the adjacent atoms of the phosphorus only backbone? There is no bond definition file (yet -- this will be changed in the future). Except for HETATMS, PyMOL connects atoms based on proximity, not dictionary lookups. The quick-and-dirty solution is to add explicit CONECT records for the atoms into the PDB file for the phosphates. My second question for now is once I bond it, will Pymol be able to render a cartoon using the P atoms to interpolate? Nope, PyMOL won't be fooled by such trickery. It will only draw ribbons between phosphates separated by six bonds (i.e. in real nucleic acids). Minor code changes will be required to accomplish what you're looking for. You might be able to comment-out the line in RepCartoon.c, but I haven't tested the idea. Look for: if(!ObjectMoleculeCheckBondSep(obj,a1,a2,6))... My only workaround ideas now are to take the pseudo-atom model, use CNS (generate.inp) to build in the rest of the bases, use that to generate the cartoon, and undisplay the stick representation (which of course will have completely bogus conformations). Im not sure what biases the built in bases will impose on the cartoon if PyMol uses them to interpolate the ribbon. Unfortunately for now you'll have to provide full coordinates in order to get ribbons. This is probably a decent way to go. At some point I would like to draw pseudo-bonds between base-paired pseudo-atoms, but I will see if I can do the above before that. Such bonds can be drawn using the dist command. Cheers, Warren
RE: [PyMOL] multiple MODEL files
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? Something like next_model or
prev_model or show_model ...?
Furthermore, I tried to use the selection command to access models.
The model operation in the selection command allows you to select objects by
number -- not models in the sense of multi-model PDB files. The first PDB file
you load is model 1, the second is model 2, etc. Sorry for the confusion.
Model was a bad choice in terminology and should be replaced with an object
operator instead. However, the chemical python package uses model instead of
object, so it's probably a hopeless case.
PyMOL treats multi-model PDB files like trajectories, in that each model is one
state of the trajectory. You can display them as a series of frames as you
were doing. You can use the left and right arrow keys to iterate through, or
the forward and back commands, or press the play button. You can use mset to
display states in a different order, etc.
color red,(model 10)
leads to
SelectorSelect1-Error: Invalid Model
PyMOL: abrupt program termination
That's a flat-out bug. Thanks for finding it.
although model 10 exists and has been read in, as shown before by the
message
As I indicated above, model/object 10 doesn't actually exist, but PyMOL
certainly shouldn't crash...I'll fix that.
How to access models in an atom selection?
You can't address atoms individually in one model or another without breaking
them into separate objects. You can do this using a Python loop and use the
create command after loading the model file.
When you create an atom selection, you are essentially selecting all states of
those atoms. However, many commands take a state argument, which is the
1-based index for which state you wish to operate on for the atom selection.
This is what allows you to change the conformations of atoms in a particular
state, for instance. NOTE the PyMOL's atom selections can span any number of
objects...
Another question: Is there a way to list details about the currently
available objects? Like sequence, secondary structure, how many
models/chains/ etc.? And the current properties like colour,
charge etc.
of an atom selection? I just browsed the manual very quickly,
so sorry
if I overlooked the information.
The manual stinks. Some volunteer with more time than myself needs to team up
with me to create a decent manual -- but one can't complain too much about free
software. I can think of more than one company that will sell you an expensive
closed-source license similar packages, and still not provide you with a decent
manual. If you prefer DeLano Scientific's open-source approach, then be sure
to support it with effort or funding.
The key commands are alter, alter_state, iterate, and label -- and they
represent the heart of PyMOL's built-in atom property manipulation capability.
However, there are a bunch of other commands for manipulating coordinates and
geometries.
iterate (all),print name
iterate (all),print color
iterate (all),print partial_charge
iterate (name ca),print resn,resi,s
alter (all),vdw=vdw*0.5
alter (all),resi=int(resi)+10
alter (chain E),chain='C'
alter_state 1,(all),x=x+2.0
label (name ca),resi
label (all),name
label (all),%1.2f%vdw
In all cases, a Python expression is evaluated for each atom in the selection.
See help iterate, etc., but note that the docs are incomplete. To see all
the properties which can be printed or altered, load a model and then try:
iterate (index 1),print locals().keys()
Note that you can also obtain and manipulate a complete copy of any model (erg,
object) at the Python level, using Python code like:
from pymol import cmd
m = cmd.get_model('old')
m.atom[0].name='C1'
cmd.load_model(m,'new')
Cheers,
Warren
RE: [PyMOL] H-bonds too thick
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 generally tweak fix hese kinds of issues using one of PyMOL's many settings -- most of them have verbose names. Try Edit All under the settings menu for a complete list. In this case: set dash_radius=0.10 ray - Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D.
RE: [PyMOL] easy (?) question
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 nothing but a new-line. This will signal PyMOL to expect explicit connectivity (of which there will be none). In the future, if you need to specify connectivity explicitly, this is how you do it using a PDB file (CONECT records followed by connectivity info) Note if you need to surface hetatms, set surface_mode=1 or alter (all),type='ATOM' followed by sort and rebuild. Same for goes for meshes. And along those lines, anyone had success with showing a Calpha trace? I tried once but couldn't figure out how to get pymol to connect the individual Calpha atoms. I think this must be easy to do but I couldn't work it out at the time. So long as the N and C atoms are also present, the ribbon representation can do this. It looks for CA atoms three bonds apart to form the trace. To get a linear C-alpha trace (no smoothing), set ribbon_sampling=1 Warren
RE: [PyMOL] Linux install problem
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 should be your starting point for Rules.make. Cheers, Warren -- 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: Gareth Stockwell [mailto:gar...@ebi.ac.uk] Sent: Friday, May 03, 2002 4:00 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Linux install problem I am having a problem installing PyMol 0.80 on my (Redhat 7.1) Linux box. I already have Tcl, Tk, Python 2.1, zlib and libpng so I just made libglut from the ext-0.79 package. cd $PYMOL_PATH/ext ./build.com glut-linux The GL libraries are in strange places on my system, so I made the following links: ln -s /usr/lib/libGL.so.1 $PYMOL_PATH/ext/lib/libGL.so ln -s /usr/lib/libGLU.so.1 $PYMOL_PATH/ext/lib/libGLU.so ln -s /usr/X11R6/lib/modules/extensions/libGLcore.a \ $PYMOL_PATH/ext/lib/libGLcore.a Then I built the PyMol program cd $PYMOL_PATH/pymol vi Rules.make make The 'make' succeeds, but when I execute pymol.com, I get Traceback (most recent call last): File /ebi/research/thornton/ligands/gareth/src/pymol-linux/pymol/m odules/launch_pymol.py, line 19, in ? import pymol File /ebi/research/thornton/ligands/gareth/src/pymol-linux/pymol/m odules/pymol/__init__.py, line 137, in ? import _cmd ImportError: /usr/X11R6/lib/libICE.so.6: shared object not open This shared object file exists - is there any reason why this error should occur? Gareth P.S. I don't have root access on this system -- - Gareth Stockwell PhD student, Thornton Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
RE: [PyMOL] Let's Introduce Your Company To China Government
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 lists by default (grumble), but I changed the settings so only list members will be able to post from now on. Contact me directly if you have any trouble posting. We lost about 5 subscribers from that PRC spam. - Warren -- 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
RE: [PyMOL] problem importing pymol.cmd module
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 DOS/Win command shell: C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe myscript.py # command-line only scripts C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe -qc myscript.py - Warren -- 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: Sorich, Michael Joseph - SORMJ001 [mailto:michael.sor...@postgrads.unisa.edu.au] Subject: [PyMOL] problem importing pymol.cmd module I have just started to use PyMol. I wish link some scripts I have written in python with PyMol using PyMol’s API. From what I understand, all I need to do is import the module pymol.cmd and call the functions contained within. However, when I attempt to import this module, I get the following error: from pymol import cmd Traceback (most recent call last): File pyshell#0, line 1, in ? from pymol import cmd File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\__init__.py, line 137, in ? import _cmd ImportError: No module named _cmd Where have I gone wrong? Any help would be appreciated.
RE: [PyMOL] Colors and ray-tracing
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 and a different one in the raytracer. Here is the general sequence of steps you'll want to follow to insure success: load prot.pdb create cpy,prot hide show cartoon,prot show sticks,cpy color red,prot color green,cpy ray -- 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: Peter Stogios [mailto:pstog...@uhnres.utoronto.ca] Sent: Tuesday, May 28, 2002 9:08 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Colors and ray-tracing This topic was touched on before but I'm still having problems with it. Somebody asked how to color sticks differently from cartoons and Warren explained that this can be done by creating duplicate objects. I managed to accomplish that, but when I ray-trace the image the cartoon takes the same color as the stick does. As soon as I move the ray-traced image, it restores back to the different colors, as I want them. For example, I colored the cartoons in one object green, while I showed only sticks in the duplicate object and colored a specific residue stick blue. When I ray-trace the image, the cartoon at that residue turns green, instead of staying blue. Is this a bug or how can I get around this? Thanks in advance. -- Peter Stogios Dept. of Medical Biophysics, Univ. of Toronto ___ Don't miss the 2002 Sprint PCS Application Developer's Conference August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Update to ScriptBox 0.3 for PyMOL
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 PyMOL commands from a shell. It starts its own thread and reads lines from a text file. This doesn't work well, but it works. Does anyone have a better idea to do this? Try launching PyMOL with the -p option. PyMOL will then accept commands on standard input using a separate thread, in a manner similar to what you describe. See 'help launching' for other command line options. Cheers, Warren
RE: [PyMOL] How to run PyMol from within Python?
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 # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module pymol -l example.py # asychronous in a new module You can also launch python programs from within PyMOL with the commands: run example.py# synchronous in pymol module run example.py,main # synchronous in __main__ module spawn example.py# asychronous in a new module spawn example.py,global # asychronous in the PyMOL module spawn example.py,main # asychronous in the __main__ module see: help launching help run help spawn Following the examples in /pymol/examples/devel I have been able to launch and controll PyMOL. The problem occur when I try to quit PyMol (version. 0.82) however I do it I end up with a fault terminating my Python interpreter. Under Redhat 7.1/Python 2.1 i get a segmentation fault and under MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same result both when quitting from the gui or within python with the command cmd.quit() How can I quit PyMol properly? I know for a fact that the Mac take-down process is currently flawed, and frequently gives a bus error. Because it only happens after you quit the program, its a low priority issue... Not sure about Redhat. Warren
RE: [PyMOL] color gradient
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 menu on prot) Cheers, Warren -- 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: jeff chao [mailto:jac...@scripps.edu] Sent: Thursday, July 11, 2002 2:40 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] color gradient i would like to make a color gradient (something like purple-cyan) from N to C. is there an easy way to do this? thanks, jeff ^^ Jeffrey A. Chao The Scripps Research Institute PHONE: (858)784-8743 Molecular Biology MB 33 FAX: (858)784-2903 10550 N. Torrey Pines Road E-MAIL: jac...@scripps.edu La Jolla, CA 92037 USA ^^
RE: [PyMOL] Re: movie -script - conversion from .png to .tga
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 Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: patricia.a.elk...@gsk.com [mailto:patricia.a.elk...@gsk.com] Sent: Monday, July 15, 2002 10:05 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Re: movie -script - conversion from .png to .tga I am trying to run the mkmov1.pml script from the Pymol page. I am stopped at the line /for i in glob(png/*):os.system(convert +i+ re.sub(png, tga, re.sub(_,.,i))) I get the errors: Traceback (innermost last): File /apps/pymol/modules/pymol/parser.py, line 98, in parse exec(com2[nest],pymol_names,pymol_names) File string, line 1 for i in glob(png/*): os.system(convert +i+ ^ SyntaxError: invalid token PyMOL+re.sub(png,tga,re.sub(_,.,i))) Traceback (innermost last): File /apps/pymol/modules/pymol/parser.py, line 234, in parse exec(com2[nest],pymol_names,pymol_names) File string, line 1 +re.sub(png,tga,re.sub(_,.,i))) ^ SyntaxError: invalid syntax Without knowing python, I haven't been able to figure out what is wrong with the input line. Can anyone help? Thanks! Trissa
RE: [PyMOL] How to run PyMol from within Python?
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 because the PyMOL launch sequence is not fixed. If you do use it, be prepared to deal with changes down the road. The reason for asking is that we are working on a python platform to run and evaluate protein-protein docking calculations. It would be a nice feature to be able to call up interaction surfaces and protein-protein clusters for display in PyMol and then interact with them from within our program. As things are now I'm forced to treat PyMol as I would treat any molecular graphics program, that is write macros macros for it. This is of course much less convenient and less flexible compared to running PyMol from within our python code. Has anyone been able to run and quit PyMol from within python without killing the interpreter? Is it possible? How? The underlying source of the limitation here is that the GLUT and Tcl/Tk libraries which PyMOL uses do not support repeated set-up/take-down -- they are both static global systems which steal threads and never return. Thus, while PyMOL is not inherently limited in this fashion, these building blocks which it employs are. Eventually there will be versions of PyMOL which are both GLUT and TCL/Tk independent -- but not today. Instead, I recommend using some kind of inter-process communication along with object serialization to pass data from your program into PyMOL. Python makes this relatively easy, but you are looking at a little bit of development. Sorry the news isn't better! Warren
RE: [PyMOL] pymol without GL
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 Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Nathaniel Echols [mailto:n...@mail.csb.yale.edu] Sent: Tuesday, July 16, 2002 12:09 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol without GL quick question: I'm trying to do batch jobs on a server. Obviously, there's no X or OpenGL installed. Is there any way to build PyMOL without any graphical frontend, and just use it as a raytracer? I don't want to go through the trouble of adding in these libraries... thanks, Nat --- This sf.net email is sponsored by: Jabber - The world's fastest growing real-time communications platform! Don't just IM. Build it in! http://www.jabber.com/osdn/xim ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] molecular sculpting
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 actually use this feature: 1. load a PDB file 2. configure the mouse for editing (Mouse menu) or click in the mouse/key matrix box 3. select auto-sculpting from the Sculpting menu 4. select Sculpting from the Wizard menu 5. ctrl-middle-click on any atom in your protein to activate sculpting the green part will be free to move the cyan part will be a fixed cushion to provide context the grey part will be excluded 6. now perform any conformational editing operation in the green region such as: ctrl-left-click-and-drag on an atom ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond You can adjust the radius and cushion using the blue pop-up menus. Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future. Warren -- 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: patricia.a.elk...@gsk.com [mailto:patricia.a.elk...@gsk.com] Sent: Thursday, July 18, 2002 4:04 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] molecular sculpting I would like to understand the molecular sculpting possibilities of pymol but haven't been able to figure it out yet. When using the wizard, the first request is to click and atom but how to proceed from there? I have used the bit of script provided on the web page and deformed the benzene ring but have not been clever enough to see the possibilities from that. Could anyone provide just enough of a step-by-step push-this, click-that lead into the molecular sculpting to get me started? Thanks! Trissa
RE: [PyMOL] Problem with Seleno-Cysteine
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. Cheers, Warren -- 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: joer...@altavista.fr [mailto:joer...@altavista.fr] Sent: Tuesday, August 06, 2002 7:43 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Problem with Seleno-Cysteine Hi everybody I have the structure of a Molybdo-CODH (CO-Dehydrogenase), which contains a Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb) The residue b/388 is denoted as EYS in the pdb file. In the cartoon representation, pymol does not display this part of the backbone (I get a hole in the cartoon structure). I can display this residue using show sticks, resi 388, and I can pick every single atom, even the selenium. Any idea how I can display the backbone without break? Thanks joerg Internet et mail gratuit AltaVista http://www.altavista.fr --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] How to ouput a PDB file with transformed coordinates?
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 ouput a PDB file with transformed coordinates? Hello PyMolers, This is probably a really stupid question, but, is there a simple way to create a PDB file with *transformed* coordinates? The save command always seems to save the original coordinates, even after altering the view with set_view etc... I apologize in advance if this is obvious, Thanks Luca Luca Jovine, Ph.D. 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 W3: http://www.mssm.edu/students/jovinl02 --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] byres, around, expand etc
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 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Michael Tallhamer [mailto:tallha...@hotmail.com] Sent: Tuesday, August 13, 2002 6:49 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] byres, around, expand etc I would like to take a look at the code for these selection keywords: (byres, around, expand ... etc) Does anyone know where to find it? Thanks, Michael Tallhamer Undergraduate Researcher Cleveland State University E-mail: tallha...@hotmail.com _ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx --- This sf.net email is sponsored by: Dice - The leading online job board for high-tech professionals. Search and apply for tech jobs today! http://seeker.dice.com/seeker.epl?rel_code=31 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol slow on a mac G4 with os 10.1
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 the other PyMOL priorities: such as new features, bug-fixes, and support, not to mention my own career and personal life, it is taking far longer to complete than I anticipated. There was an incomplete test version available with acceleration, but OS 10.2 has reportedly broken it. If you can put up with software rendering, then X-windows based Fink or GNU/Darwin versions are fine. But if you want fast PyMOL, then an x86-based PC with Windows or Linux is the only alternative (we're talking about a 10-50X performance difference of hardware over software -- huge!). Plus, PC's can do stereo -- Macs can't. If you need fast 3D graphics on a Mac, I'd encourage you to look around for other 3D viewers for at least the next couple months. VMD reportedly has a native version...though I haven't tried it myself. Warren -- 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: Russell Poyner [mailto:rpoy...@facstaff.wisc.edu] Sent: Friday, August 23, 2002 7:56 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol slow on a mac G4 with os 10.1 The machine is a newish G4 733Mhz 256K ram with a radeon 7500 card. I have installed the Fink version of pymol with the Fink supplied Xfree. It works but is noticably slower than pymol on my 500 Mhz K6/lintel box, also with a radeon 7500 and Xig xserver. It would seem that the mac installation is not benefitting from the graphics hardware despite claims of full acceleration in the xserver. If there is a trick here that I am missing please let me know. Thanks Russell Poyner --- This sf.net email is sponsored by: OSDN - Tired of that same old cell phone? Get a new here for FREE! https://www.inphonic.com/r.asp?r=sourceforge1refcode1=vs3390 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Re: Amber
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 sure that your trajectory and topology files have the same prefix and end in .top and .trj respectively. Also make sure that your topology exactly corresponds to the trajectory file (you may need to create a new topology file if you've deleted some atoms from the trajectory). (2) Now load them: load parm.top load_traj parm.trj help load_traj has some additional options, such as start, stop, average, interval, selection... So long as trajectories are generated from the same topology, you can concatentate them as follows: load_traj part1.trj,parm load_tram part2.trj,parm load_traj part3.trj,parm For now, you'll probably want to preprocess your trajectory using ptraj in order to center, average, and perhaps to remove waters. And you'll need to create a new topology file reflecting any atom deletions. Tom Cheatham and I are talking about trying to fold a copy of ptraj into PyMOL, but don't have any definite plans yet. Cheers, Warren -- 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
RE: [PyMOL] electron density maps
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] Sent: Friday, September 20, 2002 3:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] electron density maps Hello fellow PyMOL users, I am trying to display a ccp4 map over just a ligand. I have successfully read in the map and displayed it around the ligand with: isomesh msh1, map1, 1.5, myobject but the map has bits and peices of the surrounding sidechains. Is there a way to only display the map around my ligand? Thanks, Scott == Scott Classen clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 229 Stanley Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 == --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] pair_fit crashes
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 next version will definitely have it. PyMOL's command length is limit to about 1000 characters, which is probably what is causing pair_fit to crash. However, ideally it should complain gracefully instead of crashing, so if you have a sample script input PDB files which cause it to crash, please send them to me as attachments. As far as script options go, you've pointed out a hole which I had forgotten about, but Robert's suggestion on defining a function call in the script is definitely the way to go for now. Cheers, Warren -- 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: Jeremy Craven [mailto:c.j.cra...@sheffield.ac.uk] Sent: Thursday, September 26, 2002 2:00 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pair_fit crashes I have been trying to write a script to overlay two arbitrary proteins via my own alignment and the 'pair_fit' command. 1) After running into the problem I described below I looked through the pymol-users mailing list as hard as I could and found a statment that such arbitrary alignment should be in pymol anyhow from vsn 0.80. I am using 0.82 but cannot find it. Is it there ? 2) Anyhow, (and assuming that I might want to do alignments my own way anyhow), I created a script which read in an alignment and created a big long pair_fit command of the form pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr and resi 192 and name ca),(bs and resi 175 and name ca), etc The script then executed this string with cmd.do If I restricted this to about 10 atom pairs it worked fine. If I allow more atoms it crashes the program. On linux it gave segmentation violation. On irix it gave bus error. On irix it gave another message that implied that maybe the selections had got truncated. On linux it got as far as giving a sensible 'ExecutiveRMS' message (including a value for the rmsd and the number of atoms) and then froze and eventually core dumped. It therefore seems that the long selection has been accepted properly, but may it corrupts something else as a side effect ? Any ideas anyone ?? I wondered about doing all the selections invidually into named selections and then create a shorter pair_fit command, but decided I would ask here first. A second little quesion is how do you send command line arguments to a pymol python script. If I say PyMOL run test1.py abcdef it says Traceback (most recent call last): File /usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py, line 186, in parse execfile(args[nest][0],pymol_names,pymol_names) IOError: [Errno 2] No such file or directory whereas test1.py really does exist, and run test1.py works fine. Otherwise pymol is a great joy to have discovered in the last month or so, and a project that I hope I can support (e.g. by contributing scripts like this one once I can get it to work properly ...) Cheers Jeremy -- * Dr C. Jeremy Craven Department of Molecular Biology and Biotechnology University of Sheffield, Firth Court, Western Bank S10 2TN Sheffield UK e-mail: c.j.cra...@shef.ac.uk http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html Phone: x24323 From outside Sheffield: 0114 222 4323 From outside UK: +44 114 2224323 Fax: 0114 272 8697 *
[PyMOL] RE: pyMol help (Ball Sticks)
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 You can change the two numbers above to fit preferences. Cheers, Warren
RE: [PyMOL] moving one segment relative to the rest
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 interface select inter = (byres ((fab within 5 of anti)\ or (anti within 5 of fab))) color yellow,inter # splay apart orient origin fab rotate y,60,fab origin anti rotate y,-60, anti # zoom interface region zoom inter show sph,inter disable inter -Original Message- From: Shohei Koide [mailto:sko...@uchicago.edu] Sent: Monday, September 30, 2002 12:14 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] moving one segment relative to the rest Hello, I am wondering if one can move one segment (in my case, an antigen protein) relative to the rest of the complex (antibody) using PyMOL. So far I have only been able to translate/rotate the entire complex. I would like to manually undock the complex for an illustration purpose. Thanks. Shohei Koide --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Stereographics CrystalEyes problem
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 [mailto:hor...@csb.sunysb.edu] Sent: Tuesday, October 08, 2002 2:19 PM To: Schubert, Carsten Cc: pymol-users Subject: Re: [PyMOL] Stereographics CrystalEyes problem Carsten, your guess sounds very likely to me. Unfortunately, we only have ESGI emitters so I cannot confirm it for sure (but I bet you're right). Thanks a lot for the tip. Cheers, -Viktor Schubert, Carsten wrote: just a wild guess, but in order to get stereo to work on my PC (under W2K) with a Oxygen GVX card I had to use a ENT emitter from Stereographics. As far as I recall the regular emitters used on the SGI's, type ESGI, did not work. Hope it helps. Cheers Carsten -Original Message- From: Viktor Hornak [mailto:hor...@csb.sunysb.edu] Sent: Tuesday, October 08, 2002 15:45 To: pymol-users Subject: [PyMOL] Stereographics CrystalEyes problem Hello, I followed the discussion on 3D stereo support in PyMOL and saw that many people were able to get PyMOL in stereo with FireGL or Nvidia cards. Finally I got the chance to try it out myself with a new NVIDIA Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the latest nvidia drivers (1.0-3123). There were no problems to get accelerated X up with blazingly fast PyMOL rendering. So next, I tried to get stereo working. I am using Stereographics emitter and CrystalEyes which I've been using with our SGIs (so that I know they are functional; in fact PyMOL works in stereo on our SGIs without a problem). I plugged the emmiter into the DIN on my Quadro4 card, put Option Stereo 3 into my XF86Config-4, restarted X and hoped that things will just work. According to XFree log file, X was really initiated in stereo mode. The emmiter light turned on when I started PyMOL. I switched to 'quad buffered stereo' and the molecule getss rendered in stereo but when I look at it with CrystalEyes glasses nothing changes. I still see double rendered image on the screen, which means that the emmiter does not synchronize glasses correctly (or at all). I tried to change some options in XF86Config-4 but nothing helped, so I was wondering if someone experienced the same problem. Do Stereographics emmiter and CrystalEyes glasses work with Quadro4 at all? Do I need to get a different emmiter or glasses? Any help appreciated... --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] CMYK colors
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. set_color carbon= [0.00 , 0.53 , 0.22] etc, Warren -Original Message- From: Gil Prive [mailto:pr...@uhnres.utoronto.ca] Sent: Friday, October 18, 2002 1:38 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] CMYK colors This is not directly PyMOL specific, but it addresses a problem I think a lot of us have encountered in preparing hardcopy outputs. Some RGB triplets do have equivalents in CMYK space, and as a result, a figure that looks great on a screen can come out with unpredictable colors when printed. Most applications do a good job with RGB-to-CMYK conversions for photos, but do not do such a good job with graphics that use pure primary colors. For example, reds are generally OK, but pure blues and greens do not translate very well. Here are some RGB values that are within the CMYK gamut (i.e. are CMYK-safe): ## #optimized rgb values for cmyk output: set_color _dblue= [0.05 , 0.19 , 0.57] set_color _blue= [0.02 , 0.50 , 0.72] set_color _mblue= [0.5 , 0.7 , 0.9 ] set_color _lblue= [0.86 , 1.00 , 1.00] set_color _green= [0.00 , 0.53 , 0.22] set_color _lgreen=[0.50 , 0.78 , 0.50] set_color _yellow=[0.95 , 0.78 , 0.00] set_color _orange=[1.00 , 0.40 , 0.0 ] # these are trivial set_color _red= [1.00 , 0.00 , 0.00] set_color _mred= [1.00 , 0.40 , 0.40] set_color _lred= [1.00 , 0.80 , 0.80] set_color _vlred= [1.00 , 0.90 , 0.90] set_color _white= [1.00 , 1.00 , 1.00] set_color _vlgray=[0.95 , 0.95 , 0.95] set_color _lgray= [0.90 , 0.90 , 0.90] set_color _gray= [0.70 , 0.70 , 0.70] set_color _dgray= [0.50 , 0.50 , 0.50] set_color _vdgray=[0.30 , 0.30 , 0.30] set_color _black= [0.00 , 0.00 , 0.00] ## There may be a more elegant way to do this (specific to the OS and post-PyMOL application), but this is a simple solution. Wishlist: It would be useful to specify a CMYK mode in PyMOL, so that the color palate uses RGB colors that have good CMYK equivalents. This would simplify color selection when preparing hardcopy figures. With apologies to color-matching gurus, Gil == Gil Privé Ontario Cancer Institute University of Toronto pr...@uhnres.utoronto.ca http://xtal.uhnres.utoronto.ca/prive == --- This sf.net email is sponsored by: Access Your PC Securely with GoToMyPC. Try Free Now https://www.gotomypc.com/s/OSND/DD ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] distance parameters
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
RE: [PyMOL] PyMol Manual
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 to document, support, and develop PyMOL on an ongoing basis. While I am grateful for the continued assistance of PyMOL users on numerous minor tasks, it is not reasonable to expect anyone to prepare a complete well-written manual or to perform other major tasks without some form of compensation. Also, PyMOL is still immature enough in certain areas that a full manual really can't be constructed until the 1.0 features are settled upon (soon hopefully!). Understanding this situation, several large pharmaceutical companies and many smaller entities have lent support to PyMOL development through donations and license purchases. At present the flux is low, but we are getting to a point where some real headway can be made. The forthcoming Incentive PyMOL (iPyMOL) add-on will hopefully increase the flux by providing a specific reward to those who fund the PyMOL development effort. I know it may sound like PyMOL/iPyMOL is becoming commercial gray-ware, but that's not it at all. I haven't devoted thousands of hours to this project just to see it end up as yet another expensive, lousy, inflexible, and closed-source commercial tool. PyMOL will remain a vital open-source project, and iPyMOL will exist solely to accelerate PyMOL's growth and guarantee its long-term health. Nurturing PyMOL and similar efforts to fruition on such terms is central to my career vision -- it's what I stand for in this industry. I believe that well-supported, well-documented, and well-maintained open-source software will be a superior research product to what is currently offered by the major scientific software vendors. My hope is that scientists in industry and academia will eventually come to appreciate this, and then choose to make creation of such software economically viable through funding of balanced approaches such as the one I am taking with PyMOL. Free software is great once it exists, but there are far too few developers in this field to expect the kinds of dramatic successes achieved by the Linux, GNU, and BSD communities. If open-source/free-software is going to have a large impact on molecular modeling, it will need direct support from users, universities, governments, and for-profit companies. If really good open-source tools were available and able to meet the needs of research, would you be willing to pay reasonable amounts of money for their development, maintenance, and support? I hope so. Thus, pharmaceutical companies like EMD/Lexigen/Merck can choose to continue to spend millions of dollars on traditional closed-source packages with no hope of a reprieve, or they can choose to funnel a small fraction of that money into efforts like PyMOL. Over the long term, open-source packages offer vendor-independence, cost-effectiveness, flexibility, opportunities for innovation, and support for broad sharing of information and technology. These are all key ingredients in scientific progress, both within a single organization and across the industry. Realistically, it will take a year or more before PyMOL can fulfill the potential you described. How soon this happens will depend in part on whether people like yourself are content to merely gripe about the status quo, or whether you are prepared to commit resources towards improving it. Cheers, Warren L. DeLano, Ph.D. PyMOL Creator Founder, DeLano Scientific -Original Message- From: gwebs...@lexigenpharm.com [mailto:gwebs...@lexigenpharm.com] Sent: Monday, October 28, 2002 10:33 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMol Manual Fellow PyMol Users Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual. A deeper description of the program's features is required if people are seriously going to use PyMol for tricky things beyond simple visualization (simple visualization programs are ten-a-penny and PyMol could be so much more) Particularly lacking are details of structural editing (mutation, bond rotation, cut-and-paste etc.), interfaces (if any exist) to routines for enegy minimization and a detailed description of the Python command line interface with examples of scripting and how to extend PyMol's capabilities. By neglecting to adequately document what may be a really useful program, the PyMol user community might fail to attract the kind of user base and support that it deserves and that it needs to ensure its success. A good, clear and well-thought out manual really helps to make a case for using a particular piece of software (and it might also lower the odds of PyMol having to join the gray
RE: [PyMOL] Current settings list in Pymol OSX
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 x:[x,setting.get_setting_text(x)],setting.get_name_list()) etc. Cheers, Warren -Original Message- From: Kelley Moremen [mailto:more...@arches.uga.edu] Sent: Wednesday, October 30, 2002 10:13 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Current settings list in Pymol OSX Dear Pymolers, Since the Mac OSX version of Pymol does not have a menu interface that has a pull-down menu to view and alter the settings, is there any way to display and alter the full set of settings from the command line? I keep forgetting what the relevant command line syntax is for changing the settings commands (there is only a partial list in the manual) and a global list (as in the pull-down menu) is a great reminder, but alas the menu interface is not yet there in the Mac OSX version. Thanks for your help. Kelley Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705Fax: (706) 542-1759 Email: more...@arches.uga.edu (send email with large attachments to: more...@bmb.uga.edu) Website: http://bmbiris.bmb.uga.edu/moremen/lab/
RE: [PyMOL] making a two step movie in pymol
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 movie in pymol in which I rotate a molecule about the y-axis 360 deg and then immediately do a 360 deg rotation about the x-axis? I couldn't figure it out from published examples. Thanks in advance Craig L. Smith, Ph. D. Molecular Microbiology Washington University School of Medicine 660 South Euclid Box 8230 Voice: (314) 362-9054 Fax: (314) 362-1232 e-mail: sm...@borcim.wustl.edu --- This sf.net email is sponsored by: Influence the future of Java(TM) technology. Join the Java Community Process(SM) (JCP(SM)) program now. http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] help with surface parameters
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 used to create the surface? PyMOL's default surface is a water contact surface (approximates a Connolly surface). I noticed that there are a few surface settings, but I can't figure out what effects they are having on the displayed surface. Can anybody shed light on these commands? What are their default settings? You can use the settings editor to get the default (except if you're using the native OSX version on a mac). What are the high and low values they can take? surface_best surface_normal surface_proximity surface_quality These settings haven't yet been documented, but they will be in an upcoming version of the manual. I would like to create a fairly tight molecular surface and I just can't figure it out. ANy help would be appreciated. show surface set surface_quality=1 set solvent_radius=0.8 rebuild WARNING: PyMOL may crash if solvent_radius is too low. If it does, try incrementing it by 0.1 until it stabilizes. Cheers, Warren
RE: [PyMOL] Color plotting of electron density contours?
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 Subject: [PyMOL] Color plotting of electron density contours? Hi Folks: Is there a way to display a cross-section of electron density (false)-color-coded for electron density? In other words, I would like to produce a 2-D plot that looks like a contour map (eg: output of CCP4 npo) but color-coded with respect to electron density. A continuum, if possible, would actually be better than a series of contour lines. Has this by any chance been implemented in pymol or anywhere? Many thanks, Bill Scott William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) --- This sf.net email is sponsored by: To learn the basics of securing your web site with SSL, click here to get a FREE TRIAL of a Thawte Server Certificate: http://www.gothawte.com/rd522.html ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol ignores SCALE records in PDB files
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 lattice origin and axes. However, I think this is the default case with most of the standard refinement programs. At the very least, PyMOL should print a warning if it finds a SCALE record! I'll see if we can't get SCALE handling in before the next release. Cheers, Warren -Original Message- From: Keith Refson [mailto:k...@isise.rl.ac.uk] Sent: Wednesday, November 27, 2002 7:02 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol ignores SCALE records in PDB files Just to repeat the subject, it appears that pymol takes no account of the SCALE records in a PDB file. The built in assumptions of the orientation of the unit cell therefore gives an erroneous relationship between the unit cell and the atomic co-ordinates. The attached file demonstrates the problem. Show-Cell puts the long dimension of the cell perpendicular to the line of the atoms, rather than collinear with them as it ought to be. More seriously then, symexp gives a completely wrong expansion. HEADERUNKNOWN TITLE AUTHORGENERATED BY XX2PDB (Keith Refson, 1998) CRYST15.0245.0245.024 39.69 39.69 39.69 P 1 SCALE1 0.338511 0.00 0.0721210.0 SCALE2 -0.169255 0.293159 0.0721210.0 SCALE3 -0.169255 -0.293159 0.0721210.0 HETATM1 H00 NON A 1 0.000 0.000 6.933 1.00 0.00 H HETATM2 F00 NON A 1 0.000 0.000 5.792 1.00 0.00 F HETATM3 F00 NON A 1 0.000 0.000 8.073 1.00 0.00 F HETATM4 Na00 NON A 1 0.000 0.000 0.000 1.00 0.00 Na TER 4 NON A 1 END sincerely Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 778023 K.Refson@ F: 01235 445720 @rl.ac.uk --- This SF.net email is sponsored by: Get the new Palm Tungsten T handheld. Power Color in a compact size! http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Zooming in animations
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, Warren -- 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: Chris Arthur [mailto:chris.art...@bristol.ac.uk] Sent: Monday, December 02, 2002 5:20 AM To: pymol-users Subject: [PyMOL] Zooming in animations Hi Guys Sorry if this question has been asked before but does anyone know a way to zoom in on an area as an animation (eg an active site or interface). Thanks in advance Chris
RE: [PyMOL] Rolling your own functions in PyMol
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. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Stephen Graham [mailto:steph...@usyd.edu.au] Sent: Tuesday, January 07, 2003 4:14 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Rolling your own functions in PyMol Hi All, I am a recent subscriber to the list, so apologies if this question has been answered before. I am interested in finding out how you can add your own functions to PyMol such that they may be transparently called from inside PyMol's shell. The the basic question is How do I register PyMol names for home-grown functions so that they can be used like the functions in the util module. A more detailed example of what I am after is below. Also, are there any warehouses or collections of home-grown functions to which I could submit functions I write and from which I could gain examples from other users? Cheers Stephen == More detailed description of my problem == I have written a function to ramp coloring of a backbone between two or more arbitrary colors (it is really a generalization of the code in util.rainbow). I have imported the code using the general Python import command: import ramp_chain Now, let's say that I have a selection object defined as: select A,(chain A) Were I using the rainbow command I would be able to issue the command: util.rainbow A Which follows the general rules of command line parsing. Unfortunately, in my case issuing the command: ramp_chain.ramp_colors A gives the error: Syntax error: unexpected EOF (and there is an arrow under the letter A). I *can* call the command using the syntax: ramp_chain.ramp_colors( chain A ) but this syntax is not optimal - I would like to be able to use my already defined selections. -- Stephen Graham PhD candidate and nasty sysadmin Crystallography Group School of Molecular and Microbial Biosciences Building G08 University of Sydney New South Wales, 2006 Australia Ph: +61 2 9351 8197 Fax: +61 2 9351 4726 --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] measuring distances
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 import cmd
f=open('dist.txt','w')
atom = cmd.get_model(mol1ha).atom
for i in range(len(atom)-1):
sele1 = 'mol1///%s/HA'%atom[i].resi
sele2 = 'mol1///%s/HA'%atom[i+1].resi
dst=cmd.distance('tmp',sele1,sele2)
f.write(%14s %14s %8.3f\n%(sele1,sele2,dst))
f.close()
The output dist.txt would then look like:
mol1///4/HAmol1///5/HA4.748
mol1///5/HAmol1///6/HA4.828
mol1///6/HAmol1///7/HA4.861
mol1///7/HAmol1///8/HA4.784
mol1///8/HAmol1///9/HA4.936
mol1///9/HA mol1///10/HA4.833
mol1///10/HA mol1///11/HA4.933
mol1///11/HA mol1///12/HA4.813
etc.
Cheers,
Warren
--
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: Tara Sprules [mailto:tspru...@ualberta.ca]
Sent: Wednesday, January 08, 2003 3:20 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] measuring distances
Hi,
I have a file which measures a bunch of distances between
atoms (of the
form distance (mol1///25/ha), (mol1///26/ha)), and rather
than having to
look at the results on the screen I'd like to have the values output
to a text file. Is it possible to do this?
Thanks,
Tara
Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta
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RE: [PyMOL] 1pit.pdb
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 altogether remove q* Cheers, Warren -- 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: Jack Howarth [mailto:howa...@bromo.msbb.uc.edu] Sent: Sunday, January 12, 2003 6:17 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] 1pit.pdb Under linux does anyone else see the following? If one loads in the 1pit.pdb from the MOLMOL data files, the resulting structure seems to have extra bonds drawn in the side chains. For example phe's seem to have all the opposing carbons in the rings interconnected through the center of the ring. Thanks in advance for any hints on what is causing that. Jack --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] new user
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 cartoon_fl(Tab)at_sheets= Actually, that is a feature. Slowly, the PyMOL command language is becoming more consistent (and more Python like). set name,value is preferred over set name=value Since it follows the convention that arguments to PyMOL keywords are separated by commas. Nevertheless, I am a strong proponent of backwards compatibility. set parameter=value will continue to function for years to come so that old scripts will not break. Print quality doesn't seem to be as high as the image on the display. Do I need to feed the PyMol output into something else first? Increase the resolution: ray 2000,1500 etc. Can (how) I annotate the pictures in PyMol? If it's not there yet, I hope it'll be soon as annotation is an indivisible right for any figure to have. Sorry, your figures will continue to be oppressed with versions 0.86. Liberation will come in due time. Cheers, Warren
RE: [PyMOL] Separate surfaces
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 current state of the atom flags. The trivial fix to this kind of problem is to split all of the molecules into different objects and the create the surfaces independently. In this case, use three objects instead of two. That way you can ignore the flag ignore.. command and only show surfaces on the proteins. Also note that if you're planning to move objects with surfaces attached, use the object parameter in the translate command. Otherwise, PyMOL will have to recalculate the surface for each frame. translate [1,0,0],object='A+amp' or cmd.translate([1,0,0],object='A+amp') Also note that reset object='A+amp' will restore the object's original position. Cheers, Warren -- 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: Jacob Corn [mailto:jc...@uclink.berkeley.edu] Sent: Monday, January 20, 2003 1:36 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Separate surfaces Hi all, It's possible that I've run into a bug/undocumented feature, but I'd like to see if anyone has a solution to the following problem. I'm working on a movie script that will (in part) make two separate surfaces for each subunit in a dimer (excluding a drug bound between the subunits), then split the monomers apart and zoom into a drug binding site. However, I'm running into some problems when I try to create the separate surfaces. In plain english, what the script does is create two objects, one containing one subunit (B), and the other containing the other subunit AND the drug (A) (when I split the monomers apart I want the drug to follow one monomer). I then calculate the surface for subunit B, flag everything that's not subunit A as ignore, then calculate the surface for subunit A. If I input each line separately, the script works perfectly and I get two separate surfaces around each subunit and no surface around the drug. But if I run the script from the PyMOL command line or copy/paste the whole script at once into the command line, only subunit A shows a surface. The drug (correctly) does not have a surface, but (from the output in the terminal) it looks like PyMOL isn't even calculating a surface for subunit B. Any ideas would be greatly appreciated. Below are the relevant lines of the script: ## make all of the objects we'll need cmd.create(A+amp+drug,a// or l/1/ or d//) cmd.create(B+amp,b// or l/2/) cmd.select(drug,d//) cmd.select(A+amp,d// or l/1/) cmd.select(none) cmd.delete(lc03) cmd.orient() ## color it up cmd.color(orange,A+amp+drug and A+amp) cmd.color(wheat,B+amp) ## let's show separate surfaces for each subunit cmd.show(surface,B+amp) cmd.flag(ignore,not A+amp,set) cmd.show(surface) Many thanks, Jacob --- This SF.NET email is sponsored by: FREE SSL Guide from Thawte are you planning your Web Server Security? Click here to get a FREE Thawte SSL guide and find the answers to all your SSL security issues. http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] q: discrete colors and adjacent cartoon segments
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 where needed. Warren -- 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: Bartholomeus Kuettner [mailto:bkuett...@epost.de] Sent: Tuesday, January 28, 2003 3:06 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] q: discrete colors and adjacent cartoon segments Dear PyMol users, 1. I'm puzzled with a coloring problem while coloring a protein molecule accordingly to its secondary structure by using 'discrete color' option: If there are a helix and/or strand adjacent together (e.g. helix from 1-10 and sheet from 11-20) the small pseudo-loop region between (arising from atoms between last Calpha of the helix and first Calpha of the strand) gets colored like the latter partner (maybe because of its color was defined at last). What I'd like to do is to color this small pseudo loop in a different color. I've tried to color the atoms between last Calpha and next Calpha (C,N) individually but there was no effect. It seems to me, that cartoon coloring only corresponds to Calpha positions. So, is there a way around to color cartoon regions between secondary structure elements as described before? 2. Is there a way to force PyMol to draw a cartoon which shows two different secondary strcuture elements (helix, strand) ending and beginning at the same residue? Maybe one can image a scenario where the N atom makes a strand-like conformation while the CO group of the same residue starts with a helix. In another program it is/was possible to assign helix and strand ending and beginning in the same residue but when I try to perfom with PyMol only the last partner is shown correctly while the first partner gets overrided in its last residue, e.g. cartoon strand 1-10 and helix 10-20 looks the same like strand 1-9 and helix 10-20. How one could circumvent this dilemma? Many thanks in advance! Greetings, Bartholomeus --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] stop an accidental or problematic ray trace
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. When you goof up, kill the process and then reopen the session or resume the log file after editing out the offending command(s). Cheers, Warren (Hmm...A save session button might be nice...) -- 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: Anthony Duff [mailto:a.d...@staff.usyd.edu.au] Sent: Tuesday, January 28, 2003 4:29 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] stop an accidental or problematic ray trace It would be nice if there were a button to stop a ray trace, for when it is started accidentally, or if something is wrong and it is taking too long. Is there one? -- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 -- --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol and Autodock
SD is a file format for small molecule ligands based around the MDL MOL file (CTAB core). http://www.mdli.com/downloads/literature/ctfile.pdf Advantages: simplicity easy to parse supported by most cheminformatics packages captures valence, stereochem, charge 2D or 3D more extensible than PDB (arbitrary tags) Disadvantages: 999 atom limit (only useful for small molecules!) no standard conventions for storing of atom names or types. fixed field lengths Cheers, Warren -- 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: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br] Sent: Thursday, February 06, 2003 7:41 AM To: DeLano, Warren Cc: Chris; PyMOL-users Subject: Re: [PyMOL] Pymol and Autodock On Thu, 6 Feb 2003, Warren L. DeLano wrote: Read-in performace would be better if you could convert your multiligand PDB file to an SD file. Sorry, what's SD? TIA, Cheers, --- Alan Wilter S. da Silva --- Laboratório de Física Biológica Instituto de Biofísica Carlos Chagas Filho Universidade do Brasil/UFRJ Rio de Janeiro, Brasil
RE: [PyMOL] different transparencies
CC'd to list for future reference... Michal, For mixed colors, you need to use the same trick (separate objects). However, if you want the spheres to have a uniform color, in which case you can set sphere_color,white etc., without having to create separate objects. PyMOL's 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 in order to get this to work. Try the following script: load $PYMOL_PATH/test/dat/pept.pdb create cpy,pept hide show sph,pept and name ca show sph,cpy and name n set sphere_transparency,0.5,pept ray Hi Warren. Thank you for hint. Excuse me I reply directly, but I think you are the best information source in this field. Could you hint me also how to hack if I want to have different color for sphere and sticks belonging to the same atom (I want to use transparent sphere colored by element and black sticks). I wonder if built-in raytracer can render in perspective mode in near future. Regards, Michal Bozon Cheers, Warren I would like to have some spheres transparent, but some spheres leave opaque. Or to have spheres with different transparencies. Is it possible? Thanks, Michal Bozon
[PyMOL] A New Phase for PyMOL
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, DeLano Scientific LLC. This step is made possible through financial sponsorship received from a small group of PyMOL users during the past 18 months. Thank you very much for that. Your backing has given me the courage to launch even in these uncertain times. Don't let terrorism, recession, war, or epidemics dissuade you -- you only get one life in which to pursue your dreams! Fortunately, my five-year relationship with Sunesis Pharmaceuticals continues on good terms, and the company will remain an active test site for PyMOL though I will no longer be an employee. All of us owe Sunesis a debt of gratitude for nurturing the development of this package over the past several years. PyMOL now enters a critical time. We absolutely must secure additional funding in order to sustain our activities. While we hold out hope for a large influx from big pharma, so far it has not yet materialized. Nevertheless, because we are starting out small and efficient, we can succeed this year mainly on grass-roots academic and small-company sponsorship if each of you takes the initiative within your organization to support PyMOL. Thus, I urge every user to advocate for purchase of a PyMOL license and maintenance subscription for their group now that the package will be supported with rapidly improving documentation, responsive feedback, and regular updates. If you sponsored the project in 2002, then please consider renewing your maintenance subscription in 2003. http://www.pymol.org/funding.html Though PyMOL will always be unrestricted Open-Source software, DeLano Scientific will also be rewarding sponsors with extra perks known as Incentive Products. These will soon include an expanded manual and protein morphing capability, and will eventually enable electrostatic calculations, sequence editing, direct movie output, a molecular force-field, and on-site training. Please understand that my aim is to keep the package as open as possible while adopting a reliable strategy for paying the bills. Without incentives, we find that only about 5% of users contribute. If PyMOL is to eventually surpass the capabilities of traditional commercial products, we need to secure sponsorship from a majority of users. Hence this compromise. More details will follow in coming months. If you wish to know more about DeLano Scientific and our software philosophy, then please follow this link: http://www.delanoscientific.com/about.html Cheers, Warren L. DeLano, Ph.D. war...@delanoscientific.com
RE: [PyMOL] fink install fail: pymol-0.86-4
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 Fink PyMOL package. A quick workaround would be to remove the _PYMOL_NUMPY define from the PyMOL Rules.make file. Cheers, Warren -- 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: Kevin Gardner [mailto:kevin.gard...@utsouthwestern.edu] Sent: Tuesday, March 18, 2003 10:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] fink install fail: pymol-0.86-4 Hi all: I'll continue on a thread from a couple of weeks ago, re: failed fink-based installs of pymol over the past month or so. Here's the machine setup: - attempting to install pymol-0.86-4 onto OS 10.2.4 - python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs (2.2.4) all installed - running Apple's X11 (v0.2 and now 0.3) w/SDK installed, other X programs compiling OK Output from the build attached below --- anyone have any insights here? Thanks, Kevin -- cd pyopengl;make cc -ffast-math -no-cpp-precomp -g -I/sw/include -I/sw/include/python2.2 -I/usr/X11R6/include -D_HAVE_LIBPNG -D_PYMOL_MODULE -D_PYMOL_NUMPY -DHAVE_ARRAYOBJECT_H -c _glu_nummodule.c -DPythonTypes In file included from _glu_nummodule.c:8: _glumodule.c: In function `py_glu_NewTess': _glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type In file included from _glu_nummodule.c:8: _glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory _glumodule.c: In function `py_glu_Build2DMipmaps': _glumodule.c:723: `PyArrayObject' undeclared (first use in this function) _glumodule.c:723: (Each undeclared identifier is reported only once _glumodule.c:723: for each function it appears in.) _glumodule.c:723: `ap' undeclared (first use in this function) _glumodule.c:741: parse error before ')' token _glumodule.c:744: parse error before ')' token make[2]: *** [_glu_nummodule.o] Error 1 make[1]: *** [make-pyopengl] Error 2 make: *** [.contrib] Error 2 ### execution of make failed, exit code 2 Failed: compiling pymol-0.86-4 failed -- ** Kevin Gardner, Ph.D. kevin.gard...@utsouthwestern.edu Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center 214-648-8916/FAX: -8947 http://freedom7.swmed.edu --- This SF.net email is sponsored by: Does your code think in ink? You could win a Tablet PC. Get a free Tablet PC hat just for playing. What are you waiting for? http://ads.sourceforge.net/cgi-bin/redirect.pl?micr5043en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Transparent cartoons?
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. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Fred Berkovitch [mailto:fr...@mit.edu] Sent: Monday, March 17, 2003 6:41 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Transparent cartoons? Hello everyone, Can pymol make transparent cartoons? If so, how? -Fred --- This SF.net email is sponsored by:Crypto Challenge is now open! Get cracking and register here for some mind boggling fun and the chance of winning an Apple iPod: http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
