pymol-users Mailing List for PyMOL Molecular Graphics System (Page 672)

Hi!
I've got the following problem (it may be tied to python v2 that I'm
using):
[akhavr@netmaster molmov]$ PYMOL_PATH=~/src/pymol/modules/ PYTHONPATH=/homvr/src/pymol/modules/ gdb python2
GNU gdb 5.0
Copyright 2000 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux"...
(no debugging symbols found)...
(gdb) run
Starting program: /usr/bin/python2 
[New Thread 1024 (LWP 3246)]
Python 2.1.1 (#1, Aug 13 2001, 19:37:40) 
[GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-96)] on linux2
Type "copyright", "credits" or "license" for more information.
>>> from glob import glob
>>> import thread 
>>> import threading 
>>> import os
>>> import sys
>>> import time
>>> from pymol import cmd
>>> cmd.hide("lines")
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 1024 (LWP 3246)]
0x402fc2be in APIEntry () at Cmd.c:106
106	 PRINTFD(FB_API)
(gdb) bt
#0 0x402fc2be in APIEntry () at Cmd.c:106
#1 0x40301b98 in CmdShowHide (self=0x0, args=0x8113d64) at Cmd.c:2517
#2 0x80593ed in PyEval_CallObjectWithKeywords () at eval.c:41
#3 0x8057c75 in PyEval_EvalCode () at eval.c:41
#4 0x80597dd in PyEval_CallObjectWithKeywords () at eval.c:41
#5 0x8057d44 in PyEval_EvalCode () at eval.c:41
#6 0x80550d5 in PyEval_EvalCode () at eval.c:41
#7 0x806e031 in PyRun_FileExFlags () at eval.c:41
#8 0x806d0fc in PyRun_InteractiveOneFlags () at eval.c:41
#9 0x806cf5e in PyRun_InteractiveLoopFlags () at eval.c:41
#10 0x806ce2d in PyRun_AnyFileExFlags () at eval.c:41
#11 0x8051f30 in Py_Main () at eval.c:41
#12 0x40084777 in __libc_start_main (main=0x80519d0 <main>, argc=1, 
 ubp_av=0xbffff704, init=0x8050e38 <_init>, fini=0x80a48f0 <_fini>, 
 rtld_fini=0x4000dd44 <_dl_fini>, stack_end=0xbffff6fc)
 at ../sysdeps/generic/libc-start.c:129
(gdb) 
Red Hat Linux 7.2
Pmw-0.8.5-1
Numeric-20.2.1-1
pymol both 0.68 and CVS versions
This happens only if I try to run python script utilizing pymol directly
from python. Launching via 'pymol script.py' goes ok.
What I'm doing wrong?
-- 
Andrey V Khavryuchenko http://www.kds.com.ua/
Offshore Software Development

Hi!
Pymol 0.68 RPMs (both source and i386) are available at 
 http://office.kds.com.ua/~akhavr/pymol/
The packages are build for python 2.1, since latest Numeric is supported
only for python 2.
Bug reports are welcome.
-- 
Andrey V Khavryuchenko http://www.kds.com.ua/
Offshore Software Development

Hello!
Had anyone created an RPM for pymol? Even .spec would be good.
Thanks in advance!
-- 
Andrey V Khavryuchenko http://www.kds.com.ua/
Offshore Software Development

> > Does anyone know how to disable automatic normalization of an
> > input map?
The "normalize_ccp4_maps" setting is now functional in the CVS source
version, and will work in 0.69+. Note that this setting must be
changed before loading the map. On-the-fly map transformations (ala
CNS/X-PLOR) would be a cool and very easy feature to implement in
future versions...
> > Also does anyone has a script which draws a "carved" density? 
> > I've tried to
> > do this but without success.
load tst.ccp4
load ref.pdb
isomesh m1, tst, 1.0, (resi 100-105), carve=2.0
- Warren

Whoops, it looks like I created this setting without actually utilizing
it in the code. I'll fix this in the CVS repository late tonight. =20
Although I've sworn off adding any major new functionality to PyMOL for
a while, minor monthly updates are planned which will incorporate
bugfixes and outside user contributions (next one around Dec. 1st).
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> -----Original Message-----
> From: Fischmann, Thierry [mailto:thi...@sp...]
> Sent: Thursday, November 01, 2001 2:17 PM
> To: 'pym...@li...'
> Subject: [PyMOL] CCP4 density maps and PyMol
>=20
>=20
>=20
> Unless I'm mistaken (which is very possible), it appears that=20
> by default
> PyMol normalizes an input map upon loading.
>=20
> I'd like to disable this feature. Looking in the menu at=20
> Settings .../Edit
> All ... I've found the variable normalize_ccp4_maps and=20
> changed its default
> value from 1 to 0 (or in a script I've added "set=20
> normalize_ccp4_maps, 0").
> This does not appear to have any effect at all.
>=20
> Does anyone know how to disable automatic normalization of an=20
> input map?
>=20
> Also does anyone has a script which draws a "carved" density?=20
> I've tried to
> do this but without success.
>=20
> Thanks in advance for any tip,
>=20
> Thierry
>=20
> thi...@sp...
>=20
> ***************************************************************
> This message and any attachments is solely for the intended=20
> recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is=20
> prohibited --
> please immediately and permanently delete this message.
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Unless I'm mistaken (which is very possible), it appears that by default
PyMol normalizes an input map upon loading.
I'd like to disable this feature. Looking in the menu at Settings .../Edit
All ... I've found the variable normalize_ccp4_maps and changed its default
value from 1 to 0 (or in a script I've added "set normalize_ccp4_maps, 0").
This does not appear to have any effect at all.
Does anyone know how to disable automatic normalization of an input map?
Also does anyone has a script which draws a "carved" density? I've tried to
do this but without success.
Thanks in advance for any tip,
Thierry
thi...@sp...
***************************************************************
 This message and any attachments is solely for the intended recipient. If
you are not the intended recipient, disclosure, copying, use, or
distribution of the information included in this message is prohibited --
please immediately and permanently delete this message.

But that's what you should get, since alpha carbons aren't bonded
directly to other alpha carbons, right? Perhaps what you really want
to do is draw the protein "backbone only"? Try this:
hide all
show (name ca,c,n,o)
Cheers,
Ben
"Frank Vondelft" <Fra...@sy...> writes:
> Hidy Pymollers....
> 
> I *think* I've RTFMed everywhere I can, but I haven't been able to
> figure out how to draw a molecule C-alpha only. When I selected all CA
> atoms, I got a cloud of dots that were not connected. I suspect I've
> missed something fundamental...
> 
> Thanks for any tips
> Phraenquex
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

A UCSF MidasPlus style CA trace can be obtained with:
set ribbon_sampling=3D1
show ribbon
A space filling version can be had with:
set cartoon_smooth_loops=3D0
set cartoon_sampling=3D1
cartoon loop
show cartoon
All of the above can be restricted so as to apply to only a single
object as described in the manual/online help.
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> -----Original Message-----
> From: Frank Vondelft [mailto:Fra...@sy...]
> Sent: Tuesday, October 30, 2001 3:03 PM
> To: pym...@li...
> Subject: [PyMOL] ca-trace
>=20
>=20
> Hidy Pymollers....
>=20
> I *think* I've RTFMed everywhere I can, but I haven't been able to
> figure out how to draw a molecule C-alpha only. When I=20
> selected all CA
> atoms, I got a cloud of dots that were not connected. I suspect I've
> missed something fundamental...
>=20
> Thanks for any tips
> Phraenquex
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hidy Pymollers....
I *think* I've RTFMed everywhere I can, but I haven't been able to
figure out how to draw a molecule C-alpha only. When I selected all CA
atoms, I got a cloud of dots that were not connected. I suspect I've
missed something fundamental...
Thanks for any tips
Phraenquex

I've folded Numeric Python 20.0.0 into the Windows binaries for PyMOL 0.68
(released today). This is the most recent version of Numeric which works
with both 1.5.2 and Python 2.1. 
For those with an insatiable hunger for eye candy, PyMOL 0.68 also 
contains transparent surfaces. 8-)
Cheers,
Warren
On 2001年10月26日, Paul Sherwood wrote:
> All,
> 
> I would like to try and use parts of PyMOL that use Numeric
> on the Windows platform. The "out-of-the-box" install
> procedures for PyMOL, Python (2.1.1) and Numeric lead to
> problems importing the Numeric module as follows.
> 
> ImportError: No module named Numeric
> 
> Is there a way to fix this?
> 
> thanks
> 
> Paul
> 

All,
I would like to try and use parts of PyMOL that use Numeric
on the Windows platform. The "out-of-the-box" install
procedures for PyMOL, Python (2.1.1) and Numeric lead to
problems importing the Numeric module as follows.
ImportError: No module named Numeric
Is there a way to fix this?
thanks
Paul
-- 
======================================================================
Dr Paul Sherwood, email: p.s...@da...
CLRC Daresbury Lab, tel: +44-1925-603553
Warrington, fax: +44-1925-603634
WA4 4AD, UK. http: http://www.cse.clrc.ac.uk
======================================================================

> From: Peter Haebel [mailto:p.h...@au...]
> anyway, playing around I realised that it would be nice to be=20
> able to read
> out the pymol settings, such as 'bg_color', 'antialias' and any other
> variables. is there such a pymol function?
For well defined settings, this can be easily done, although the API is
somewhat incomplete.
(in python)
from pymol import cmd
print cmd.get_setting_tuple('bg_rgb')
my_variable =3D cmd.get_setting_tuple('antialias')
etc.
You will get a tuple of length 2. The first field is a type identifier,
and the second is the value corresponding to the setting. =20
Current type identifiers: 3 for a float, 4 for a nested tuple of three
floats. In the future, 1 will be a boolean, and 2 will be an int. =20
Settings are still in the process of being de-homogenized from being
pure floating point values. Eventually we will supplement this function
with something more descriptive and user-friendly -- it only exists this
early because I needed it to support the first external GUI.
Please contribute your extension for inclusion in util.py when it is
done.
Note that you can use cmd.extend to bind it to a command for maximum
convenience.=20
Cheers,
Warren
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> -----Original Message-----
> From: Peter Haebel [mailto:p.h...@au...]
> Sent: Wednesday, October 24, 2001 1:12 PM
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #2 - 2 msgs
>=20
>=20
> Hi Warren,
>=20
> I have a related question. just wrote a little extension for=20
> pymol that
> generates stereo figures and merges the right and left stereo image to
> complete the figure.
>=20
> util.stpng(["filename"]).
>=20
> the extension is written in python and uses PIL (the python=20
> image library)
> to manipulate the images. It can output the merged figures in=20
> all standard
> image formats (png, tiff, jpeg, ps, pdf, etc only depends on=20
> the libraries
> you have installed) and derives the format from the extension of the=20
> output filename.
>=20
> anyway, playing around I realised that it would be nice to be=20
> able to read
> out the pymol settings, such as 'bg_color', 'antialias' and any other
> variables. is there such a pymol function?
>=20
> cheers
>=20

Hi Warren,
I have a related question. just wrote a little extension for pymol that
generates stereo figures and merges the right and left stereo image to
complete the figure.
util.stpng(["filename"]).
the extension is written in python and uses PIL (the python image library)
to manipulate the images. It can output the merged figures in all standard
image formats (png, tiff, jpeg, ps, pdf, etc only depends on the libraries
you have installed) and derives the format from the extension of the 
output filename.
anyway, playing around I realised that it would be nice to be able to read
out the pymol settings, such as 'bg_color', 'antialias' and any other
variables. is there such a pymol function?
cheers
peter
 :)__________________________________________
 Peter Haebel
 Laboratory of Structural Biology, Phone: +64-9-373 7599 ext. 7237
 School of Biological Sciences, Fax: +64-9-373 7414
 University of Auckland Email: p.h...@au...
 New Zealand http://www.netcolony.com/life/phaebel
 Meet LISA at http://lisa.sbs.auckland.ac.nz
On 2001年10月24日 pym...@li... wrote:
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
> 1. getting image sizes (Ben Cornett)
> 2. RE: getting image sizes (DeLano, Warren)
> 
> --__--__--
> 
> Message: 1
> To: pym...@li...
> From: Ben Cornett <ac...@em...>
> Date: 24 Oct 2001 09:09:18 -0400
> Subject: [PyMOL] getting image sizes
> 
> Does anyone know how to get the size (pixels) of the viewer? I'd like
> to be able to write a python script that orients and colors a molecule
> and then renders it at whatever dpi I provide as a command-line
> argument.
> 
> Best,
> 
> Ben
> 
> 
> 
> --__--__--
> 
> Message: 2
> Subject: RE: [PyMOL] getting image sizes
> Date: 2001年10月24日 09:06:42 -0700
> From: "DeLano, Warren" <wa...@su...>
> To: "Ben Cornett" <ac...@em...>,
> 	<pym...@li...>
> 
> Welcome everybody to the PyMOL mailing list. There are over 30
> subscribers. I am very pleased that so many people want to use (and
> thereby improve) the package.
> 
> > From: Ben Cornett=20
> 
> > Does anyone know how to get the size (pixels) of the viewer? I'd like
> > to be able to write a python script that orients and colors a molecule
> > and then renders it at whatever dpi I provide as a command-line
> > argument.
> 
> Ben,
> 
> Hmm, not all of those features may exist yet, but the following will
> help.
> 
> The "viewport" command can be used to change the window size.
> Alternatively, the "ray" command can take width and height arguments.
> 
> Remember that two options exist for scripting: PyMOL commands and
> Python. The former is easier for quick-and-dirty tasks.
> 
> # SCRIPT fig1.pml (PyMOL command language)
> # RUN AS "pymol -c fig1.pml"
> viewport 1024,768
> load example.pdb
> color marine
> orient
> ray=20
> png fig1.png
> # END
> 
> versus=20
> 
> # SCRIPT fig2.py (Python)
> # RUN AS "pymol -c fig2.py"
> from pymol import cmd
> cmd.viewport(1024,768)
> cmd.load("example.pdb")
> cmd.color("marine")
> cmd.orient()
> cmd.ray()
> cmd.png("fig2.png")
> # END
> 
> also equivalent to=20
> # SCRIPT fig3.pml (PyMOL)
> # RUN AS "pymol -c fig3.pml"
> load example.pdb
> color marine
> orient
> ray 1024,768
> png fig3.png
> # END
> 
> Passing additional command arguments can't yet be done reliably, but you
> might try playing around with -d (at least on unix). Note single quotes
> and no spaces within the quote.
> 
> pymol -d 'w=3D1024;h=3D768'
> 
> should define "w" and "h" in the interpreter namespace.
> 
> Thus, the following works...
> 
> # SCRIPT fig3.py (Python)
> # RUN AS "pymol -c -d 'w=3D1024;h=3D768' fig3.py "
> from pymol import cmd
> cmd.load("example.pdb")
> cmd.color("marine")
> cmd.orient()
> cmd.ray(w,h)
> cmd.png("fig3.png")
> # END
> 
> You might even be able to pass in the input and output filenames:
> 
> pymol -c -d 'w=3D1024;h=3D768;i=3Dexample.pdb;o=3Dfig4.png' fig4.py
> 
> # SCRIPT fig4.py (Python)
> from pymol import cmd
> cmd.load(i)
> cmd.color("marine")
> cmd.orient()
> cmd.ray(w,h)
> cmd.png(o)
> # END
> 
> - Warren
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> End of PyMOL-users Digest
> 

> From: Ezequiel Panepucci [mailto:za...@SL...]
> Hi There,
> How would I go about selecting a specific model from a
> PDB file which includes several NMR conformations?
Zac,
load 1NGR.pdb
create mod6,1NGR,6,1 =20
# takes state/model 6 of 1NGR and puts it in frame 1
# of a new object called "mod6"
save mod8.pdb,1NGR,8
# saves state/model 8 of 1NGR to a new PDB file.
See "help create" and "help save"
- Warren
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
>=20

Hi There,
How would I go about selecting a specific model from a
PDB file which includes several NMR conformations?
Thanks,
	Zac

Welcome everybody to the PyMOL mailing list. There are over 30
subscribers. I am very pleased that so many people want to use (and
thereby improve) the package.
> From: Ben Cornett=20
> Does anyone know how to get the size (pixels) of the viewer? I'd like
> to be able to write a python script that orients and colors a molecule
> and then renders it at whatever dpi I provide as a command-line
> argument.
Ben,
Hmm, not all of those features may exist yet, but the following will
help.
The "viewport" command can be used to change the window size.
Alternatively, the "ray" command can take width and height arguments.
Remember that two options exist for scripting: PyMOL commands and
Python. The former is easier for quick-and-dirty tasks.
# SCRIPT fig1.pml (PyMOL command language)
# RUN AS "pymol -c fig1.pml"
viewport 1024,768
load example.pdb
color marine
orient
ray=20
png fig1.png
# END
versus=20
# SCRIPT fig2.py (Python)
# RUN AS "pymol -c fig2.py"
from pymol import cmd
cmd.viewport(1024,768)
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray()
cmd.png("fig2.png")
# END
also equivalent to=20
# SCRIPT fig3.pml (PyMOL)
# RUN AS "pymol -c fig3.pml"
load example.pdb
color marine
orient
ray 1024,768
png fig3.png
# END
Passing additional command arguments can't yet be done reliably, but you
might try playing around with -d (at least on unix). Note single quotes
and no spaces within the quote.
pymol -d 'w=3D1024;h=3D768'
should define "w" and "h" in the interpreter namespace.
Thus, the following works...
# SCRIPT fig3.py (Python)
# RUN AS "pymol -c -d 'w=3D1024;h=3D768' fig3.py "
from pymol import cmd
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png("fig3.png")
# END
You might even be able to pass in the input and output filenames:
pymol -c -d 'w=3D1024;h=3D768;i=3Dexample.pdb;o=3Dfig4.png' fig4.py
# SCRIPT fig4.py (Python)
from pymol import cmd
cmd.load(i)
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png(o)
# END
- Warren

Does anyone know how to get the size (pixels) of the viewer? I'd like
to be able to write a python script that orients and colors a molecule
and then renders it at whatever dpi I provide as a command-line
argument.
Best,
Ben

Ben,=20
 If all you have is a single structure loaded, then you can get
unambiguous identifiers corresponding to the atom positions in the
macromodel file by cmd.identify.
For example, if the user put some atoms into the "lb" selection using
the mouse, then you could get a Python list of their indices as follows:
print cmd.identify("(lb)")
[1,4,7,8,4,50]
(one based atom indices from the macromodel file).
Example usage with a Python function...
from pymol import cmd
def color_sele_red(sele):
 lst =3D cmd.identify(sele)
 cmd.color("white")
 for a in lst:
 cmd.color("red","(id %d)"%a)
color_sele_red("lb")
 =20
Note that if you have multiple objects loaded, you will need some way of
determining which identifiers correspond in which object. Right now
that is complicated. In version 0.67, you can pass a mode argument to
"identify" which will give you the object names and identifiers as a
list of tuples...
print cmd.identify("(lb)")
[('pept',2),('pept',6),('pept',11)]
It is also possible to grab user selections directly with the Wizard
capabilities. That interface isn't documented, but several working
examples exist:
pymol/modules/pymol/wizard/*.py
Cheers,
Warren
Ben Wrote:
>Let me help break the new mailing list in. I haven't been using pymol
>for very long, but I've been impressed with some of its features and
>with its potential. At the moment, I'm working on a program that
>could benefit by integrating pymol. Specifically, I need to be able
>to read in a molecule (macromodel format) and allow the user to select
>various atoms. Does pymol provide a way for my code to access these
>selections? Thanks.
--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Scientist=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 fax: (650)-266-3501=20

Let me help break the new mailing list in. I haven't been using pymol
for very long, but I've been impressed with some of its features and
with its potential. At the moment, I'm working on a program that
could benefit by integrating pymol. Specifically, I need to be able
to read in a molecule (macromodel format) and allow the user to select
various atoms. Does pymol provide a way for my code to access these
selections? Thanks.
Best,
Ben