[PyMOL] PyMOL and cctbx

[Roger Dodd]

Dear Simon and other pymolers,

I have realised that the solution to getting cctbx working with pymol on
windows I posted no longer works with recent builds of cctbx. I have
found that the following solution works:

1. Download and install python (to the default location - C:\Python24)

--> http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi

(1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

-->
http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download)

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources

-->
http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

--> http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

   @python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. One other thing, it's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.

Hopefully this should work OK... I know it is working on at least one
other system than my own. Let me know if it works for you. I'll post
this up on the wiki ASAP.

Cheers

Roger
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org:University of Cambridge;Department of Medicine
adr:Addenbrooke's Hospital, Hills Road;;CIMR, Wellcome Trust/MRC Building;Cambridge;Cambridgeshire;CB2 2XY;UK
email;internet:rb...@cam.ac.uk
title:Post-Doctoral Research Associate
tel;work:+44-1223-762629
note;quoted-printable:MSN - rogerd...@hotmail.com=0d=0a=
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[PyMOL] question on cctbx and pymol

[Roger Dodd]

Hi all,

I hesitated to post this because I thought someone would have a more
elegant solution, but I have got the draw_cell/symmops scripts working
on windows with cctbx. I have had it working with all versions of PyMOL
including the latest betas. I install PyMOL as usual in C:\Program
Files\Delano Scientific\PyMOL. I also got hold of python 2.4.1
(http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi) and cctbx
(http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe)
and installed them to C:\python24 and C:\cctbx_build & C:\cctbx_sources,
respectively.

In order to get things working together, I launch PyMOL with the
following batch file:

@ECHO off
set LIBTBX_DIST_ROOT=C:\cctbx_sources
if not defined PYTHONPATH set PYTHONPATH=
set
PYTHONPATH=C:\cctbx_sources\boost_adaptbx;C:\cctbx_sources\scitbx;C:\cctbx_sources\cctbx;C:\cctbx_sources\iotbx;C:\cctbx_build\libtbx;C:\cctbx_sources\libtbx;%PYTHONPATH%
set LIBTBX_BUILD=C:\cctbx_build
set LIBTBX_PYTHON_EXE=C:\Python24\python.exe
if not defined PATH set PATH=
set PATH=C:\cctbx_build\libtbx\bin;C:\cctbx_build\libtbx;%PATH%
set SCITBX_DIST=C:\cctbx_sources\scitbx
set IOTBX_DIST=C:\cctbx_sources\iotbx
set CCTBX_DIST=C:\cctbx_sources\cctbx
set BOOST_ADAPTBX_DIST=C:\cctbx_sources\boost_adaptbx
set LIBTBX_DIST=C:\cctbx_sources\libtbx
if not defined PATHEXT set PATHEXT=
set PATHEXT=.PX;.PY;%PATHEXT%
call "%LIBTBX_PYTHON_EXE%" "%LIBTBX_DIST%\libtbx\assoc_ftype.py"
"C:\Program Files\DeLano Scientific\PyMOL\PyMOLWin.exe"  +2

 just save as PyMOL.bat and run it (this is basically the cctbx
setpaths.bat with a pymol command tagged on the end). I hope this helps.

Cheers

Roger
begin:vcard
fn:Roger Dodd
n:Dodd;Roger
org:University of Cambridge;Department of Medicine
adr:Addenbrooke's Hospital, Hills Road;;CIMR, Wellcome Trust/MRC Building;Cambridge;Cambridgeshire;CB2 2XY;UK
email;internet:rb...@cam.ac.uk
title:Post-Doctoral Research Associate
tel;work:+44-1223-762629
note;quoted-printable:MSN - rogerd...@hotmail.com=0d=0a=
	ICQ - 100657240=0D=0A=
	Skype - rogerdodd=0D=0A=
	Gizmo - rogerdodd=0D=0A=
	SIP (VoIP) -  17476057995
x-mozilla-html:TRUE
url:http://www.cus.cam.ac.uk/~rbd22/
version:2.1
end:vcard

[PyMOL] Help/suggestions for illustrating lattice arrangement

[Roger Dodd]

Hi,

I am trying to prepare a figure illustrating a fairly complex packing 
arrangement in a large H32 (R32) unit cell, where the packing may 
actually have some biological relevance. To try and show the packing 
I've been generating symmetry related molecules using the symexp 
command. The problem I've been running into is that things become too 
complex and cluttered, whether I use lines, ribbons, cartoons, etc. My 
asymmetric unit contains 2 homo-pentamers and my question is - would it 
be possible to replace each monomer with, for example, an ellipsoid of 
roughly the same size centred on the subunit's centre of mass to 
simplify things? Is this the sort of thing that could be done with a cgo 
object? Any help or other suggestions would be greatly appreciated.


Cheers

Roger

[PyMOL] rgb to cmyk woes

[Roger Dodd]

Hi all,

I'm trying to prepare some figures for publication and of course the 
journal requires them in cmyk format. I have produced the images in 
pymol using the cmyk color space and saved them as png files. However, 
the png files themselves are in 24 bit rgb format if I'm correct. Trying 
to subsequently convert them to cmyk format tiff files in photoshop or 
coreldraw results in all the colors being mangled (becoming duller and 
darker). Is there some trick to converting to the cmyk color space 
without altering the colors - I assumed working in the cmyk mode in 
PyMOL would ensure this didn't occur?


Thanks in advance for any help

Roger Dodd

[PyMOL] Pymol segmentation fault - fedora core 1

[Roger Dodd]

Hi everyone,

I've recently updated to the 0.97 release of pymol and although it ran 
fine to start with, it's now generating a segmentation fault. I 
installed from the * pymol-0_97-bin-linux-libc6-i386.tgz* 
 
file into /usr/local/pymol and ran setup.sh. Then when running the 
pymol.com script I get the following:


./pymol.com: line 14: 31156 Segmentation fault  $PYMOL_PATH/pymol.exe $*

I'm not sure exactly what's causing this and any help would be 
appreciated. I've tried completely removing the pymol directory and 
reinstalling but I still get the same error.


Cheers

Roger

[PyMOL] Error in sequence viewer

[Roger Dodd]

The sequence viewer is a brilliant addition to pymol and I'm already 
finding it quite useful after playing around with it a bit. However, 
I've noticed a possible bug, although I don't know what's causing it. 
When viewing the pdb file 1fe6 (a coiled coil protein) and using the 
sequence viewer, the sequence RLT it displayed as RLR (residues 14-16) 
despite the graphics correctly showing a threonine residue. You can see 
a screenshot here http://www.cus.cam.ac.uk/~rbd22/Screenshot.png.

Any ideas?

Cheers

Roger

[PyMOL] Restrict surface transparency to limited region

[Roger Dodd]

Dear PyMOL users/devs,

I am trying to produce a figure with a molecular surface and would like to make 
this surface transparent only covering certain residues. I have tried creating 
a separate surface for these residues and the rest of the protein and setting 
transparency for the object covering only those residues, but this gives a very 
discontinuous looking surface representation. Is it possible to just enable 
transparency on a limited region of a surface?

Thanks

Roger

--
Roger Dodd
CIMR
University of Cambridge
Wellcome Trust / MRC Building
Addenbrooke's Hospital
Hills Road
Cambridge
CB2 2XY

[PyMOL] Display of electrostatic potential surfaces

[Roger Dodd]

Dear PyMOL users,

I would like to generate a figure of my protein where the surface electrostatic 
potential is displayed. PyMOL now comes with a demo function for display of 
such a surface. However, when I apply the commands used in this demo, i.e.

cmd.set("coulomb_dielectric",80.0)
 cmd.map_new("e_pot","coulomb",1.0,"pept",5)
 cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
 cmd.set("surface_color","e_lvl","pept")
 cmd.refresh()

to the model from my pdb file, I get a uniformly blue surface. I believe this 
must be due to the lack of assignment of partial/formal charges to the atoms in 
the pdb file. So, my questions are:

1. Is it possible to automatically assign the correct charges to atoms within 
PyMOL
2. If not, is there a program that will do this and if so can the output from 
this program be understood by PyMOL in some way.

Thanks for your help

Roger

--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge