pymol-users

[PyMOL] question on cctbx and pymol

[Yi Z. <yz...@xr...>]

Dear all,

I am trying some of pymol scripts from Prof. Robert L. Campbell, which 
require cctbx module. but I don't know how to put pymol and cctbx togther. 
I download window version of cctbx/python2.4 bundle. and I download 
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I got 
an error message that pymol can't locate python when I tried to install 
pymol into site-packages directory. I don't know how to solve this problem 
since I am new to python scripting. Could anyone give me a hand? Thanks!

Sincerely,

Yi Zhang 

[PyMOL] question on cctbx and pymol

[Roger D. <rb...@ca...>]

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

Re: [PyMOL] question on cctbx and pymol

[Sabuj P. <sab...@va...>]

Actually I was wondering the same thing, except how to set it up in 
linux. I was able to compile the cctbx but I'm not sure how to get it to 
show up as a python module so that Pymol scripts (e.g. Dr. Campbell's 
draw_cell.py) can work. Any help would be greatly appreciated.

Yi Zhang wrote:
> Dear all,
> 
> I am trying some of pymol scripts from Prof. Robert L. Campbell, which 
> require cctbx module. but I don't know how to put pymol and cctbx 
> togther. 
> 
> Sincerely,
> 
> Yi Zhang

Re: [PyMOL] question on cctbx and pymol

[Robert C. <rl...@po...>]

Hi,

* Sabuj Pattanayek <sab...@va...> [2005-08-18 16:08] wrote:
> Actually I was wondering the same thing, except how to set it up in 
> linux. I was able to compile the cctbx but I'm not sure how to get it to 
> show up as a python module so that Pymol scripts (e.g. Dr. Campbell's 
> draw_cell.py) can work. Any help would be greatly appreciated.
> 
> Yi Zhang wrote:
> >Dear all,
> >
> >I am trying some of pymol scripts from Prof. Robert L. Campbell, which 
> >require cctbx module. but I don't know how to put pymol and cctbx 
> >togther. 

I suggested that Yi Zhang ask this on the list, since I have no
experience with trying to make this work under Windows.  Under Linux,
though, I can say that you need to build both cctbx and PyMOL from
source to make sure that they are using the same python executable and
therefore they can "see" all the available modules for importing and to
ensure that all modules are byte-compiled with the same version of
Python.  Otherwise, even if the modules are visible, you may get version
conflict errors when trying to import a module.

I use PyMOL built from the CVS source (I like to have the latest and
greatest features!).  Once this is done the first time, it is a simple
process to rebuild it when the CVS entries are updated. 

The cctbx is easily built from source. Follow the "Downloads" link on
http://cctbx.sourceforge.net and look for either the "Self-extracting
binary distributions" and use the "cctbx only" version or install the
"Self-extracting cctbx sources for Unix". I use the latter just to make
sure that it is compiled for the system libraries I have available on my
computers.  The installation is done with:

  perl cctbx_bundle.selfx

and this will create a setup file that needs to be run:
 
  source cctbx_build/setpaths.sh (or .csh if you use a csh variant).

The installation is exactly the same with the "self-extracting binary
distributions" (apart from the file name used in the "perl" command).

I hope this is sufficiently clear.  I guess I should create a page of
these instructions and link to it from my PyMOL scripts page.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] question on cctbx and pymol

[Sabuj P. <sab...@va...>]

Hi,

Thank you for replying.

In fact this is what I did. Gentoo automatically compiles pymol (pymol 
ebuild) with all required dependencies against the system-wide 
python-2.4.1. I then manually installed cctbx, did "source 
/usr/lib64/python-2.4/site-packages/setpaths_all.csh" and "source 
/usr/lib64/python-2.4/site-packages/setpaths.csh", ran pymol, opened up 
a pdb with CRYST header and tried to run the draw_cell.py script and I 
got this error:

PyMOL>run draw_cell.py
Traceback (most recent call last):
   File "/usr/lib64/python2.4/site-packages/pymol/parser.py", line 270, 
in parse
     execfile(exp_path(args[nest][0]),pymol_names,pymol_names)
   File "draw_cell.py", line 3, in ?
     from cctbx import uctbx, sgtbx
ImportError: No module named cctbx

When I ran the command "python $SCITBX_DIST/run_tests.py" all the tests 
completed with OK status.

I tried adding:

from libtbx import uctbx, sgtbx
import libtbx.load_env

as it has in the run_tests.py file but it gave the same error (No module 
named libtbx).

What else needs to be done so that the python scripts can see the module 
when loaded through pymol? Could it possibly be that when pymol is 
executed it loads a new environment and thus the cctbx paths are not set 
in this new environment?

Thanks,
Sabuj Pattanayek

Robert Campbell wrote:
> Hi,
> 
> * Sabuj Pattanayek <sab...@va...> [2005-08-18 16:08] wrote:
> 
>>Actually I was wondering the same thing, except how to set it up in 
>>linux. I was able to compile the cctbx but I'm not sure how to get it to 
>>show up as a python module so that Pymol scripts (e.g. Dr. Campbell's 
>>draw_cell.py) can work. Any help would be greatly appreciated.
> 
> I use PyMOL built from the CVS source (I like to have the latest and
> greatest features!).  Once this is done the first time, it is a simple
> process to rebuild it when the CVS entries are updated. 
> 
> The cctbx is easily built from source. Follow the "Downloads" link on
> http://cctbx.sourceforge.net and look for either the "Self-extracting
> binary distributions" and use the "cctbx only" version or install the
> "Self-extracting cctbx sources for Unix". I use the latter just to make
> sure that it is compiled for the system libraries I have available on my
> computers.  The installation is done with:
> 
>   perl cctbx_bundle.selfx
> 
> and this will create a setup file that needs to be run:
>  
>   source cctbx_build/setpaths.sh (or .csh if you use a csh variant).
> 
> The installation is exactly the same with the "self-extracting binary
> distributions" (apart from the file name used in the "perl" command).
> 
> I hope this is sufficiently clear.  I guess I should create a page of
> these instructions and link to it from my PyMOL scripts page.
> 
> Cheers,
> Rob

Re: [PyMOL] question on cctbx and pymol

[Robert C. <rl...@po...>]

Hi Sabuj,

* Sabuj Pattanayek <sab...@va...> [2005-08-22 18:03] wrote:
> Hi,
> 
> Thank you for replying.
> 
> In fact this is what I did. Gentoo automatically compiles pymol (pymol 
> ebuild) with all required dependencies against the system-wide 
> python-2.4.1. I then manually installed cctbx, did "source 
> /usr/lib64/python-2.4/site-packages/setpaths_all.csh" and "source 
> /usr/lib64/python-2.4/site-packages/setpaths.csh", ran pymol, opened up 
> a pdb with CRYST header and tried to run the draw_cell.py script and I 
> got this error:
> 
> PyMOL>run draw_cell.py
> Traceback (most recent call last):
>   File "/usr/lib64/python2.4/site-packages/pymol/parser.py", line 270, 
> in parse
>     execfile(exp_path(args[nest][0]),pymol_names,pymol_names)
>   File "draw_cell.py", line 3, in ?
>     from cctbx import uctbx, sgtbx
> ImportError: No module named cctbx
> 

I just tested it and of course it failed for me, too! It must be that
there was a slight change in the cctbx since my previous compilation
of it. Or else I had modified something to take it into account and have
since forgotten. 

When you run the setpaths.sh script, it adds the cctbx_build/bin
directory to the *front* of your $PATH. In that directory is a shell
script called "python" that sets the environment necessary to import
cctbx. So, to get cctbx to work, you have to call python without 
prefixing a directory path.  If you were like me and had:

    /usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*

in your pymol.com file, then it would not run that
cctbx_build/bin/python script. So you need to either change the above
line to:

   python  $PYMOL_PATH/modules/launch_pymol.py $*

(assuming you've already run the setpaths.sh script) or you need to
copy the cctbx_build/bin/python contents (without the actual "python"
command) into your pymol.com file or some other file that you source
before pymol.com.

Within pymol, type the command:

  print sys.path

and you should now see the cctbx directories show up.

I hope this is clear enough!

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] question on cctbx and pymol

[Sabuj P. <sab...@va...>]

Hi,

This worked.

Thanks,
..Sabuj

Robert Campbell wrote:
> prefixing a directory path.  If you were like me and had:
> 
>     /usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*
> 
> in your pymol.com file, then it would not run that
> cctbx_build/bin/python script. So you need to either change the above
> line to:
> 
>    python  $PYMOL_PATH/modules/launch_pymol.py $*

Re: [PyMOL] question on cctbx and pymol

[Jianghai Z. <zh...@pu...>]

Hi,

I could not get cctbx work under either MacPymol or PymolX11Hybrid in 
Mac OS X.  Anywhere I can find some instructions to get cctbx work in 
OS X?

Thanks.

Jianghai

On Aug 23, 2005, at 1:18 PM, Sabuj Pattanayek wrote:

> Hi,
>
> This worked.
>
> Thanks,
> ..Sabuj
>
> Robert Campbell wrote:
>> prefixing a directory path.  If you were like me and had:
>>     /usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*
>> in your pymol.com file, then it would not run that
>> cctbx_build/bin/python script. So you need to either change the above
>> line to:
>>    python  $PYMOL_PATH/modules/launch_pymol.py $*
>

Re: [PyMOL] question on cctbx and pymol

[Robert C. <rl...@po...>]

Hi,

* Jianghai Zhu <zh...@pu...> [2005-08-24 01:59] wrote:
> 
> I could not get cctbx work under either MacPymol or PymolX11Hybrid in 
> Mac OS X.  Anywhere I can find some instructions to get cctbx work in 
> OS X?

There is a page on the cctbx with special instructions for using it on
the Mac:

    http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html

Note that you need to use the "Framework" build of PyMOL:

    http://delsci.com/frameworkpymol/

Unfortunately there isn't a Mac around here for me to test this stuff
on.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] question on cctbx and pymol

[Peter A. M. <pa...@co...>]

> I am trying some of pymol scripts from Prof. Robert L. Campbell, which
require cctbx module. but I don't know how to put pymol and cctbx
togther.
> I download window version of cctbx/python2.4 bundle. and I download
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I
got
> an error message that pymol can't locate python when I tried to install
pymol into site-packages directory. I don't know how to solve this
problem
> since I am new to python scripting. Could anyone give me a hand? Thanks!

There could be a couple of things.
The first thing to check is that the python path (called PYTHONHOME on
unix; not sure about windows) is set up correctly (the executable path may
need adjusting as well, maybe try running with the full path).  A
workaround for python path that should work on windows is to add few lines
to the beginning of a python script: import sys (may not be needed if sys
module has already been imported), followed by sys.path.append("full path
to the python/cctbx/pymol modules you want to install).
For python on windows, any compiled modules (which includes parts of cctbx
and pymol) have to be compiled with the same compiler (VisualC++,gcc,
etc), and possible same version, as the python interpreter was complied
with.  I'm not sure how you'd go about resolving this, other than hoping
the compiler versions happened to match, or trying to compile both with
the same compiler.
The third possible problem could be that both cctbx and pymol can come
packaged with their own python interpreters (I'm not sure how the windows
executable versions are packaged), so you'll need to make sure that both
are using the same interpreter.

For unix/linux(/os x?), this the fix would be to install everything from
source, and use environmental variables to make sure that pymol knows
about the cctbx packages, and cctbx knows which python to install itself
to.  For windows it's likely to be more difficult, if it was me I'd
install cygwin (unix emulator for windows), and just install everything
there.

Hope some of this is helpful,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University