pymol-users Mailing List for PyMOL Molecular Graphics System

Hey all,

sorry for taking to the list what seems to me a trivial problem.  But I=20
can't get over it and I'm afraid to modified my system too much since I=20
don't know what I'm doing.

Basically, what I've done is download the pymol sources=20
(pymol-0_98-src.tgz) from delsci.com.  I made sure I've installed all=20
the requirements (python2.3.4, Numeric, Pmw, tcl8.4, tk8.4.7, libpng,=20
zlib, freeglut2.2).  This is on a standard Fedora Core 3 system, nothing=20
fancy.

I run `python2.3 setup.py install` and get a bunch of error messages=20
relating to the absence of GL/gl.h and GL/glu.h.  Supposedly, freeglut=20
combines them into GL/glut.h.  So I change all occurences of GL/gl.h and=20
GL/glu.h in the pymol source to GL/glut.h.  More errors!  It turns out=20
that freeglut is also asking for GL/gl.h and GL/glu.h.  I have the faint=20
notion that Mesa provides GL/gl.h and GL/glu.h, but aren't Mesa and=20
freeglut supposed to do the same thing?  Both provide libGLU.so.  Should=20
I install Mesa?  And wasn't there some FireGL/xorg/Mesa incopatibility=20
issue?


Any suggestions?


Andreas


--=20
    -->       Andreas F=F6rster       <--
  8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
       www.biochem.utah.edu/~andreas
    b5foan at skype and yahoo messenger
docandreas & andreasenfrance.blogspot.com

Hi,

i just set auto_sculpt and after I protect all my protein but the=
=20
residue (group of residues) i want to sculpt. I wrote several .pml to=
=20
switch to the next residue or deprotect only the side_chain,fix an at=
om=20
  (protect pk1) etc... that I call from the script_box (see the links=
 on=20
the web-site).
It works really well for me it's twice faster than with O (but i'm no=
t=20
really good with O).

Thanks to warren for this software.

Jim Nettles a =E9crit :
> Hello all,
>=20
> Perhaps I'm awaking from hibernation or something, but the communic=
ation=20
> below came as a surprise to me.
>=20
> Do I read this correctly that Pymol does real space refining into=
=20
> electron density using the sculpting function? If so, that is great=
! I=20
> apologize if this has been discussed before and I missed it. Could=
=20
> someone please clue me in as to how to best use this function?
>=20
> Thanks,
>=20
> Jim Nettles
>=20
> On Aug 30, 2005, at 8:33 AM, Warren DeLano wrote:
>=20
>     Mathieu,
>     =20
>     Deselect Sculpting from the builder menu or "unset sculpting"
>     =20
>     Note that if you're doing this a lot, then create some custom o=
n/off
>     function keys as follows:
>     =20
>     # F1 to turn on sculpting
>     cmd.set_key('F1',lambda :(cmd.set("sculpting"),cmd.set("auto_sc=
ulpt")))
>     =20
>     # F2 to turn off sculpting
>     cmd.set_key('F2',lambda
>     :(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))
>     =20
>     Cheers,
>     Warren
>=20
>     *From:* pym...@li... on behalf of Ma=
thieu
>     Coincon
>     *Sent:* Mon 8/29/2005 8:26 AM
>     *To:* pym...@li...
>     *Subject:* [PyMOL] Refinement in auto_sculpt
>=20
>=20
>=20
>=20
>     Hi,
>     i'm usinig pymol for modelling my protein in electron density.
>     I like it very much but there is one thing I would like to unde=
rstand.
>     Is there a way to stop the refinement of the geometry:
>         I'm using auto_sculpt and I protect/deprotect the protein b=
ut
>     sometimes the
>     refinemt run during a long time I would like to stop it ? i pla=
yed
>     with the
>     number  of cycles and other parameters but it didn't work.
>=20
>=20
>=20
>=20
>=20
>     -------------------------------------------------------
>     SF.Net email is Sponsored by the Better Software Conference & E=
XPO
>     September 19-22, 2005 * San Francisco, CA * Development Lifecyc=
le
>     Practices
>     Agile & Plan-Driven Development * Managing Projects & Teams *
>     Testing & QA
>     Security * Process Improvement & Measurement *
>     http://www.sqe.com/bsce5sf
>     _______________________________________________
>     PyMOL-users mailing list
>     PyM...@li...
>     https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20

Mathieu,
=20
Deselect Sculpting from the builder menu or "unset sculpting"
=20
Note that if you're doing this a lot, then create some custom on/off =
function keys as follows:
=20
# F1 to turn on sculpting
cmd.set_key('F1',lambda :(cmd.set("sculpting"),cmd.set("auto_sculpt")))
=20
# F2 to turn off sculpting
cmd.set_key('F2',lambda =
:(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))
=20
Cheers,
Warren

________________________________

From: pym...@li... on behalf of Mathieu =
Coincon
Sent: Mon 8/29/2005 8:26 AM
To: pym...@li...
Subject: [PyMOL] Refinement in auto_sculpt





Hi,
i'm usinig pymol for modelling my protein in electron density.
I like it very much but there is one thing I would like to understand.
Is there a way to stop the refinement of the geometry:
    I'm using auto_sculpt and I protect/deprotect the protein but =
sometimes the
refinemt run during a long time I would like to stop it ? i played with =
the
number  of cycles and other parameters but it didn't work.





-------------------------------------------------------
SF.Net email is Sponsored by the Better Software Conference & EXPO
September 19-22, 2005 * San Francisco, CA * Development Lifecycle =
Practices
Agile & Plan-Driven Development * Managing Projects & Teams * Testing & =
QA
Security * Process Improvement & Measurement * =
http://www.sqe.com/bsce5sf
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,
i'm usinig pymol for modelling my protein in electron density.
I like it very much but there is one thing I would like to understand.
Is there a way to stop the refinement of the geometry:
    I'm using auto_sculpt and I protect/deprotect the protein but sometimes the
refinemt run during a long time I would like to stop it ? i played with the
number  of cycles and other parameters but it didn't work.

PyMOL Users:

We are looking to identify a few collaborators with existing Java
application (not applet!) development efforts already in progress that
would be ripe for inclusion of a simple real-time molecular
visualization component.

If this is you, then please make contact at your convenience and please
provide a concise list of the capabilities you would minimally need for
such a component to be useful to you.  If we think our current
development code may be able to meet your needs, then we are prepared to
share pre-release builds with you in exchange for your participation and
feedback.  If we can't meet your needs yet, then we won't waste your
time.

The ideal developer/collaborator would be someone familiar with PyMOL's
Python API, but who would prefer to eschew Python altogether and access
PyMOL-quality molecular visualization directly from Java. =20

Cheers,
Warren

PS. We'll be at ACS next week, so no hurry on this...

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

> Why don't we?  Because we do most PyMOL development on Mac OS and Linux=
,
> using free or open-source tools, such as GCC, GDB, and Apple's wonderfu=
l
> XCode, with CHUD and OpenGL profilers.  Even on Windows, we are now
> bypassing Microsoft Visual Tools altogether and using MingW and GCC to
> build our native Java extension.

native Java extension?  Is this something new, something I didn't notice
before, or a typo?

Pete

>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> wenming hu
>> Sent: Wednesday, August 24, 2005 6:29 PM
>> To: Warren DeLano; pym...@li...
>> Subject: [PyMOL] Re=EF=BC=9A RE: [PyMOL] question about _cmd.pyd
>>
>> I see. thank you for your answer. and i'm wondering, how do u
>> develop python modules like _cmd.pyd? only via setup.py, and
>> type python setup.py build to compile it? how do u debug it
>> on the procudure of development? for me, it's not easy to
>> develop _cmd.pyd only via setup.py script, i think, there
>> must have some other way to debug python extend modules.
>>
>> thank you.
>>
>>
>> Warren DeLano <wa...@de...>
>>
>>
>> 	Wen,
>>
>> 	The only form of end-user PyMOL compilation we support
>> on Windows is via Python's distutils facility.
>>
>> 	Assuming that your system paths are set up correctly,
>> distutils compilations will work fine with msvc6 -- no
>> Makefile is required.
>>
>> 	Your own c/c++ code should be built as a standalone DLL
>> -- separate from _cmd.*, and you should use the Python
>> interpreter to bring all of the native components together at runtime.
>>
>> 	Cheers,
>> 	Warren
>>
>> 	--
>> 	Warren L. DeLano, Ph.D.
>> 	Principal Scientist
>>
>> 	. DeLano Scientific LLC
>> 	. 400 Oyster Point Blvd., Suite 213
>> 	. South San Francisco, CA 94080 USA
>> 	. Biz:(650)-872-0942 Tech:(650)-872-0834
>> 	. Fax:(650)-872-0273 Cell:(650)-346-1154
>> 	. mailto:wa...@de...
>>
>>
>> ________________________________
>>
>> DO YOU YAHOO!?
>> =E9=9B=85=E8=99=8E=E5=85=8D=E8=B4=B9G=E9=82=AE=E7=AE=B1=EF=BC=8DNo.1=E7=
=9A=84=E9=98=B2=E6=AF=92=E9=98=B2=E5=9E=83=E5=9C=BE=E8=B6=85=E5=A4=A7=E9=82=
=AE=E7=AE=B1
>> <http://cn.mail.yahoo.com>
>>
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Hugues,

1) PyMOL will not render identical overlapping surface triangles =
correctly -- it is a weakness in the current algorithm.

2) If the surfaces are truly distinct are distinct, then you'll only see =
one of the unless you select multilayer transparency, in which case =
you'll see both sides of transparent surfaces (which doesn't look so =
great either).

Sorry!

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Hugues Nury
> Sent: Thursday, August 25, 2005 5:15 AM
> To: pym...@li...
> Subject: [PyMOL] Overlapping surfaces
>=20
> Hi,
>=20
> I have a problem raytracing an image with overlapping surface.
> Ok I have a protein and a lipid close to it, I draw surfaces=20
> (transparency .7) of both, and there are slightly=20
> overlapping. To see the whole lipid surface, I have to hide=20
> and show again the protein, otherwise the ovelapping part do=20
> not appear. Don't know why. When raytracing, this small=20
> overlapping surface is missing again.
>=20
> (I guess this is not perfectly clear, so you can see the images at
> http://pagesperso.laposte.net/huguesnury/Pymol/pymol_temp.html)
>=20
> Does anyone have an idea ?
>=20
> Thanks,
> Hugues
>=20
> --
> Hugues Nury
> PhD Student
> Laboratoire des Prot=E9ines Membranaires
> Institut de Biologie Structurale
> 41 rue Jules Horowitz - F 38027 Grenoble Cedex 1 - France=20
> tel. +33 (0)4 38 78 95 92
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices Agile & Plan-Driven Development *=20
> Managing Projects & Teams * Testing & QA Security * Process=20
> Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

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Hi,

I have a problem raytracing an image with overlapping surface.
Ok I have a protein and a lipid close to it, I draw surfaces=20
(transparency .7) of both, and there are slightly overlapping. To see=20
the whole lipid surface, I have to hide and show again the protein,=20
otherwise the ovelapping part do not appear. Don't know why. When=20
raytracing, this small overlapping surface is missing again.

(I guess this is not perfectly clear, so you can see the images at=20
http://pagesperso.laposte.net/huguesnury/Pymol/pymol_temp.html)

Does anyone have an idea ?

Thanks,
Hugues

--
Hugues Nury
PhD Student
Laboratoire des Prot=E9ines Membranaires
Institut de Biologie Structurale
41 rue Jules Horowitz - F 38027 Grenoble Cedex 1 - France
tel. +33 (0)4 38 78 95 92=

I see. thank you for your answer. and i'm wondering, how do u develop python modules like _cmd.pyd? only via setup.py, and type python setup.py build to compile it? how do u debug it on the procudure of development? for me, it's not easy to develop _cmd.pyd only via setup.py script, i think, there must have some other way to debug python extend modules.
 
thank you.
 

Warren DeLano <wa...@de...>

Wen,

The only form of end-user PyMOL compilation we support on Windows is via Python's distutils facility. 

Assuming that your system paths are set up correctly, distutils compilations will work fine with msvc6 -- no Makefile is required. 

Your own c/c++ code should be built as a standalone DLL -- separate from _cmd.*, and you should use the Python interpreter to bring all of the native components together at runtime.

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC 
. 400 Oyster Point Blvd., Suite 213 
. South San Francisco, CA 94080 USA 
. Biz:(650)-872-0942 Tech:(650)-872-0834 
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:wa...@de... 

		
---------------------------------
DO YOU YAHOO!?
  雅虎免费G邮箱－No.1的防毒防垃圾超大邮箱  

hi,

while using kabsch.py by Jason Vertrees from the pymolwiki site (http://www=
.pymolwiki.org/index.php/Kabsch#The_Code)

i am getting the following error message:=20

Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", =
line 191, in parse
    result=3Dapply(kw[nest][0],args[nest],kw_args[nest])
  File "kabsch.py", line 578, in optAlign
    U, T1, T2, RMSD, c1, c2 =3D K.align(stored.sel1, stored.sel2, [])
  File "kabsch.py", line 161, in align
    R =3D self.calcR(c1, c2)
  File "kabsch.py", line 254, in calcR
    R[i][j] =3D R[i][j] + (1 * (c2[k][i] * c1[k][j]) )
TypeError: only rank-0 arrays can be converted to Python scalars.

on contacting Jason and trying to backtrace the error source it appears tha=
t this error occurs=20
only on the Windows platform and the error message originates from within p=
ymol.exe and not=20
from anywhere within the Numeric package. i have tried different versions o=
f Numeric and pymol.

anyone have insight regarding this?=20=20
i am using pymol 0.99beta12 and Numeric 23.8 on Windows XP SP2.

thanks,
shiven


--=20
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i have written python extend module by c/c++, but i saw a module of pyMOL called
_cmd.pyd instead of _cmd.dll. and it is written by c/c++ also, the author
use makefile to compile it into _cmd.pyd. i have some question about it:
1. what's the difference between them? i saw the code is same as common c++
extended python module, can i use microsoft visual C++ to create a dll
project for compiling it as _cmd.dll?
2. i have never written a module with extension *.pyd, how to make a *.pyd?
and, i doubt, how the author debug the _cmd.pyd, only by Makefile?
3. i have a common problem about writting a extend module by c/c++, i often
use msvc to write it, but i only can invoke release dll, not debug dll, even
i use command like this: python_d test.py, in which case, test.py import
test.dll, and invoke test.hello() api. why? anybody has nice way to debug
it? thank you.

4. how does the author use msvc compile it as cmd.pyd? i did not find any legal makefile for msvc6.


any help would be appreciated.


with my best regards,
    Wen



		
---------------------------------
DO YOU YAHOO!?
  雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱 

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

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 $*
>

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 $*

I find that MacPyMol 0.98 will not load certain pdb files which are  
readily handled by other viewing programs. A common error message I  
receive is:

  File  
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/ 
parser.py", line 356, in parse
     exec(com2[nest]+"\n",pymol_names,pymol_names)
   File "<string>", line 1, in ?
   File  
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/ 
importing.py", line 549, in load
     discrete,quiet,multiplex,zoom)
   File  
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/cmd.py",  
line 771, in _load
     finfo = tmp_file.read(tmp_file) # WARNING: will block and hang --  
thread instead?
AttributeError: addinfourl instance has no attribute '__int__'

Paul Fitzpatrick
Department of Biochemistry and Biophysics
Texas A&M University
College Station, TX 77843-2128
ph: 979-845-5487
fax: 979-845-4946
email: fi...@ta...

hmmm....most likely the IR emmiter is connected to the v-sync on the SVGA 
port w/t Active3D/OpenGL interperter software to produce the left 
eye/right eye images.
Some of the ones like this one that i have seen only works with Active3D 
based software.  AND not all active3d software will work.  (ditto w/t 
OpenGL)

LCD monitors?  My understanding is that 3D "works" with LCD 
monitors....you just get A LOT of ghosting.  its a physics thing....  the 
hack would be to delay the shutters in the glasses to match the slow 
pixel-flip of the LCD monitor.  a marketing hack would be to list only the 
newer LCD monitors with the faster pixel-flip rate as the ones "that 
work".

Last time i looked at these, they all had an issue with keeping track of 
which eye was being displayed.

i'm always looking for cheaper alternatives to the StereoGraphics 
equipment.  So, if anyone else has some other suggestions, feel free to 
list them.

MK


pym...@li... wrote on 08/23/2005 08:11:39:

> 
> Hi,
> I would like to know if someone tried these glassesunder windows/linux.
> http://www.edimensional.com/index.php?cPath=21
> They are cheap and should work with non-pro graphics card and LCD (??).
> Thanks to share your experience.
> 
> Mathieu Coincon
> Graduate Student
> Universite de Montreal
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & 
QA
> Security * Process Improvement & Measurement * 
http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

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

Hi,
I would like to know if someone tried these glassesunder windows/linux.
http://www.edimensional.com/index.php?cPath=21
They are cheap and should work with non-pro graphics card and LCD (??).
Thanks to share your experience.

Mathieu Coincon
Graduate Student
Universite de Montreal

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

Hi,

I just downloaded a PyMOL v0.98 standalone executable and have it
running under Mandrake linux 10. I just noticed that the distance wizard
does not show the actual distance labels. Does anybody know how to turn
these on?

Thanks,

Anton Vila

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

On Mon, August 22, 2005 2:55 pm, Warren DeLano said:
>
> Hold on -- from the end-user's standpoint, the only thing that matters
> is: "does the image I see on the screen match what comes out of the
> printer".  Who cares about the "printer's point of view"?!

The printer (a person running the press) does; not the little ink-jet
thingy on the table :-)

Printing a PyMol image to a local device (ink-jet or laser probably) needs
RGB data not CMYK (anyone who has a printing device that takes CMYK
directly and knows how to use it doesn't need any help, they've got all
this stuff down pat) which it then converts to its own internal CMYK or
CcMmYK definitions. Feeding it CMYK simply results in the printer driver
converting  first to RGB and back to it's own CMYK.

>
> In the real world, scientists do not have time or resources to mess with
> color profiles and color-calibrated hardware.  They simply want to go
> from screen to hardcopy knowing their colors will not be grossly
> distorted by their hardware, which is often consumer-grade,
> non-calibrated equipment.

Pretty much.

>
> Though CMYK is indeed device-dependent, there are some color regions
> that, *in practice*, are more problematic than others when printing from
> an RGB source.  If you stick to safer regions of RGB space that are
> pragmatically captured through PyMOL's "CMYK" space command, then you
> will get closer to a WYSIWYG experience even in the absense of
> calibration.

Wouldn't it be better to rename this colour space as printRGB or something
to more accurately reflect what it is: a reduced gamut RGB space that trys
to avoid some of the colours that routinely produce unwnted colour shifts?

>
> On the other hand, blithely working in RGB space and then relying upon
> automatic RGB->CMYK color translations in the *absense* of color
> calibration for both display and printer almost always results in
> unacceptably poor color quality, and that is the practical real-world
> issue facing PyMOL users.

But the journals all have professional printers (the people) who are quite
capable of re-casting an RGB file into a CMYK file for their printing
conditions. I'm not saying it isn't easier to do that with PyMol's reduced
gamut space just that if you want or need a larger colour gamut there is
nothing preventing you from using one as long as you have some tools to
help you.

>
> So I would recast your advice as follows:  Unless you have calibrated
> hardware for both display and printer, then you are definitely not "far
> better off getting the RGB image out of pymol to look just the way you
> want it to".    Instead, you are far better off avoiding areas of RGB
> color space that are difficult or impossible to handle without
> professional-grade color hardware, and that is the sole task PyMOL's
> CMYK capability is designed to help you with.

If somebody has gotten to the point where they are worrying about their
own CMYK separations then telling them to just use a reduced gamut space
to limit the conversion problems is less than helpful to my mind. They
need to understand what is going on so they can make the decisions that
are necessary if they are to get the best colour reproduction on the
journal pages.

Rich

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