pymol-users Mailing List for PyMOL Molecular Graphics System

Dear Pymolers:

I am sure that this has been beaten to death on this email list but I am
having a heck of a time trying to figure out the following:

I am trying to make simple animations with movement, rotation, zoom and
other simple transitions in Pymol.  I have a basic understanding of the
simple movement commands as follows:

mset 1 x100
movie.roll(20, 50,axis="x")
mdo 51: move x,10
mdo 54: turn x, 5; turn y,5

The problem comes when I want to make defined rolls, zooms, or moves that
start and stop at specific places.  There must be a better way than
concatenating a collection of "move x,10" commands.  I have seen in several
scripts containing the following syntax:

for a in range(702,802):
   cmd.mdo(a,"translate [0.40,-0.5,0],object=lambda2")

Could somebody please explain what this syntax means and how to employ it
(in detail and in simple terms, if possible, for the many of us out there
who don't quite grasp all of the nuances of Pymol and Pythol command
syntax).  

When I try to incorporate a similar usage as follows:
for a in range(55,70):
   cmd.mdo(a,"move x,10,object=proteinA")

I get an error message that says:
     for a in range(55,70):
   cmd.mdo(a,"move x,10,object=proteinA")
                           ^
 SyntaxError: invalid syntax

I have tried MANY variations on this theme and seem to be stumbling around
in the dark.  Any help would be greatly appreciated.

Thanks,
Kelley



Dr. Kelley Moremen 
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229

Dear Kristian,

Thank you for your quick answer concerning pymol and python scripts.=20
You answered questions 1-3, indeed. Generator functions are described=20
at http://www.python.org/doc/2.2.2/whatsnew/node5.html and require=20
python 2.2.

Questions 4 and 6 I can now answer myself:
> 4) Can I temporarily return control to pymol from within a running a=20=

> python script and continue running the script after I have finished=20
> interacting with pymol?
The spawn command does the trick. I did not check out this ScriptBox=20
Utility yet.

> 6) How do I generate symmetry molecules for one selected state of a=20
> molecule only? I have a molecule with 144 states and generating=20
> symmetry objects for all states simultaneously takes too long time and=20=

> finally crashes pymol, because all memory is used up.
Copy the desired state into a new object and generate the symmetry=20
molecules of this new object:

def sym_state(s):
   cmd.delete("sym*")
   cmd.delete("tmp")
   cmd.create("tmp", "MyObject", s, 1)
   cmd.symexp("sym", "tmp", "tmp", 30)
   cmd.do("show cell")
   print("Generated symmetry objects for state " + `s`)
   return

Cheers,
Markus

On Wednesday, March 26, 2003, at 02:51  pm, Kristian Rother wrote:

>
> Dear Markus,
>
>> 1) How can I supply arguments to a python script,
>> when I invoke it from
>> the pymol command line?
>
> Write the python script like
>
> def bla(arg1,arg2):
>     any.python.commands(arg1,arg2)
>     return
>
> from pymol import cmd
> cmd.extend('blacommand',bla)
>
> Now you can call your function 'bla' from the PyMOL
> command line:
>
> PyMOL> blacommand pdb1cso,42
>
> Which would be like in Python:
>
> bla('pdb1cso','42')
>
>
>
>> 2) Can I set user variables in the pymol command
>> line and access them
>> in a python script?
>
> same answer as for 1).
>
>
>> 3) Can I rerun a python script and use generator
>> functions that I
>> initialised in the run before?
>
> Sorry, I did not understand this question completely
> (might be same answer as above two).
>
>
>> 4) Can I temporarily return control to pymol from
>> within a running a
>> python script and continue running the script after
>> I have finished
>> interacting with pymol?
>
> You should probably check out the Script Box utility,
> if You have not already (http://www.rubor.de/bioinf
>
>
>> 5) Can I query the active state of a pymol object
>> (and other properties
>> as well) from withing a python script?
>
> Yes. Look at:
> http://www.rubor.de/bioinf/pymol_tips.html#getcoord
>
>
>> 6)
> dunno
>
>> 7)
> also.
>
> Good luck,
>
> Kristian Rother

Markus Meier
M. E. M=FCller Institut
Biozentrum der Universit=E4t Basel
Klingelbergstrasse 70
CH-4056 Basel
Tel.: +41 61 267 20 91
Fax: +41 61 267 21 09

If your question is how to maintain a "colored" cross-section rather than
the black one, use "two-sided lighting" option from the Display menu.  I
think there are a couple other switches that may help, but I found that
the two-sided lighting takes care of the blackened surfaces.

Denis

On Fri, 28 Mar 2003, Tsjerk Wassenaar wrote:


Hi guys,

Was wondering if it is possible to get the spheres filled when clipping.
Couldn't find this in the mail archive. Sorry if I just overlooked.

Cheers,

Tsjerk

-- 
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-- :) 	Dept. of Biophysical Chemistry
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Hi guys,

Was wondering if it is possible to get the spheres filled when clipping. 
Couldn't find this in the mail archive. Sorry if I just overlooked.

Cheers,

Tsjerk

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
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Pedro,

That is the default behavior of PyMOL -- surfaces are given the color of
the underlying atoms.

To select a uniform color, such as white, try:

set surface_color,white

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D. 
Principal Member
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Pedro
Antonio Reche
Sent: Thursday, March 27, 2003 8:15 AM
To: pym...@li...
Subject: [PyMOL] coloring surface

Hi all,

I have just started using pymol and I wonder if it is possible to
transfer or map residue/atoms colors to their surface as with GRASP. If
so, I would like to know how is done. Tanks in advance for any positive
consideration.
Cheers


pedro

Hi all,

I have just started using pymol and I wonder if it is possible to
transfer or map residue/atoms colors to their surface as with GRASP. If
so, I would like to know how is done. Tanks in advance for any positive
consideration.
Cheers

pedro
-- 
*******************************************************************
PEDRO A. RECHE , pHD		    TL: 617 632 3824
Bioinformatics Research Scientist   FX: 617 632 4569
Dana-Farber Cancer Institute,	    EM: re...@re...
Molecular Immunology Foundation,    EM: ped...@df...
Harvard Medical School,		    W3: http://www.mifoundation.org 
44 Binney Street, D1510A,
Boston, MA 02115   						
*******************************************************************

Hello All,

is there a self-contained PyMOL windows executable that doesn't require 
the installation of Python?

Thanks,

John

Dear Markus,

> 1) How can I supply arguments to a python script,
> when I invoke it from 
> the pymol command line?

Write the python script like

def bla(arg1,arg2):
    any.python.commands(arg1,arg2)
    return

from pymol import cmd
cmd.extend('blacommand',bla)

Now you can call your function 'bla' from the PyMOL 
command line:

PyMOL> blacommand pdb1cso,42

Which would be like in Python:

bla('pdb1cso','42')



> 2) Can I set user variables in the pymol command
> line and access them 
> in a python script?

same answer as for 1).

 
> 3) Can I rerun a python script and use generator
> functions that I 
> initialised in the run before?

Sorry, I did not understand this question completely
(might be same answer as above two).


> 4) Can I temporarily return control to pymol from
> within a running a 
> python script and continue running the script after
> I have finished 
> interacting with pymol?

You should probably check out the Script Box utility,
if You have not already (http://www.rubor.de/bioinf

 
> 5) Can I query the active state of a pymol object
> (and other properties 
> as well) from withing a python script?

Yes. Look at: 
http://www.rubor.de/bioinf/pymol_tips.html#getcoord


> 6) 
dunno
 
> 7) 
also.

Good luck,

Kristian Rother

__________________________________________________
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Hi everyone

I have a couple of observations/problems, more in the irritating rather
than serious category, but which I'd still like explanations for.

1.  I have a Dell Precision machine with Nvidia graphics which generally
works extremely well with Pymol.  It's recognised like this

 OpenGL based graphics front end:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro2 MXR/AGP/SSE2
  GL_VERSION: 1.3.1 NVIDIA 29.60

and is wonderfully fast.

Occasionally, however, I start pymol and it's clear that the hardware
acceleration isn't there - everything works but *slowly*.  Sometimes just
starting Pymol from a different terminal does the trick, sometimes not.
Any explanations for this?  I can't see any common factors in the
situations where I've seen this behaviour.

2.  Today, facing this problem, I was getting nowhere trying differnt
(Konsole) terminals so I thought - what about trying a Gnome terminal.  I
did and the whole machine froze completely immediately after I pressed
return.  Had to reboot.

Any thoughts much appreciated.

Daniel Rigden

+-------------------------------------------------------------------------+
|                       Dr Daniel John Rigden                             |
| CENARGEN/EMBRAPA                 | e-mail: da...@ce...   |
| Parque Estacao Biologica         | http://www.cenargen.embrapa.br       |
| PqEB - Final - Av. W3 Norte      |  Phone:  +55 (61)448-4741            |
| 70770-900, Brasilia-D.F.-BRAZIL  |  Fax:    +55 (61)340-3658            |
+-------------------------------------------------------------------------+

Dear all,

I have some questions mainly regarding command-line and python scripts=20=

in pymol:

1) How can I supply arguments to a python script, when I invoke it from=20=

the pymol command line?

2) Can I set user variables in the pymol command line and access them=20
in a python script?

3) Can I rerun a python script and use generator functions that I=20
initialised in the run before?

4) Can I temporarily return control to pymol from within a running a=20
python script and continue running the script after I have finished=20
interacting with pymol?

5) Can I query the active state of a pymol object (and other properties=20=

as well) from withing a python script?

6) How do I generate symmetry molecules for one selected state of a=20
molecule only? I have a molecule with 144 states and generating=20
symmetry objects for all states simultaneously takes too long time and=20=

finally crashes pymol, because all memory is used up.

7) How do I search the archived mailing list? If I go to=20
http://sourceforge.net/mailarchive/forum.php?forum_id=3D60 and use the=20=

search button, I only get:
      No matches found
      for whatever search word I type in
     (I remember it working before)

Best regards,
Markus

Markus Meier
M. E. M=FCller Institut
Biozentrum der Universit=E4t Basel
Klingelbergstrasse 70
CH-4056 Basel
Tel.: +41 61 267 20 91
Fax: +41 61 267 21 09=

Hi!

I want to color the cartoon of a protein that has been aligned to 
another protein where the color changes as the RMSD changes. My python 
programmer husband is helping me by adapting Robert Campbell's 
color_b.py script but I am not sure where to get the RMSD values. I was 
thinking intra_fit, or intra_rms or intra_rms_cur would work because 
they return an array which could be used but it is not clear to me how 
they work. I don't see where to put the two sets of atoms; rms and fit 
have the seemingly correct input but don't return the array, right?

Thanks for any clues.

Cheers,
Holly

I am working with a molecule from PDB which has negative residue numbers
for some chains. There is a logical reasoning for this numbering scheme.
Unfortunately, PyMol appears to translate atom selections with negative
residues into incomplete range specifications and generates an error. Is
there any trick or workaround?

Thanks.

Andrew.

Hi All!

Has anyone worked much with session saves? I tried it for the first time 
yesterday. I saved what I was working on. This morning I tried to open 
the session and pymol just quits. No error message.

I am using Windows XP, pymol version 0.86, and python 2.2.

If anyone wants, I can send the session file to them. I don't want to 
attach it to list mail.

Cheers,
Holly

-- 
____________________________________________________________________________

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Res. Asst. Prof.                 FAX:  631 444-7641
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On Friday, Mar 21, 2003, at 08:45 Australia/Sydney, Balaji Bhyravbhatla 
wrote:

> Hello All,
> I am new to the OS-X environment and would like some help getting the 
> program running
> on a laptop.
> For practice I setup pymol on an older G3 and all went fine. Complete 
> new install by me.
> Next I get a laptop of a student and I follow the same instructions of 
> Bill Scott's but get
> a "Bus error" when the program is started from an xterm.
>
> The first time around immediate "Bus error" message.
> So then I do a "fink selfupdate-cvs" and a "fink update-all". No errors
> but this time around, a pymol window opens up before crashing with a 
> "Bus error"
>
> Any help would be greatly appreciated.
>
> Thanks, please email me if you need further information (also how to 
> get that
> info!!)

What version of fink 'fink -V' and are you running stable or unstable 
tree.

What version of OSX

Matt

Hello All,
I am new to the OS-X environment and would like some help getting the 
program running
on a laptop.
For practice I setup pymol on an older G3 and all went fine. Complete 
new install by me.
Next I get a laptop of a student and I follow the same instructions of 
Bill Scott's but get
a "Bus error" when the program is started from an xterm.

The first time around immediate "Bus error" message.
So then I do a "fink selfupdate-cvs" and a "fink update-all". No errors
but this time around, a pymol window opens up before crashing with a 
"Bus error"

Any help would be greatly appreciated.

Thanks, please email me if you need further information (also how to get 
that
info!!)

Balaji

David,

	By default, when HETATMs are loaded from a PDB file, the "ignore" flag =
is set, which means that they are excluded from surface & mesh =
calculations.  You can clear these flags with:

flag ignore,all,clear
rebuild

Alternatively, you can just tell the surface and mesh algorithms to =
disregard the ignore flag by changing the surface mode.

set mesh_mode,1
set surface_mode,1

mode 0: consider all atoms except those with ignore set
mode 1: consider all atoms
mode 2: consider all non-hydrogen atoms

Cheers,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: David P. Chimento [mailto:dp...@un...]
> Sent: Thursday, March 20, 2003 7:09 AM
> To: pym...@li...
> Subject: [PyMOL] Surface on HETATM groups
>=20
>=20
> I would like to display a surface for a HETATM group in my=20
> structure, but
> PYMOL is not doing so.  Has anyone ever done this and if so=20
> how?  Thanks.
>=20
>=20
>  David Chimento 	University of Virginia
>  dp...@vi...
>  W (804) 243-2730 or 924-9599
>  H (804) 984-0877
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Tablet PC. =20
> Does your code think in ink? You could win a Tablet PC.=20
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>=20

I would like to display a surface for a HETATM group in my structure, but
PYMOL is not doing so.  Has anyone ever done this and if so how?  Thanks.


 David Chimento 	University of Virginia
 dp...@vi...
 W (804) 243-2730 or 924-9599
 H (804) 984-0877

Hi, I am trying to make a movie out of 50 pdb
snapshots. I want to show the surrounding residues and
water 4 angstroms away from the substrate. If I only
work on one snapshot it seems fine--there are three or
four water molecules. When I load all 50 snapshots at
the same time as different mov states, there are a few
dozen if not hundred water in each rendered snapshot.
Here is part of my script:

...
select near, (byres (resi 219 around 4))
show spheres, (near and resn WAT)
set sphere_scale=0.2
...
mset 1 -50
set ray_trace_frames=1
set cache_frames=0
mclear
mpng mov

Thank you for your input!

Regards,
-Yunfeng

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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:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Fred Berkovitch [mailto:fr...@MI...]
> Sent: Monday, March 17, 2003 6:41 PM
> To: pym...@li...
> Subject: [PyMOL] Transparent cartoons?
>=20
>=20
> Hello everyone,
>=20
> Can pymol make transparent cartoons?  If so, how?
>=20
> -Fred
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by:Crypto Challenge is now open!=20
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>=20

On Wednesday, Mar 19, 2003, at 07:42 Australia/Sydney, DeLano, Warren 
wrote:

> 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.

No this is a problem in the fink unstable tree due to python-2.3 and 
numeric being install in the wrong spot.

Cheers
Matt

Do this,

fink install python-2.2.2

fink rebuild numeric

fink rebuild pmw

fink install pymol

Cheers
Matt



On Wednesday, Mar 19, 2003, at 05:58 Australia/Sydney, Kevin Gardner 
wrote:

> 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.                  Kev...@ut...
> Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
> 214-648-8916/FAX: -8947        		     http://freedom7.swmed.edu
>
>
>
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On 18/3/03 8:42 pm, "DeLano, Warren" <wa...@su...> wrote:

> 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.

I installed PyMOL using Fink Commander on MacOS X 10.2.4. Fink Commander
will download the source files and compile them automatically.

PyMOL works nicely under Apple's X11 beta.

Ian
-- 
Ian Robinson - Belfast - UK
<http://www.canicula.com>

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:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Kevin Gardner [mailto:Kev...@ut...]
> Sent: Tuesday, March 18, 2003 10:59 AM
> To: pym...@li...
> Subject: [PyMOL] fink install fail: pymol-0.86-4
>=20
>=20
> 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:
>=20
> 	- 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
>=20
> Output from the build attached below --- anyone have any insights
> here?
>=20
> Thanks,
> Kevin
>=20
> ------
>=20
> cd pyopengl;make
> cc -ffast-math -no-cpp-precomp -g -I/sw/include=20
> -I/sw/include/python2.2=20
> -I/usr/X11R6/include -D_HAVE_LIBPNG  -D_PYMOL_MODULE -D_PYMOL_NUMPY=20
> -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=20
> incompatible pointer type
> _glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from=20
> incompatible pointer type
> _glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from=20
> incompatible pointer type
> _glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from=20
> incompatible pointer type
> _glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from=20
> 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=20
> 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
>=20
> --=20
> **********************************************************************
> Kevin Gardner, Ph.D.                  Kev...@ut...
> Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
> 214-648-8916/FAX: -8947        		    =20
http://freedom7.swmed.edu



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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.                  Kev...@ut...
Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
214-648-8916/FAX: -8947        		     http://freedom7.swmed.edu

Hello everyone,

Can pymol make transparent cartoons?  If so, how?

-Fred