pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] resolution of th eimage

[Mirek C. <mir...@br...>]

Hi,
	The images produced by PyMOL are really nice. Is there a way to define the
resolution of the image file? Say I would like to get an image with a
resolution of 1600 x 1200 pixels but my screen is only 1400 x 1050?

                                                Mirek

[PyMOL] electron density 'surface'

[Manfred W. B. <ma...@uk...>]

I would like to display an electron density as a surface instead of a mesh.
Is this somehow possible with PyMOL?

Thanks in advance for any help

Manfred

RE: [PyMOL] CSD .dat files

[DeLano, W. <wa...@su...>]

Charles,

   ".dat" is a hopefully oversubscribed file extension, and the .dat
which PyMOL currently recognizes is for Macromodel.  If you are have
some development skills, consider writing a Python-based CSD file parser
for the Chemical Python portion of PyMOL.  Any ChemPy model can be
loaded straight into PyMOL.  This approach doesn't have quite the
performance as native C reads but, it will suffice for
moderate-throughput applications.

  Example Python code for reading MOL files can be found in
modules/chempy/mol.py.  The code is just over 105 lines and supports
both reads and writes.  One should be able to add a CSD reader with just
an hour or two starting with a description of the CSD file format.  Just
focus on the atom symbols, coordinates, bonds, and bond orders...the
rest can be dealt with later on.

  I propose using the extension ".csd" for csd structure files.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> From: Ross, Charles [mailto:Cha...@st...]
>=20
> I am running latest version (0.73) on an SGI Octane running=20
> IRIX 6.5.14m.
> Structures extracted from the Cambridge Structural Database have the
> extension .dat.  This extension is recognized by PyMol,=20
> although perhaps not
> as a structure file - when I read it, I get no errors, but I get no
> structure either.  Does PyMol recognize CSD structure files,=20
> and if so, what
> is the proper extension?
>=20
> thanks
> Charles Ross
>=20
> Department of Structural Biology
> St. Jude Children's Research Hospital
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] CSD .dat files

[Ross, C. <Cha...@st...>]

I am running latest version (0.73) on an SGI Octane running IRIX 6.5.14m.
Structures extracted from the Cambridge Structural Database have the
extension .dat.  This extension is recognized by PyMol, although perhaps not
as a structure file - when I read it, I get no errors, but I get no
structure either.  Does PyMol recognize CSD structure files, and if so, what
is the proper extension?

thanks
Charles Ross

Department of Structural Biology
St. Jude Children's Research Hospital

[PyMOL] problems downloading pymol

[palmira <pa...@is...>]

Dear all:

I tried to install pymol in my Linux box (Mandrake 8.0) and I've been having 
some problems downloading the external dependencies packages (both the 
required and the optional one). When I try to untar them I get a message 
saying that the packages are not complete or corrupted. 

I don't know if the problem resides in my school connection (10,000 students 
and a very narrow bandwidth) or with the files (shouldn't the req one be 
10MB? when I'm downloading I get the information it is only 3,6...)

Thanks
Palmira

[PyMOL] installation on WindowsXP operating system

[Sue H. <she...@hs...>]

Dear PyMol users:
I recently upgraded to WindowsXP from WindowsMe, in doing so I had some =
problems that ultimately resulted in wiping out my hard drive.  I have =
tried to downlad and reinstall PyMol and I am experiencing some difficulty.=
 I have ben able to download and install Python-2.1 successfully; however, =
I have been unable to install PyMol.  I downloaded pymol-0_68-bin-win32-py2=
1 and also pymol-0_73-bin-win32-py21, when I try to unzip these files I =
get an error that says the file is corrupt or there are no files to unzip. =
 I have tried several times.  Is this a conflict with XP or a problem with =
my computer or a problem with the files?  Thanks ion advance for your =
feedback.  Sue

RE: [PyMOL] add hydrogens

[DeLano, W. <wa...@su...>]

Addis,

  Yes, I am aware of this issue and plan to address it in later
versions.  Hydrogen adding needs to become residue-aware. =20

Note that when you are building amino acids, they do start out with
qausi-correct hydrogen names.  There is still some ambituity as to which
convention is followed for 4-letter names 2HH1 vs. HH12.  Unfortunately,
certain packages make assumptions about this, so PyMOL should probably
support both, as well as on-the-fly interconversion.

Cheers,
Warren

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



> -----Original Message-----
> From: Addis [mailto:ad...@ds...]
> Sent: Thursday, December 13, 2001 10:13 AM
> To: pym...@li...
> Subject: [PyMOL] add hydrogens
>=20
>=20
> I start to work in computational chemistry and I use as imput=20
> file of my=20
> algorithm a pdb standard format, I need all atoms for my calculation=20
> (also hydrogens), but frequently the examples I found are without=20
> hydrogens. I have used the command h_add and it works: it add=20
> hydrogens,=20
> but the names are diffrent from the standard pdb format. I explain in=20
> pdb format the name of hydrogen depends on the position that=20
> it has in=20
> the aminoacyd structure ( for example 1HB is the first=20
> hydrogen linked=20
> to C-beta  , but if I add hydrogens with h_add I obtain a sequence of=20
> hydrogens labeled as H01,H02,...
> Is it possible to obtain labels in standard pdb format?
> Thank you very much,
> 	Bernardetta Addis
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] add hydrogens

[Addis <ad...@ds...>]

I start to work in computational chemistry and I use as imput file of my 
algorithm a pdb standard format, I need all atoms for my calculation 
(also hydrogens), but frequently the examples I found are without 
hydrogens. I have used the command h_add and it works: it add hydrogens, 
but the names are diffrent from the standard pdb format. I explain in 
pdb format the name of hydrogen depends on the position that it has in 
the aminoacyd structure ( for example 1HB is the first hydrogen linked 
to C-beta  , but if I add hydrogens with h_add I obtain a sequence of 
hydrogens labeled as H01,H02,...
Is it possible to obtain labels in standard pdb format?
Thank you very much,
	Bernardetta Addis

[PyMOL] Suggested stereo parameter settings

[Dirk K. <dir...@ps...>]

Dear PyMOL users,

in case that you may find the current stereo parameters not optimal, here
are my suggestions:
put the following lines in your .pymolrc file (copy from
<yourinstallation>/pymol/sample.pymolrc):

set stereo_angle=6.0
set stereo_shift=0.0

At least on our SGIs these settings produce a significantly better stereo
picture than the default values 2.1 and 2.0, respectively.
Many thanks to Warren who told me which parameters to change and their
default values.

Regards,

Dirk.


*****************************************************
Dirk Kostrewa
Paul Scherrer Institut   e-mail: dir...@ps...
Life Sciences             phone: +41-56-310-4722
OSRA/007                    fax: +41-56-310-4556
CH-5232 Villigen PSI        WWW: http://sb.web.psi.ch
Switzerland
*****************************************************

RE: [PyMOL] Selecting objects to move

[DeLano, W. <wa...@su...>]

Leslie,=20

   Well it seems a mis-spoke.  I tried to write a script which does what
you layed out, but it turns out that the current the API functions for
moving moleculs don't have quite enough power to do this efficiently
(even in version 0.73).  My time is probably better spent refining
"rotate" and "translate" than describing some kind of elaborate
work-around which would enable you to do this right now.   Can we
revisit this in a month or two?

   Electrostatic surfaces are also a few months away still, unless
someone can provide me with source code for a drop-in PB solver.

Cheers,
Warren

> From: Leslie Hall [mailto:HA...@ut...]

>  I am trying to make these changes automatically. =20
> Essentially, I would
> like to have a script to make a movie where;
>=20
> First, I want to load pdb files that contain four molecules=20
> (A, A, B, and
> B).   Initially, I what to hide all four molecules.  Then=20
> show the dimer AA
> in the center of the screen.  Have this dimer rotate around=20
> X.  Then show a
> conformational change in this dimer where you hold one of the=20
> molecules (A)
> stationary, while you rotate the other molecule A in X by 100 degrees.
> After this is done, I then want to show one molecules of B on=20
> the left side
> and the other molecule B on the right side of the dimer of=20
> AA.  Finally I
> want to show the molecule B's moving and docking with the=20
> dimer (AA) in its
> new conformation.
>=20
> Also, is it posible to make this movie showing electrostatic surface?
>=20
> Les
>=20
>=20
>=20

[PyMOL] Re: Installing Pymol on SuSE 7.3 again (Andrey Khavryuchenko)

[Marc S. <mar...@mp...>]

> Marc,
> 
> I'm the person, who build the rpm.  I'm using Red Hat and package works
> flawlessly (as far as I need).

Actually that might be the problem. As Warren has pointed out, rpm's are 
not neccessarily interchangeable between distributions. Therefore 
something might be broken if installed on SuSE (for example it seems 
that the package expects python to be in a different path or under a 
different name (I have a working python 2.1.1, but one package 
complains, that python > 2.1 is neccessary).

Pymol now runs (compiled from source) so anyway.

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] Re: Installing Pymol on SuSE 7.3 again

[Andrey K. <ak...@kd...>]

Marc,

"MS" == Marc Saric wrote:

 MS> Bottomline: The precompiled rpm-binaries seem to be broken -at least
 MS> they don't for SuSE 7.3.

They work for me :)

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

[PyMOL] Installing Pymol on SuSE 7.3 again

[Marc S. <mar...@mp...>]

Hi,

disregard my message from yesterday.

Today I downloaded the pymol 0.73-sources and the ext-req-package and 
now it works (I also sorted out some problems with rpm-packages of 
Numeric and other external stuff not directly related to Pymol).

But still I had some problems compiling:

1. glut complained that glutbitmap.h was not there (but should'nt it be 
there, otherwise downloading a complete ext-package does not make 
sense???). I installed mesaglut-devel from SuSE 7.3, and after that, it 
worked.

2. after compilation (apparently without error, but with some warnings) 
of both the required ext-packages (I excluded png1 because I have the 
png2-lib installed, as described in the INSTALL-manual) and pymol, I 
tried to start pymol, but got an error from _cmd complaining, that 
python 152.so-something had an undefined symbol "stat".

I changed the Makefile-scripts to use my preinstalled SuSE 7.3 Python 
2.1 (why use 1.52 anyway) and after that it worked (i.e. demos ran 
without problems and program did not crash for 10 minutes or so ;-) ).

So now I need to test-check it a bit more and see if everything is ok.
Any hints for ready-made self-tests or so?

Bottomline: The precompiled rpm-binaries seem to be broken -at least 
they don't for SuSE 7.3.

There is a missing (really??) header-file in glut in the ext-package.

The default compilation of Python 1.52 as in the ext-package does not 
work either (for me -don't know why) but with a precompiled Python 2.1.1 
it is ok.

Cheers!

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] Re: Installing Pymol on SuSE-Linux 7.3 fails

[Andrey K. <ak...@kd...>]

Marc,

I'm the person, who build the rpm.  I'm using Red Hat and package works
flawlessly (as far as I need).

"MS" == Marc Saric wrote:

 MS> Hi all,
 MS> I recently downloaded the rpm-packages available from the
 MS> pymol-sourceforge-site


 MS> (i.e.
 MS> Numeric-20.2.1-1.i386.rpm
 MS> Pmw-0.8.5-1.i386.rpm
 MS> pymol-0_68-1.i386.rpm
 MS> )

 MS> and installed them, but after starting pymol, I got the following error:

 MS> -------------------------------

 MS> saric@m99106:/home/saric> pymol
 MS> Traceback (most recent call last):
 MS> File "/usr/lib/pymol/launch_pymol.py", line 6, in ?
 MS> import pymol
 MS> File "/usr/lib/python2.1/site-packages/pymol/__init__.py", line 24, in ?
 MS> import _cmd
 MS> File "/usr/lib/python2.1/site-packages/pymol/_cmd.py", line 57, in ?

That line is strange.  Do you really have _cmd.py file???
There's no such file in rpm.  Neither in my site-packages/pymol.

This might be the cause of malfunction.

 MS> import parsing
 MS> File "/usr/lib/python2.1/site-packages/pymol/parsing.py", line 592, in ?
 MS> import cmd
 MS> File "/usr/lib/python2.1/site-packages/pymol/cmd.py", line 97, in ?
 MS> lock_api = pymol.lock_api
 MS> AttributeError: 'pymol' module has no attribute 'lock_api'

Other generic recommendation would be to rebuild rpm from src.rpm.  That's
simple: just issue
        rpm --rebuild pymol-xxx.src.rpm


-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] Learning Python for PyMOL

[Frank V. <Fra...@sy...>]

vim (Improved Vi editor) which is on RedHat and probably most other
Linux, also is python-sensitive.  It does pretty colours and stuff, so
for all you vi loyalists, there's no need to go over to the Dark Side.
:)

phx.

> -----Original Message-----
> From: DeLano, Warren [mailto:wa...@su...]
> Sent: Monday, December 10, 2001 9:13 AM
> To: David J. Schuller
> Cc: pym...@li...
> Subject: [PyMOL] Learning Python for PyMOL
>=20
>=20
>=20
> David Schuller asked about the best books for learning Python.  There
> are two key resources:
>=20
> (1) Guido's online tutorial is a good starting point for learning the
> language.
>=20
> http://www.python.org/doc/current/tut/tut.html
>=20
> and (2) "Python Essential Reference" by David M. Beazley, (New Riders)
> is a must-have reference for writing Python code.
>=20
> These tare what got me going a couple years back along with the other
> documentation files on the Python web site.=20
> http://www.python.org/doc/current/
>=20
> NOTE: In order to write Python effectively, you need an editor which
> supports its indentation scheme.  The top choices are (1)=20
> emacs running
> python-mode, or (2) IDLE, the editor included with most Python
> distributions. =20
>=20
> Writing Python without a Python-aware editor is a thankless=20
> task due to
> Python's sensitive block structures which would be a chore to=20
> maintain.
> I recommend that you use spaces instead of tabs to indent=20
> Python code --
> PyMOL's convention is 3 spaces per block.
>=20
> The relavent portions of my .emacs file are included below in case
> anyone is interested.  I think most modern Linux=20
> distrubutions include a
> python mode in emacs by default.
>=20
> For simple tasks, the PyMOL command language (.pml files) is=20
> easier than
> Python because you can ignore the identation issue.  However,=20
> .pml files
> are suited for real programming.
>=20
> Cheers,
> Warren
>=20
> -- BEGIN .emacs excerpt
>=20
> (setq-default visible-bell t)
> (setq-default backup-inhibited t)
> (setq-default auto-save-default nil)
>=20
> (global-set-key "\C-c\C-w" 'goto-line)
>=20
> (setq-default tab-stop-list '(3 6 9 12 15 18 21 24 27 30 33=20
> 36 39 42) )
>=20
> (setq-default tab-width 3)
> (setq-default py-indent-offset 3)
> (setq-default indent-tabs-mode nil)
>=20
> (setq auto-save-default nil)
> (setq auto-save nil)
> (setq load-path (cons "/usr/share/emacs/site-lisp/" load-path))
> (autoload 'python-mode "python-mode" "Python editing mode." t)
> (setq auto-mode-alist
> 	  (cons '("\\.py$" . python-mode) auto-mode-alist))
> (setq auto-mode-alist
> 	  (cons '("\\.pym$" . python-mode) auto-mode-alist))
> (setq interpreter-mode-alist
> 	  (cons '("python" . python-mode) interpreter-mode-alist))
> (global-font-lock-mode)
>=20
> -- END .emacs excerpt
>=20
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
> Informatics Manager
> Sunesis Pharmaceuticals, Inc.
> 341 Oyster Point Blvd.
> S. San Francisco, CA 94080
> (650)-266-3606 fax: (650)-266-3501
>=20
>=20
>=20
> > -----Original Message-----
> > From: DeLano, Warren=20
> > Sent: Monday, December 10, 2001 7:40 AM
> > To: Glen L. Prosise
> > Cc: pym...@li...
> > Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux)
> >=20
> >=20
> >=20
> > Gang,
> >=20
> > Last night I posted binaries of PyMOL 0.73 for Windows and=20
> > Linux to the
> > downloads page.  Read more at http://www.pymol.org
> >=20
> > This is the first version to support fragment and residue-based
> > molecular building.  However, you may find the process=20
> > challenging with
> > the current rudimentary interface. =20
> >=20
> > Cheers,
> > Warren
> >=20
> >=20
> >=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Re: [PyMOL] Selecting objects to move

[Leslie H. <HA...@ut...>]

"DeLano, Warren" wrote:

> > From: Leslie Hall [mailto:HA...@ut...]
>
> > I have just started using PyMol and had a question about
> > moving selected
> > objects in an animation.
> > Here is basically what I want to do.
> >
> > 1.    Load two separate pdb files.
> > 2.    Be able to move the two molecules independently of each other.
> > 3.    Show a conformational change in one of the molecules.
> > 4.    Move the two molecules independently and show them docking with
> > each other.
>
> Leslie,
>
>    Are you trying to perform these changes manually using the mouse, or
> automatically using the Python API?  The manual approach is documented
> in the manual, but the Python API approach was neither documented nor
> complete in 0.68.
>
>    It is complete now in version (0.73) but still isn't well documented.
> If you provide some more details about how you're planning on doing
> this, I could probably post a couple examples for you.

Warren,

 I am trying to make these changes automatically.  Essentially, I would
like to have a script to make a movie where;

First, I want to load pdb files that contain four molecules (A, A, B, and
B).   Initially, I what to hide all four molecules.  Then show the dimer AA
in the center of the screen.  Have this dimer rotate around X.  Then show a
conformational change in this dimer where you hold one of the molecules (A)
stationary, while you rotate the other molecule A in X by 100 degrees.
After this is done, I then want to show one molecules of B on the left side
and the other molecule B on the right side of the dimer of AA.  Finally I
want to show the molecule B's moving and docking with the dimer (AA) in its
new conformation.

Also, is it posible to make this movie showing electrostatic surface?

Les

[PyMOL] Learning Python for PyMOL

[DeLano, W. <wa...@su...>]

David Schuller asked about the best books for learning Python.  There
are two key resources:

(1) Guido's online tutorial is a good starting point for learning the
language.

http://www.python.org/doc/current/tut/tut.html

and (2) "Python Essential Reference" by David M. Beazley, (New Riders)
is a must-have reference for writing Python code.

These tare what got me going a couple years back along with the other
documentation files on the Python web site.=20
http://www.python.org/doc/current/

NOTE: In order to write Python effectively, you need an editor which
supports its indentation scheme.  The top choices are (1) emacs running
python-mode, or (2) IDLE, the editor included with most Python
distributions. =20

Writing Python without a Python-aware editor is a thankless task due to
Python's sensitive block structures which would be a chore to maintain.
I recommend that you use spaces instead of tabs to indent Python code --
PyMOL's convention is 3 spaces per block.

The relavent portions of my .emacs file are included below in case
anyone is interested.  I think most modern Linux distrubutions include a
python mode in emacs by default.

For simple tasks, the PyMOL command language (.pml files) is easier than
Python because you can ignore the identation issue.  However, .pml files
are suited for real programming.

Cheers,
Warren

-- BEGIN .emacs excerpt

(setq-default visible-bell t)
(setq-default backup-inhibited t)
(setq-default auto-save-default nil)

(global-set-key "\C-c\C-w" 'goto-line)

(setq-default tab-stop-list '(3 6 9 12 15 18 21 24 27 30 33 36 39 42) )

(setq-default tab-width 3)
(setq-default py-indent-offset 3)
(setq-default indent-tabs-mode nil)

(setq auto-save-default nil)
(setq auto-save nil)
(setq load-path (cons "/usr/share/emacs/site-lisp/" load-path))
(autoload 'python-mode "python-mode" "Python editing mode." t)
(setq auto-mode-alist
	  (cons '("\\.py$" . python-mode) auto-mode-alist))
(setq auto-mode-alist
	  (cons '("\\.pym$" . python-mode) auto-mode-alist))
(setq interpreter-mode-alist
	  (cons '("python" . python-mode) interpreter-mode-alist))
(global-font-lock-mode)

-- END .emacs excerpt

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



> -----Original Message-----
> From: DeLano, Warren=20
> Sent: Monday, December 10, 2001 7:40 AM
> To: Glen L. Prosise
> Cc: pym...@li...
> Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux)
>=20
>=20
>=20
> Gang,
>=20
> Last night I posted binaries of PyMOL 0.73 for Windows and=20
> Linux to the
> downloads page.  Read more at http://www.pymol.org
>=20
> This is the first version to support fragment and residue-based
> molecular building.  However, you may find the process=20
> challenging with
> the current rudimentary interface. =20
>=20
> Cheers,
> Warren
>=20
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] PyMOL 0.73 Released (Win,Linux)

[Warren L. D. <wa...@su...>]

Gang,

Last night I posted binaries of PyMOL 0.73 for Windows and Linux to the
downloads page.  Read more at http://www.pymol.org

This is the first version to support fragment and residue-based
molecular building.  However, you may find the process challenging with
the current rudimentary interface.  

Cheers,
Warren

[PyMOL] Installing Pymol on SuSE-Linux 7.3 fails

[Marc S. <mar...@mp...>]

Hi all,

I recently downloaded the rpm-packages available from the 
pymol-sourceforge-site

(i.e.
      Numeric-20.2.1-1.i386.rpm
      Pmw-0.8.5-1.i386.rpm
      pymol-0_68-1.i386.rpm
)

and installed them, but after starting pymol, I got the following error:

-------------------------------

saric@m99106:/home/saric> pymol
Traceback (most recent call last):
   File "/usr/lib/pymol/launch_pymol.py", line 6, in ?
     import pymol
   File "/usr/lib/python2.1/site-packages/pymol/__init__.py", line 24, in ?
     import _cmd
   File "/usr/lib/python2.1/site-packages/pymol/_cmd.py", line 57, in ?
     import parsing
   File "/usr/lib/python2.1/site-packages/pymol/parsing.py", line 592, in ?
     import cmd
   File "/usr/lib/python2.1/site-packages/pymol/cmd.py", line 97, in ?
     lock_api = pymol.lock_api
AttributeError: 'pymol' module has no attribute 'lock_api'

------------------------------

Further details of my setup:

P2/400 with Matrox-graphics-board running SuSE Linux 7.3
(kernel 2.4.10-4GB, glibc 2.2.4, XFree86 4.1.0/mga/glx, KDE 2.2.1, 
Python 2.1.1)

Here is the startup-message of python (the package included with
SuSE-Linux):

saric@m99106:/home/saric> python
Python 2.1.1 (#1, Sep 24 2001, 05:28:47)
[GCC 2.95.3 20010315 (SuSE)] on linux2
Type "copyright", "credits" or "license" for more information.
 >>>

importin of Pmw and Numeric works so far (I haven't tested it further 
though), but pymol won't start.

3D-acceleration works with a lot of other programs, and I use python as 
a scripting language now and then, so it should work in principle.

Can anybody point me to a possible sollution for this problem?

Thanks in advance!

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] Re: Selecting objects to move

[Andrey K. <ak...@kd...>]

Glen,

"GLP" == Glen L Prosise wrote:

 GLP> Is 0.73 out?  I only see 0.68 on your download site.

I guess it's in CVS.  Right?

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] Selecting objects to move

[Glen L. P. <gpr...@ea...>]

Warren,
Is 0.73 out?  I only see 0.68 on your download site.

Thanks,

Glen


>
>    It is complete now in version (0.73) but still isn't well documented.
> If you provide some more details about how you're planning on doing
> this, I could probably post a couple examples for you...
>
> Warren
>
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
> Informatics Manager
> Sunesis Pharmaceuticals, Inc.
> 341 Oyster Point Blvd.
> S. San Francisco, CA 94080
> (650)-266-3606 fax: (650)-266-3501
>
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] Selecting objects to move

[DeLano, W. <wa...@su...>]

> From: Leslie Hall [mailto:HA...@ut...]

> I have just started using PyMol and had a question about=20
> moving selected
> objects in an animation.
> Here is basically what I want to do.
>=20
> 1.    Load two separate pdb files.
> 2.    Be able to move the two molecules independently of each other.
> 3.    Show a conformational change in one of the molecules.
> 4.    Move the two molecules independently and show them docking with
> each other.

Leslie,

   Are you trying to perform these changes manually using the mouse, or
automatically using the Python API?  The manual approach is documented
in the manual, but the Python API approach was neither documented nor
complete in 0.68. =20

   It is complete now in version (0.73) but still isn't well documented.
If you provide some more details about how you're planning on doing
this, I could probably post a couple examples for you...
 =20
Warren

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

Re: [PyMOL] Selecting objects to move

[Ricardo A. <apa...@if...>]

I'm new too but I think on-line manual can help you.

http://pymol.sourceforge.net/html/toc.html

Good luck,

Ricardo







Leslie Hall wrote:
> 
> Hello,
> 
> I have just started using PyMol and had a question about moving selected
> objects in an animation.
> Here is basically what I want to do.
> 
> 1.    Load two separate pdb files.
> 2.    Be able to move the two molecules independently of each other.
> 3.    Show a conformational change in one of the molecules.
> 4.    Move the two molecules independently and show them docking with
> each other.
> 
> Thanks,
> 
> Les
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] Selecting objects to move

[Leslie H. <HA...@ut...>]

Hello,

I have just started using PyMol and had a question about moving selected
objects in an animation.
Here is basically what I want to do.

1.    Load two separate pdb files.
2.    Be able to move the two molecules independently of each other.
3.    Show a conformational change in one of the molecules.
4.    Move the two molecules independently and show them docking with
each other.

Thanks,

Les

[PyMOL] Install problem

[thal <th...@ka...>]

Hi All,

I have Python 2.1 installed on a Win 95 box, and have completed
installation
of pymol-0_68-bin-win32-py21, but when I try to run it I get this error
message:

Error Starting Program
The PYMOL.EXE file is linked to missing export
GLU32.DLL:glu:gluTessProperty

Does anyone have any ideas?