pymol-users Mailing List for PyMOL Molecular Graphics System

Dear PyMOLers

I have a pdb containing many models how would I load just one of the models 
into pymol?
Or is this even posible without making a seperate pdb file from the model.

Thanks
Mike




_________________________________________________________________
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Dear Mike,

> Where would I store the reference to the object (containing my data) so
> that I can retrieve it on the second call?  Can I link it to the CGO ob=
ject
> or something?

You can reference the object in Your Python script just like:

my_data =3D []

(but i'd prefer using a class for that). What is important is that a=20
cmd.extend(x,y) call should be called somewhere in the script, otherwise=20
Python thinks the data will be no longer used and calls the Garbage=20
Collection.

Kristian


> ----- Original Message -----
> From: "Kristian Rother" <kri...@ch...>
> To: "Mike Liang" <ml...@St...>
> Cc: <pym...@li...>
> Sent: Thursday, January 30, 2003 3:53 AM
> Subject: Re: [PyMOL] Associating data structure with CGO object
>
> > Dear Mike,
> >
> > You can at least do the following:
> >
> > *** first call of command ***
> > - parse the file
> > - store the data in an object (dictionary, list, etc.) - you can prob=
ably
> > store the Strings that make up the CGO object.
> > - refine the data using the cutoff
> > - create CGO object from refined data
> >
> > *** second call of command ***
> > - delete CGO object
> > - refine the data using the cutoff
> > - create CGO object from refined data
> >
> > Message: You can create objects in Python scripts that are persistent=
 as
> long
> > as PyMOL is running.
> > This should work a lot faster than parsing the file several times.
> >
> > Kristian
> >

Dear Kristian,

Where would I store the reference to the object (containing my data) so that
I can retrieve it on the second call?  Can I link it to the CGO object or
something?

Thanks!
Mike


----- Original Message -----
From: "Kristian Rother" <kri...@ch...>
To: "Mike Liang" <ml...@St...>
Cc: <pym...@li...>
Sent: Thursday, January 30, 2003 3:53 AM
Subject: Re: [PyMOL] Associating data structure with CGO object


>
> Dear Mike,
>
> You can at least do the following:
>
> *** first call of command ***
> - parse the file
> - store the data in an object (dictionary, list, etc.) - you can probably
> store the Strings that make up the CGO object.
> - refine the data using the cutoff
> - create CGO object from refined data
>
> *** second call of command ***
> - delete CGO object
> - refine the data using the cutoff
> - create CGO object from refined data
>
> Message: You can create objects in Python scripts that are persistent as
long
> as PyMOL is running.
> This should work a lot faster than parsing the file several times.
>
> Kristian
>
>
> > What I want to do is parse a file that has a bunch of coordinates and
draw
> > the spheres in PyMOL.  But then I want to be able to adjust the cutoff
for
> > which points are to be drawn.
> >
> > What I was doing now was first to run the script to bind the function to
a
> > command.  Then the function will load the file and draw the spheres at a
> > particular cutoff.  If I rerun the function, it will delete the old CGO
> > object, parse the file again, and recreate a new CGO.  But if the file
is
> > really big, this becomes cumbersome.
> >
> > Or maybe what I need to do is create a "pymol object" and then have it
> > create the CGO object everytime it needs to be drawn.  Then have my
> > function be able to update the cutoff parameter for the object.
> >
> > Thanks!
> > Mike
> >
>
>
>
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld
http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

On Wed, Jan 29, 2003 at 08:11:27PM +0100, Eugen Leitl wrote:
> On Wed, 29 Jan 2003, Naveen Michaud-Agrawal wrote:
> 
> > Hi, this is more a general question related to using pymol on linux, but
> > does anyone have any 3D graphics card recommendations for linux; ie good
> > driver support, supports more of OpenGL than is just required by games.
> 
> Check out the VMD users list archives.

As well as the o-info mailing list archives:

http://o-info.imsb.au.dk/pipermail/o-info/

I've gotten stereo to work with PyMOL on Mandrake 8.1 boxes, running the
proprietary XIG X server for an ATI Radeon 8500 (easier to get than the
FireGL from what I can tell).

--Joe

Dear Mike,

You can at least do the following:

*** first call of command ***
- parse the file
- store the data in an object (dictionary, list, etc.) - you can probably=
=20
store the Strings that make up the CGO object.
- refine the data using the cutoff
- create CGO object from refined data

*** second call of command ***
- delete CGO object
- refine the data using the cutoff
- create CGO object from refined data

Message: You can create objects in Python scripts that are persistent as =
long=20
as PyMOL is running.
This should work a lot faster than parsing the file several times.

Kristian


> What I want to do is parse a file that has a bunch of coordinates and d=
raw
> the spheres in PyMOL.  But then I want to be able to adjust the cutoff =
for
> which points are to be drawn.
>
> What I was doing now was first to run the script to bind the function t=
o a
> command.  Then the function will load the file and draw the spheres at =
a
> particular cutoff.  If I rerun the function, it will delete the old CGO
> object, parse the file again, and recreate a new CGO.  But if the file =
is
> really big, this becomes cumbersome.
>
> Or maybe what I need to do is create a "pymol object" and then have it
> create the CGO object everytime it needs to be drawn.  Then have my
> function be able to update the cutoff parameter for the object.
>
> Thanks!
> Mike
>

Hi!  Is there a way to associate data with an object and access it from a
script?

What I want to do is parse a file that has a bunch of coordinates and draw
the spheres in PyMOL.  But then I want to be able to adjust the cutoff for
which points are to be drawn.

What I was doing now was first to run the script to bind the function to a
command.  Then the function will load the file and draw the spheres at a
particular cutoff.  If I rerun the function, it will delete the old CGO
object, parse the file again, and recreate a new CGO.  But if the file is
really big, this becomes cumbersome.

Or maybe what I need to do is create a "pymol object" and then have it
create the CGO object everytime it needs to be drawn.  Then have my function
be able to update the cutoff parameter for the object.

Thanks!
Mike

Hi!  I would like to create a GUI that interacts with PyMOL.  What I'm
thinking of doing is running PyMOL to visualize a molecule and then create a
GUI that interacts with the visualization, such as draw new objects, add
labels, etc.

How would I go about extending PyMOL with new GUIs (using wxPython)?

Take as a toy example, I want to create a GUI that is a little frame with a
slider in it.  As the slider is dragged right/left, more or less random
spheres will be drawn into the visualization area, or maybe it'll adjust
their radius.

Ultimately what I'm hoping to do is to start up a GUI within Python that
will decorate the molecule with addition objects.  The GUI will allow the
objects to customized (like setting their color, size, etc.).

Thanks!
Mike

I would like to show ribbons and cartoons based upon Calpha coordinates.

Is there a way this can be done short of generating the other mainchain atoms?


Anthony




----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-7817   Fax. 61-2-9351-4726
----------------------------------------------------------------------

Hi--

This sounds a bit offtopic, but it's related to a project that would
probably be built off of PyMOL.  Does anyone have any experience with
protein dynamics software that runs on clusters and performs energy
minimization?  I've seen all sorts of pure MD packages that run on
clusters (GROMACS, NAMD, etc.) but all I want to do is adiabatic mapping.
None of these programs seem to be designed for this.  I've been using CNS
for everything and as far as I know this does not come in an MPI-based
flavor.  I've seen reference to an MPI version of CHARMm, but I'm not sure
how to get ahold of it (we have a Harvard CHARMm license, at least).

thanks,
Nat

----------------------------------------------------------------------------
Nathaniel Echols                                                  Programmer
na...@bi...                                        Gerstein Lab
203-589-6765                                                 Yale University
----------------------------------------------------------------------------

Naveen,

We've had great results with the FireGL series, and the OpenGL =
performance of the FireGL X1 is excellent =
(http://www.spec.org/gpc/opc.data/vp7/summary.html). =20

However, the trick with these cards is to allow ATI's binary driver =
compatibility to dictate your choice of Linux distribution and version.  =
This is fine for new dedicated 3D workstations (read SGI replacements), =
but not so good for existing linux setups.

Stereo support is trouble-free.

Warren

PS. These card's aren't cheap -- they're not designed for gamers.

--
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: Naveen Michaud-Agrawal [mailto:nmi...@jh...]
> Sent: Wednesday, January 29, 2003 11:06 AM
> To: pym...@li...
> Subject: [PyMOL] 3D on linux
>=20
>=20
>=20
> Hi, this is more a general question related to using pymol on=20
> linux, but
> does anyone have any 3D graphics card recommendations for=20
> linux; ie good
> driver support, supports more of OpenGL than is just required=20
> by games.
> I've looked around a bit on the web, but I figured since my=20
> primary use
> would be for molecular visualization I would ask here to see=20
> if anyone has
> had experience with this issue. Thanks.
>=20
> Naveen
>=20
> ---------------------------------------------------------------------
> Naveen Michaud-Agrawal
> Program in Molecular Biophysics
> Johns Hopkins University
> (410) 614 4435
>=20
> -- Tomorrow will be cancelled due to lack of interest
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld =3D Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Naveen,
I recommend graphics cards with the nvidia quadro4 xgl chips.
We several PNY Quadro4 700 XGL and they work great.
The caveat is that if you have it configured for quad buffered
Stereo then mono display (the usual) will be low performance.
zac

Naveen Michaud-Agrawal wrote:
> Hi, this is more a general question related to using pymol on linux, but
> does anyone have any 3D graphics card recommendations for linux; ie good
> driver support, supports more of OpenGL than is just required by games.
> I've looked around a bit on the web, but I figured since my primary use
> would be for molecular visualization I would ask here to see if anyone has
> had experience with this issue. Thanks.

On Wed, 29 Jan 2003, Naveen Michaud-Agrawal wrote:

> Hi, this is more a general question related to using pymol on linux, but
> does anyone have any 3D graphics card recommendations for linux; ie good
> driver support, supports more of OpenGL than is just required by games.

Check out the VMD users list archives.

> I've looked around a bit on the web, but I figured since my primary use
> would be for molecular visualization I would ask here to see if anyone has
> had experience with this issue. Thanks.

Hi, this is more a general question related to using pymol on linux, but
does anyone have any 3D graphics card recommendations for linux; ie good
driver support, supports more of OpenGL than is just required by games.
I've looked around a bit on the web, but I figured since my primary use
would be for molecular visualization I would ask here to see if anyone has
had experience with this issue. Thanks.

Naveen

---------------------------------------------------------------------
Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

-- Tomorrow will be cancelled due to lack of interest

Hi all,

I recently installed the very nice new rTools 0.5.2 with the latest 
release of Pymol (0.8.6) on a PC running SuSE-Linux 8.1.

After setup of all external programs I tried to run HBExplore, but got 
an error from the pulldown-menu. When invoking hbond from the 
command-line, everything works fine.

Any suggestions?

I don't have the exact output of the error-message here unfortunately, 
but I could provide it if needed.

-- 
Bye,  Marc Saric

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

Anthony,

I agree that we need one, but it doesn't currently exist.  The same can =
be said for surface calculations, especially when you've loaded a 500 =
frame MD trajectory and accidentally "show surface" (doh!).

My advice: save sessions often and make liberal use of PyMOL's logging =
capability.  When you goof up, kill the process and then reopen the =
session or resume the log file after editing out the offending =
command(s).

Cheers,
Warren

(Hmm...A save session button might be nice...)
--
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: Anthony Duff [mailto:A....@st...]
> Sent: Tuesday, January 28, 2003 4:29 PM
> To: pym...@li...
> Subject: [PyMOL] stop an accidental or problematic ray trace
>=20
>=20
>=20
>=20
>=20
> It would be nice if there were a button to stop a ray trace,=20
> for when it is=20
> started accidentally, or if something is wrong and it is=20
> taking too long.
>=20
>=20
> Is there one?
>=20
>=20
>=20
>=20
> ----------------------------------------------------------------------
> Anthony Duff
> Postdoctoral Fellow
> School of Molecular and Microbial Biosciences
> Biochemistry Building, G08
> University of Sydney, NSW 2006 Australia
> Phone. 61-2-9351-7817   Fax. 61-2-9351-4726
> ----------------------------------------------------------------------
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld =3D Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

It would be nice if there were a button to stop a ray trace, for when it is 
started accidentally, or if something is wrong and it is taking too long.


Is there one?




----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-7817   Fax. 61-2-9351-4726
----------------------------------------------------------------------

Thanks for the reply ...

Do you have a list of which programs pymol might accept input from?

Thanks again-
Doug

DeLano, Warren wrote:

>Doug,
>
>	(1) I've got a hard deadline to have this capability in the program less than 1 month from now...not the pot. calc., just the import, rendition, and coloring.
>
>	(2) no clue
>
>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: Douglas Kojetin [mailto:djk...@un...]
>>Sent: Tuesday, January 28, 2003 3:14 PM
>>To: pym...@li...
>>Subject: [PyMOL] non-related question & related: electrostatics
>>
>>
>>Hi All-
>>
>>I'll ask my related question first: does anyone know if/when 
>>electrostatic calculations might be incorporated into pymol?  
>>Or if you 
>>can import calcs from another (hopefully free) program?
>>
>>Unrelated question: does anyone know of a secondary structure 
>>prediction 
>>program that outputs "pretty" graphics to related 'helix' and 'sheet' 
>>structures?  similar to how ESPript outputs ... but i do not have an 
>>input PDB file (yet) to use that program
>>
>>Thanks,
>>Doug
>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.NET email is sponsored by:
>>SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
>>http://www.vasoftware.com
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>    
>>
>
>
>  
>

Bartholomeus,

You have run into limitations in PyMOL's handling of single objects.

The answer to both these questions is to split your molecule into =
multiple object and color/show independently.  Use the "create" command =
to make copies, and then use alter to reassign secondary structure codes =
where needed.

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: Bartholomeus Kuettner [mailto:bku...@ep...]
> Sent: Tuesday, January 28, 2003 3:06 PM
> To: pym...@li...
> Subject: [PyMOL] q: discrete colors and adjacent cartoon segments
>=20
>=20
> Dear PyMol users,
>=20
> 1.
> I'm puzzled with a coloring problem while coloring a protein molecule
> accordingly to its secondary structure by using 'discrete=20
> color' option:
> If there are a helix and/or strand adjacent together (e.g.=20
> helix from 1-10
> and sheet from 11-20) the small pseudo-loop region between=20
> (arising from
> atoms between last Calpha of the helix and first Calpha of=20
> the strand) gets
> colored like the latter partner (maybe because of its color=20
> was defined at
> last). What I'd like to do is to color this small pseudo loop=20
> in a different
> color. I've tried to color the atoms between last Calpha and=20
> next Calpha
> (C,N) individually but there was no effect. It seems to me,=20
> that cartoon
> coloring only corresponds to Calpha positions. So, is there a=20
> way around to
> color cartoon regions between secondary structure elements as=20
> described
> before?
>=20
> 2.
> Is there a way to force PyMol to draw a cartoon which shows=20
> two different
> secondary strcuture elements (helix, strand) ending and=20
> beginning at the
> same residue? Maybe one can image a scenario where the N atom makes a
> strand-like conformation while the CO group of the same=20
> residue starts with
> a helix. In another program it is/was possible to assign=20
> helix and strand
> ending and beginning in the same residue but when I try to=20
> perfom with PyMol
> only the last partner is shown correctly while the first partner gets
> overrided in its last residue, e.g. cartoon "strand 1-10" and=20
> "helix 10-20"
> looks the same like "strand 1-9" and "helix 10-20". How 
> could circumvent
> this dilemma?
>=20
> Many thanks in advance!
>=20
> Greetings,
> Bartholomeus
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld =3D Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Doug,

	(1) I've got a hard deadline to have this capability in the program =
less than 1 month from now...not the pot. calc., just the import, =
rendition, and coloring.

	(2) no clue

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: Douglas Kojetin [mailto:djk...@un...]
> Sent: Tuesday, January 28, 2003 3:14 PM
> To: pym...@li...
> Subject: [PyMOL] non-related question & related: electrostatics
>=20
>=20
> Hi All-
>=20
> I'll ask my related question first: does anyone know if/when=20
> electrostatic calculations might be incorporated into pymol? =20
> Or if you=20
> can import calcs from another (hopefully free) program?
>=20
> Unrelated question: does anyone know of a secondary structure=20
> prediction=20
> program that outputs "pretty" graphics to related 'helix' and 'sheet'=20
> structures?  similar to how ESPript outputs ... but i do not have an=20
> input PDB file (yet) to use that program
>=20
> Thanks,
> Doug
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld =3D Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hi All-

I'll ask my related question first: does anyone know if/when 
electrostatic calculations might be incorporated into pymol?  Or if you 
can import calcs from another (hopefully free) program?

Unrelated question: does anyone know of a secondary structure prediction 
program that outputs "pretty" graphics to related 'helix' and 'sheet' 
structures?  similar to how ESPript outputs ... but i do not have an 
input PDB file (yet) to use that program

Thanks,
Doug

Dear PyMol users,

1.
I'm puzzled with a coloring problem while coloring a protein molecule
accordingly to its secondary structure by using 'discrete color' option:
If there are a helix and/or strand adjacent together (e.g. helix from 1-10
and sheet from 11-20) the small pseudo-loop region between (arising from
atoms between last Calpha of the helix and first Calpha of the strand) gets
colored like the latter partner (maybe because of its color was defined at
last). What I'd like to do is to color this small pseudo loop in a different
color. I've tried to color the atoms between last Calpha and next Calpha
(C,N) individually but there was no effect. It seems to me, that cartoon
coloring only corresponds to Calpha positions. So, is there a way around to
color cartoon regions between secondary structure elements as described
before?

2.
Is there a way to force PyMol to draw a cartoon which shows two different
secondary strcuture elements (helix, strand) ending and beginning at the
same residue? Maybe one can image a scenario where the N atom makes a
strand-like conformation while the CO group of the same residue starts with
a helix. In another program it is/was possible to assign helix and strand
ending and beginning in the same residue but when I try to perfom with PyMol
only the last partner is shown correctly while the first partner gets
overrided in its last residue, e.g. cartoon "strand 1-10" and "helix 10-20"
looks the same like "strand 1-9" and "helix 10-20". How one could circumvent
this dilemma?

Many thanks in advance!

Greetings,
Bartholomeus

I found the receipes on your homepage to install PyMol on Macs kind of 
convoluted, so here is what I figured after some working hours:

Installation on Mac-OsX 10.2

1) Download fink from www.apple.com and install
2) add "source /sw/bin/init.csh" to /etc/csh.login to let the system know about 
fink
3) sudo fink configure (give as proxy something like http://www-cache.fh-
giessen.de:3128)
4) get cvs-proxy......info and cvs-proxy....patch from http://
fink.sourceforge.net/faq/usage-fink.php and put them into /sw/fink/dists/local/
main/finkinfo
5) sudo fink install cvs-proxy
6) cd to folder pymol-0.86; sudo fink update-all
7) open X11-Terminal
8) start pymol: /sw/bin/pymol & 

Best
Uwe Hobohm

I've trying to make an external GUI for pymol and I'm new to python. I try to 
import the module cmd as follows:

from pymol import cmd

But I recieve the following error message:

Traceback (most recent call last):
  File "GUI.py", line 7, in ?
    from cmd import _cmd
  File "/home/panderso/software/pymol/modules/pymol/cmd.py", line 48, in ?
    import _cmd
ImportError: No module named _cmd

Any input would be greatly appreciated. Thanks in advance.

Paul

> I was wondering if there is a way to colour by a structure by 
> hydrophobicity.

Hi Carly,

This is a quick hack I wrote some time ago, but it kind of does the 
job... (of course I see much room for improvement!)

# color_h
# -------
# PyMOL command to color protein molecules according to the Eisenberg 
hydrophobicity scale
#
# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
# Amino acid scale: Normalized consensus hydrophobicity scale
# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
# Reference: J. Mol. Biol. 179:125-142 (1984)
#
# Amino acid scale values:
#
# Ala:  0.620
# Arg: -2.530
# Asn: -0.780
# Asp: -0.900
# Cys:  0.290
# Gln: -0.850
# Glu: -0.740
# Gly:  0.480
# His: -0.400
# Ile:  1.380
# Leu:  1.060
# Lys: -1.500
# Met:  0.640
# Phe:  1.190
# Pro:  0.120
# Ser: -0.180
# Thr: -0.050
# Trp:  0.810
# Tyr:  0.260
# Val:  1.080
#
# Usage:
# color_h (selection)
#
def color_h(selection="(all)"):
	s = str(selection)
	cmd.set_color('color_ile',[0.996,0.062,0.062])
	cmd.set_color('color_phe',[0.996,0.109,0.109])
	cmd.set_color('color_val',[0.992,0.156,0.156])
	cmd.set_color('color_leu',[0.992,0.207,0.207])
	cmd.set_color('color_trp',[0.992,0.254,0.254])
	cmd.set_color('color_met',[0.988,0.301,0.301])
	cmd.set_color('color_ala',[0.988,0.348,0.348])
	cmd.set_color('color_gly',[0.984,0.394,0.394])
	cmd.set_color('color_cys',[0.984,0.445,0.445])
	cmd.set_color('color_tyr',[0.984,0.492,0.492])
	cmd.set_color('color_pro',[0.980,0.539,0.539])
	cmd.set_color('color_thr',[0.980,0.586,0.586])
	cmd.set_color('color_ser',[0.980,0.637,0.637])
	cmd.set_color('color_his',[0.977,0.684,0.684])
	cmd.set_color('color_glu',[0.977,0.730,0.730])
	cmd.set_color('color_asn',[0.973,0.777,0.777])
	cmd.set_color('color_gln',[0.973,0.824,0.824])
	cmd.set_color('color_asp',[0.973,0.875,0.875])
	cmd.set_color('color_lys',[0.899,0.922,0.922])
	cmd.set_color('color_arg',[0.899,0.969,0.969])
	cmd.color("color_ile","(resn ile and "+s+")")
	cmd.color("color_phe","(resn phe and "+s+")")
	cmd.color("color_val","(resn val and "+s+")")
	cmd.color("color_leu","(resn leu and "+s+")")
	cmd.color("color_trp","(resn trp and "+s+")")
	cmd.color("color_met","(resn met and "+s+")")
	cmd.color("color_ala","(resn ala and "+s+")")
	cmd.color("color_gly","(resn gly and "+s+")")
	cmd.color("color_cys","(resn cys and "+s+")")
	cmd.color("color_tyr","(resn tyr and "+s+")")
	cmd.color("color_pro","(resn pro and "+s+")")
	cmd.color("color_thr","(resn thr and "+s+")")
	cmd.color("color_ser","(resn ser and "+s+")")
	cmd.color("color_his","(resn his and "+s+")")
	cmd.color("color_glu","(resn glu and "+s+")")
	cmd.color("color_asn","(resn asn and "+s+")")
	cmd.color("color_gln","(resn gln and "+s+")")
	cmd.color("color_asp","(resn asp and "+s+")")
	cmd.color("color_lys","(resn lys and "+s+")")
	cmd.color("color_arg","(resn arg and "+s+")")
cmd.extend('color_h',color_h)

Hope this helps,

Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma... - luc...@ms...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

Carsten,

    You're bumping up against a 63-character limit I currently have for =
any one individual argument in PyMOL's internal parser.  Obviously I =
need to either safeguard that limitation to prevent a crash or eliminate =
it. You can still do this in a single selection, as follows

select pocket =3D (P_338437 and (resi =
16,17,18,19,54,55,57,58,59,60,61,62,67 or resi =
72,73,74,75,82,86,91,93,95,96,97,99,100,103))

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=20
-----Original Message-----
From: Schubert, Carsten [mailto:Car...@3d...]
Sent: Thursday, January 23, 2003 12:41 PM
To: pym...@li...
Subject: [PyMOL] Bug in selections


Hi,=20
there is a problem in pymol 0.86 under W2K using a long list of residues =
in a selection.=20
When I use:=20
select pocket =3D (P_338437 and (resi =
16,17,18,19,54,55,57,58,59,60,61,62,67,72,73,74,75,82,86,91,93,95,96,97,9=
9,100,103))
pymol generates an error and exits.=20
Splitting the selection into 2 parts prevents the crash:=20
select p1 =3D (P_338437 and (resi =
16,17,18,19,54,55,57,58,59,60,61,62,67,72,73,74,75,82,86,91,93))=20
select pocket =3D (p1 or (P_338437 and (resi 95,96,97,99,100,103))=20
Is there a maximum number of elements in a selection statement?=20
BTW the script worked fine in the previous release, 0.82 I guess?=20
Any thoughts?=20


Cheers=20
        Carsten=20