pymol-users Mailing List for PyMOL Molecular Graphics System

Could anyone tell me how to replace amino acid residues in Pymol. 
Specifically, I want to replace Proline 30 and Isoleucine 32 with 
cysteines in horse cytochrome c (PDB: 2FRC).  Can I do energy 
minimization? I am using MAC OSX version.

Also, is there any way to position a ligand such as Ca ion or Mg ion?

Thanks

Xiang

Sorry Ulrich,
 
            The file got left off verson 0.88 - will be in 0.90, which
will be released this week.
 
Cheers,
Warren
 
 
--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Ulrich
Baumann
Sent: Sunday, June 29, 2003 6:39 AM
To: pym...@li...
Subject: [PyMOL] Missing cmyk.png
 
Dear Warren and other pymolers,


I am using Pymol 0.89 under Windows XP, Python 2.1.  When I try to =
change the color space using the DISPLAY menu COLORSPACE  the following
=
error message appears:


ColorTableLoad-Error: unable to load 'c:\program =
files\pymol-0.89/data/pymol/cmyk.png'=20


The file cmyk.png does not exist, can I download it from some other =
location?


Cheers,

Ulrich

Dear Warren and other pymolers,


I am using Pymol 0.89 under Windows XP, Python 2.1.  When I try to =3D
change the color space using the DISPLAY menu COLORSPACE  the following =
=3D
error message appears:


ColorTableLoad-Error: unable to load 'c:\program =3D
files\pymol-0.89/data/pymol/cmyk.png'=3D20


The file cmyk.png does not exist, can I download it from some other =3D
location?


Cheers,

Ulrich

Hello..

I have my electrostatic potential in avs format, and I wonder if anyone
knows how to convert it into phi format in order to read it into pymol
??

Best wishes,

Stefan B=E4ckstr=F6m
UCMP
Ume=E5 University
Sweden

I am making C-alpha ribbon traces with two different sets of 
coordinates. Each time, when I type "ray" to render, the resulting 
image has the C-terminal C-alpha clipped off. The missing carbon is 
visible in the non-ray traced image, however. Please send suggestions 
to fix this asap.


***************************
Casey M. Finnerty, Ph. D.
Dept. of Microbiology
University of Guelph
Guelph, ON, Canada
N1G 2W1

Tsjerk,

	Not currently.  The closest you can achieve is to write out the
PDB file, delete the object, and then read it back in.

- Warren

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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Tsjerk Wassenaar
> Sent: Friday, June 27, 2003 1:48 AM
> To: pym...@li...
> Subject: [PyMOL] Bonds
> 
> 
> Hi all!
> 
> I've written a script to position all atoms into a simulation box, but
> the connectivity stays, thus generating a beautiful image of bonds all
> across the box. Though not too clear. Is there a way to update the
> connectivity directly (other than saving the coordinates and
reloading)?
> 
> 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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Hi all!

I've written a script to position all atoms into a simulation box, but 
the connectivity stays, thus generating a beautiful image of bonds all 
across the box. Though not too clear. Is there a way to update the 
connectivity directly (other than saving the coordinates and reloading)?

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!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> Has anyone been succesful in depicting a membrane surface in pymol?  The
> archives showed a similar question from John Maynes but no answer.
> I would like to render my protein above a membrane surface as cover art for a
> soon-to-be published paper.

I'm not entirely sure I understand the question, but what about this:

http://bioinfo.mbb.yale.edu/people/nat/bilayer.png

There are obviously lots of visible pockets (this is with a solvent
radius of 1.4 - I don't know what the default is), but this seems normal.
If I crank the solvent area up to 2.5, I get this:

http://bioinfo.mbb.yale.edu/people/nat/bilayer2.png

(These are just OpenGL rendered, of course.)

The PDB file I used for this is
http://bioinfo.mbb.yale.edu/people/nat/bilayer.pdb
and I got it from here:
http://moose.bio.ucalgary.ca/Downloads

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

David,

	Try turning off "roving_origin"

set roving_origin,0

Also, I think the zooming only happens in orthoscopic mode -- I may be
able to get rid of that side-effect.


Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of David P. Chimento
> Sent: Tuesday, June 24, 2003 11:25 AM
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #346 - 14 msgs
> 
> Hi
> 
> Has anyone notice this change in PYMOL 0.89?
> 
> When I use the mouse to change the clipping level, the zoom also
changes.
> This did not happen until  I started using the newest version of
Pymol.
> 
> Also it only seems to happen on Window 2000, but not Windows XP.
> 
> -Thanks
> 
>  David Chimento 	University of Virginia
>  dp...@vi...
>  W (804) 243-2730 or 924-9599
>  H (804) 984-0877
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: INetU
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I've created .phi files using Grasp and DelPhi.  When
I use the Grasp .phi files in PyMOL, everything works
great, but when I use the DelPhi .phi files, things go
wrong.  The range goes to insane numbers and the
surface coloring doesnt work.  Grasp would be fine to
use, but Grasp is only on the SGI computer which is
being disposed of, so I must resort to the
DelPhi/PyMOL combination.  Anyone have any
ideas/suggestions/similar problems?

  Thanks,
  Julius

__________________________________
Do you Yahoo!?
The New Yahoo! Search - Faster. Easier. Bingo.
http://search.yahoo.com

Pymolians -


Has anyone been succesful in depicting a membrane surface in pymol?  The 
archives showed a similar question from John Maynes but no answer.

I would like to render my protein above a membrane surface as cover art for a 
soon-to-be published paper.

Anyone willing to share their work would of course receive full credit for their 
contribution.

Cheers,

Byron


-- 
Byron DeLaBarre
Stanford University / HHMI
Dept. of Molecular and Cellular Physiology
P250 MSLS Building//(L)650 736 1714 (C)650 468 5677

That's likely the problem.

If you need to reduce RAM consumption during raytracing (at the cost of
performance), try reducing hash_max to 80 or 60.

set hash_max,60

Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of an...@bi...
> Sent: Wednesday, June 25, 2003 12:28 PM
> To: Nat Echols
> Cc: pymol
> Subject: Re: [PyMOL] pymol crashes with large pdb files
> 
> Limited physical memory might indeed be the problem.
> When I ray-trace under WinXP, memory usage increases sharply (to about
> 500MB) and after a second or so, pymol crashes.
> When I ray-trace under linux, almost all physical memory (1GB) is
being
> used. Barely 40MB available.
> 
> We should be getting new computers next week. We'll see if 2GB will do
the
> trick for Windows.
> 
> 
> Andreas
> 
> 
> >> Now there is a twist to the story. We also run linux (redhat with
> 2.4.18
> >> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII.
Working
> >> speed is much slower but no crashes when ray-tracing from the exact
> same
> >> pml script.
> >> Can it be that linux makes better use of its physical memory or
that
> the
> >> 2GB of swap make the difference?
> >
> > When you ray-trace an image, PyMOL will tell you exactly how much
memory
> > it's using.  My suspicion is that this is painfully close to the
> physical
> > memory limit.  From what I understand, swap space does not give you
more
> > memory but Linux will transfer idle programs to swap, freeing up
more
> > RAM for PyMOL.  I have no idea how Windows works (other than
"badly").
> >
> > 'top' in Linux or the Task Manager in WinXP should tell you how much
> > physical memory is being used at any time.
> >
> >
------------------------------------------------------------------------
> ----
> > Nathaniel Echols
> > Programmer
> > na...@bi...
Gerstein
> > Lab
> > 203-589-6765                                                 Yale
> > University
> >
------------------------------------------------------------------------
> ----
> 
> 
> 
> -------------------------------------------------------
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Two suggestions:

If you know that residues will always contain one and only one of a
given atom type, then you can just use "count_atoms"

For example:

number=cmd.count_atoms("name ca")

Alternatively, you can have PyMOL create a dictionary of all residues:

import pymol
pymol.stored.dict = {}
iterate (all),stored.dict[(segi,chain,resn,resi)]=1
number= len(pymol.stored.dict)

Your cmd.get_model() approach is fine too.  Note that you don't need to
define a selection before using it...

number= len(cmd.get_model("name ca").atom)


Cheers,
Warren

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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Cameron Mura
> Sent: Wednesday, June 25, 2003 3:39 PM
> To: PyM...@li...
> Subject: [PyMOL] extracting number of residues
> 
> Hello,
> I'm wondering what's the easiest way to extract the number of residues
> from a PyMOL molecular object?? I need to be able to do this in an
> automated way for a python script I'm writing. I guess a roundabout
way
> would be to define a selection (say "X_ca") from an object ("X"), and
> then use something like this to extract the number of atoms in the
X_ca
> object:
> 
> 	calphas = cmd.get_model("X_ca");
> 	num_residues = length(calphas.atom);
> 
> But, this seems unneccesary? I thought I could load in the chempy
> "models" module and then use its "get_residues()" function, but the
> command fails as follows:
> 
> ###
> models.get_residues("all")
> PyMOL>models.get_residues("all")
> Traceback (most recent call last):
>    File "modules/pymol/parser.py", line 251, in parse
>      exec(com2[nest]+"\n",pymol_names,pymol_names)
>    File "<string>", line 1, in ?
> AttributeError: 'module' object has no attribute 'get_residues'
> ###
> 
> So, I'm wondering what I'm missing...is there an easy way to do this?
> 
> Thanks anyone,
> 	Cameron
> 
> 
> 
> 
> -------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hello,
I'm wondering what's the easiest way to extract the number of residues 
from a PyMOL molecular object?? I need to be able to do this in an 
automated way for a python script I'm writing. I guess a roundabout way 
would be to define a selection (say "X_ca") from an object ("X"), and 
then use something like this to extract the number of atoms in the X_ca 
object:

	calphas = cmd.get_model("X_ca");
	num_residues = length(calphas.atom);

But, this seems unneccesary? I thought I could load in the chempy 
"models" module and then use its "get_residues()" function, but the 
command fails as follows:

###
models.get_residues("all")
PyMOL>models.get_residues("all")
Traceback (most recent call last):
   File "modules/pymol/parser.py", line 251, in parse
     exec(com2[nest]+"\n",pymol_names,pymol_names)
   File "<string>", line 1, in ?
AttributeError: 'module' object has no attribute 'get_residues'
###

So, I'm wondering what I'm missing...is there an easy way to do this?

Thanks anyone,
	Cameron

Limited physical memory might indeed be the problem.
When I ray-trace under WinXP, memory usage increases sharply (to about
500MB) and after a second or so, pymol crashes.
When I ray-trace under linux, almost all physical memory (1GB) is being
used. Barely 40MB available.

We should be getting new computers next week. We'll see if 2GB will do the
trick for Windows.


Andreas


>> Now there is a twist to the story. We also run linux (redhat with 2.4.18
>> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working
>> speed is much slower but no crashes when ray-tracing from the exact same
>> pml script.
>> Can it be that linux makes better use of its physical memory or that the
>> 2GB of swap make the difference?
>
> When you ray-trace an image, PyMOL will tell you exactly how much memory
> it's using.  My suspicion is that this is painfully close to the physical
> memory limit.  From what I understand, swap space does not give you more
> memory but Linux will transfer idle programs to swap, freeing up more
> RAM for PyMOL.  I have no idea how Windows works (other than "badly").
>
> 'top' in Linux or the Task Manager in WinXP should tell you how much
> physical memory is being used at any time.
>
> ----------------------------------------------------------------------------
> Nathaniel Echols
> Programmer
> na...@bi...                                        Gerstein
> Lab
> 203-589-6765                                                 Yale
> University
> ----------------------------------------------------------------------------

> Now there is a twist to the story. We also run linux (redhat with 2.4.18
> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working
> speed is much slower but no crashes when ray-tracing from the exact same
> pml script.
> Can it be that linux makes better use of its physical memory or that the
> 2GB of swap make the difference?

When you ray-trace an image, PyMOL will tell you exactly how much memory
it's using.  My suspicion is that this is painfully close to the physical
memory limit.  From what I understand, swap space does not give you more
memory but Linux will transfer idle programs to swap, freeing up more
RAM for PyMOL.  I have no idea how Windows works (other than "badly").

'top' in Linux or the Task Manager in WinXP should tell you how much
physical memory is being used at any time.

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

Sorry I didn't mention the operating system. It's WinXPpro. The
computers are a Xeon 2.8GHz (1GB RAM, Nvidia Quadro4 900XGL) and a P4
1.4GHz (768MB RAM, Nvidia GeForce2 GTS). Both run pymol 0.89.

Now there is a twist to the story. We also run linux (redhat with 2.4.18
kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working
speed is much slower but no crashes when ray-tracing from the exact same
pml script.

The linux computer runs pymol 0.88. When I was using pymol 0.88 on
either of the WinBoxes they were crashing just like now with pymol 0.89.

Can it be that linux makes better use of its physical memory or that the
2GB of swap make the difference?

Andreas


On Wed, 2003-06-25 at 09:40, Nat Echols wrote:
> > Is there a limitation to the number of atoms or subunits pymol can handle?
> > I reset max_triangles from 10^6 to 10^7. Didn't change a thing.
> 
> Exactly how much memory does your computer have?  And what OS are you
> running?  I've definitely crashed PyMOL before on a Linux system when I
> tried to do things with huge structures like bacterial chaperonin.  It's
> not that hard to run out of physical memory, or even to hit the
> addressible memory limit.
> 
> ----------------------------------------------------------------------------
> Nathaniel Echols                                                  Programmer
> na...@bi...                                        Gerstein Lab
> 203-589-6765                                                 Yale University
> ----------------------------------------------------------------------------

-- 
                    Andreas Förster
Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
Salt Lake City, UT 84132, phone: 001.801.585.3919
home: 1736 Kensington, SLC, UT 84108, 001.801.463.3607
        http://www.biochem.utah.edu/~andreas

Whoops - I meant to delete that message, must have spaced out and hit
the accept button.  Sorry for (accidentally) propagating spam.  

DeLano Scientific does not endorse "Chief Mgbe" or his ilk...these are
all scams.  Any email with the words "Nigeria" "bank" and "million"
should be moved straight to the trash.

Cheers,
Warren

> Is there a limitation to the number of atoms or subunits pymol can handle?
> I reset max_triangles from 10^6 to 10^7. Didn't change a thing.

Exactly how much memory does your computer have?  And what OS are you
running?  I've definitely crashed PyMOL before on a Linux system when I
tried to do things with huge structures like bacterial chaperonin.  It's
not that hard to run out of physical memory, or even to hit the
addressible memory limit.

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

Hi all,

I'm running pymol 0.89 on quite capable machines. When I ray-trace large
pdb files (proteasome; 1pma, 1ryp, 1fnt straight off the pdb), pymol
crashes. Doesn't matter if surface or cartoon representation. When I
decrease the number of subunits from 28 (or 42 in case of 1fnt) to less
than 20 (cut-open or end-on view), ray-tracing works fine.

Is there a limitation to the number of atoms or subunits pymol can handle?
I reset max_triangles from 10^6 to 10^7. Didn't change a thing.

Any suggestions? Just work on Ubiquitin instead??


Thanks

Andreas

From: Chief Mgbe momodu 
Director of Finance and Accounts Department 
Independent National Electoral Commission (INEC) 


Attention: The Managing Director 

Subject: Partnership Negotiations 

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Pls Reply to nc...@ju... 


-- 
Ziskejte kvalitu, kterou si zasluhujete. Za minimalni mesicni
poplatek vam nabizime Antivir, Antispam nebo dalsi kapacitu pro
vas Mailbox. Vice na: http://sluzby.volny.cz/product/postpaid/

Hi

Has anyone notice this change in PYMOL 0.89?

When I use the mouse to change the clipping level, the zoom also changes.
This did not happen until  I started using the newest version of Pymol.

Also it only seems to happen on Window 2000, but not Windows XP.

-Thanks

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

Tara,

	By default, PyMOL loads models as states rather than as separate
molecular objects.  That can make it hard for you to refer to any
particular model.  Using a discrete objects helps a bit with
mouse-driven interaction, but the selection language doesn't do too well
with molecular states.

	Some development will be required to address this.  What would
people like to see?

Possibilities:

	A) A setting which loads MODEL records as independent objects.
	B) "state" keyword added to selection language (exists, but
buggy)
	C) ???

Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Tara Sprules
> Sent: Friday, June 20, 2003 10:35 AM
> To: pym...@li...
> Subject: [PyMOL] show model
> 
> Hi,
> 
> How does one display and access the multiple models found in a pdb
file
> for a nmr structure from the command line? I have loaded in all the
> models, but cannot figure out how to specify them (ie in the format
> /model/segment...).
> 
> Thanks,
> 
> Tara
> 
> Tara Sprules
> Post-Doctoral Fellow
> Department of Chemistry
> University of Alberta
> Edmonton, AB
> Canada
> 
> 
> 
> 
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Scott,

	Currently they are hard-coded in the C, but can be changed after
loading the molecule using:

alter selection, vdw=number

for example:

alter elem c, vdw=1.8
alter elem n, vdw=1.4
alter elem h, vdw=1.1


etc.

Cheers,
Warren


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

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Scott Classen
> Sent: Friday, June 20, 2003 12:56 PM
> To: pym...@li...
> Subject: [PyMOL] default atomic radii
> 
> Hi Warren,
> What are the default atomic radii in PyMol? How are they
> calculated/determined?
> Thanks,
> Scott Classen
> 
> 
> ==============================================
>    Scott Classen, Ph.D.
>    cl...@uc...
>    University of California, Berkeley
>    Department of Molecular & Cell Biology
>    237 Hildebrand Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ==============================================
> 
> 
> 
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On Tuesday, June 24, 2003, at 01:32 PM, RichGB wrote:

> I'd like to experiment with the rTools 0.5.2 package with PyMol0.88  
> (MacOSX 10.2.6 using the
> PyMol binary from the sourceforge site). But the installation 'hints'  
> don't appear to describe a
> functional method of getting rTools to work with PyMol on this  
> platform. Does anyone have this
> working so they could provide some directions?

Hello Richard,

Just after 0.88 was released I installed the rTools package under OSX  
(10.2.6), and it seems to work just fine.
Here is a log of what I did (you'll obviously need to modify the file  
paths depending on where you unpack the rTools distribution etc.):

OSX> cd /sw/lib/pymol/modules/pmg_tk/startup
OSX> sudo cp  
/Users/luca/applications/PyMOL/Extensions/rtools/rTools0.5.2/rubor.py .
OSX> sudo mkdir rubor
OSX> cd rubor
OSX> sudo mkdir scripts
OSX> sudo cp  
/Users/luca/applications/PyMOL/Extensions/rtools/rTools0.5.2/rubor/* .
OSX> sudo cp  
/Users/luca/applications/PyMOL/Extensions/rtools/rTools0.5.2/rubor/ 
scripts/* scripts/
OSX> sudo mkdir /pdb
OSX> sudo chmod 775 /pdb

To test, start xpymol (i.e. the Fink version of the program), and issue  
this command:

PyMOL>pdb 1cse

the above should fetch the PDB file for entry 1CSE and put it in  
/pdb/cs/

OSX> cd /sw/lib/pymol/modules/pmg_tk/startup/rubor/scripts
OSX> sudo cp /pdb/cs/pdb1cse.ent ./1cse.ent
OSX> sudo chmod 644 1cse.ent

and finally edit the single line of file 1cse.pml as follows:

OSX> sudo vi 1cse.pml

	load /sw/lib/pymol/modules/pmg_tk/startup/rubor/scripts/1cse.ent

now you can automatically load entry 1CSE from ScriptBox within rTools.

Hope this helps!

Good luck, Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Brookdale 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
--------------------------------------------------------