pymol-users Mailing List for PyMOL Molecular Graphics System

Happy New Year ....

Is there a facility for outputting a 3d-molecular object from PyMol in
VRML ? I want to load this into a general animation/rendering package
(Blender) which will read VRML. Alternatively, does anyone know of a
good Linux/Mac Povray->VRML convertor so I could convert the .pov file
optionally generated by PyMol's ray command.

Laurence Pearl


--------------------------------------------------------------------------------
Laurence H. Pearl
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
Phone +44-207-970 6045 : Secretary +44-207-970 6046 : FAX   +44-207-970
6051
--------------------------------------------------------------------------------
"Live Simply and do Serious Things .. "
- Dorothy Crowfoot Hodgkin
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Hi all,

 I have a ThinkPad T40p (WinXP) with an ATI Mobility Fire GL 9000 video
driver. After installing PyMol, I try to run the executable but it crashes
and I get the standard Windows error message asking me to submit an error
report to Microsoft. I never got this error before on any PC I ran PyMOL
on, so I'm utterly confused as to its origin. I don't think it's a GL
issue because I am able to run VMD ok.

 I really, really, need PyMOL for my research and would honestly appreciate
any help any of you could offer. Thank you very much,

Shantanu Sharma

===================================================================
|   shantanu sharma - 056Bc beckman institute - mail code 127-72  |
|   division of chemistry and chemical engineering - caltech      |
|             http://www.its.caltech.edu/~ssharma                 |
|              http://www.its.caltech.edu/~ch213                  |
|                 http://www.wag.caltech.edu                      |
===================================================================

Hi,

I would like to know how to fill in a ribonucleotide base and/or ribose with 
planes. Ribbons has a command called "pdb-nuc-ring" that generates polygons 
that fills the base ring. VMD can fill both the base and sugar rings in 
RNA/DNA. Is there a easy way to do the same in Pymol?

Thanks for helping!

Ailong

Ailong Ke, Ph.D.
305 Hildebrand Hall, Mail stop 3206
University of California, Berkeley
Berkeley, CA, 94720
Tel: (510) 643-0108
Fax: (510) 528-0080

Hi,
Someone sent out a question about this a month or so ago, but I never
saw a reply, so I'll ask it again.
In the Windows v0.93 pyMOL, it seems that I'm stuck with
ribbon_sampling=1 (CA trace, instead of smoothed ribbon). I can change
the setting, but the representation does not change. This behavior is
not evident in the native OSX pyMOL currently under development.

Has anyone else run into this problem? Is it a Windows-distribution
only problem? Are there any solutions?

Jacob

Hi Michele:

You don't have glut on OS X unless you installed it, for example, with 
fink.  Looking at the fink pymol package (0.86) you will
need to have installed these dependencies:

Depends: libpng3-shlibs, numeric, tcltk, pmw (>= 0.8.5-2), python (>= 
2.2.1-8), glut-shlibs (>= 3.7-3)
BuildDepends: libpng3, glut (>= 3.7-3), db3 (>= 3.3.11-23), readline 
(>= 4.3-15), gdbm, gmp (>= 4.1.2-11), expat, tcltk-dev, dlcompat-dev

I have all of those and I still can't get 0.93 to compile.  I am hoping 
the fink package will come out sometime soon.  Meanwhile the native OS 
X pymol is really nice.  It is well worth supporting I think...

Fink seems really behind now in all things python.  All of 2.3 is in 
the "unstable" tree, which seems odd to me given that 2.3 has been 
around for a year and is now part of OS X, albeit in the usual 
lobotomized form.  I've used fink to compile python 2.3, numeric, 
scientific, scipy, etc., and they all seem to work fine.

I'll try to hack on it a bit more, but it might be worth dropping Matt 
Stephenson a line.

Bill Scott


> Date: Sun, 21 Dec 2003 15:39:52 -0500
> To: pym...@li...
> From: Michele Fuortes <mfu...@me...>
> Subject: [PyMOL] Re: PyMOL 0.93 and MacOS X
>
> Hi everybody,
>
> I know I'm an idiot, but I cannot build pymol 0.93 on Mac OS 10.3 to 
> save
> my life.
> After getting and resolving a lot of gl.h and glut.h complaints now I'm
> stuck with:
>
> building 'pymol._cmd' extension
> .................
> -L/usr/X11R6/lib -lGL -lGLU -lglut -lpng -o
> build/lib.darwin-7.2.0-Power_Macintosh-2.3/pymol/_cmd.so
> ld: can't locate file for: -lglut
>
>
> Any kind soul there willing to help me?
>
> Thanks
>
>
> Michele
>
>
> -- 
>
>
>
>
>
> --
> Michele Fuortes, M.D., Ph.D.
> Assistant Professor
> Departments of Surgery and of Cell and Developmental Biology
> Cornell University  - Weill Medical College
> E-mail: mfu...@RE...
>
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>
>
>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)
url:          http://chemistry.ucsc.edu/~wgscott/

Hi everybody,

I know I'm an idiot, but I cannot build pymol 0.93 on Mac OS 10.3 to save
my life.
After getting and resolving a lot of gl.h and glut.h complaints now I'm
stuck with:

building 'pymol._cmd' extension
.................
-L/usr/X11R6/lib -lGL -lGLU -lglut -lpng -o
build/lib.darwin-7.2.0-Power_Macintosh-2.3/pymol/_cmd.so
ld: can't locate file for: -lglut


Any kind soul there willing to help me?

Thanks


Michele


-- 





--
Michele Fuortes, M.D., Ph.D.
Assistant Professor
Departments of Surgery and of Cell and Developmental Biology
Cornell University  - Weill Medical College
E-mail: mfu...@RE...

PyMOL Users,

This is the final reminder that I am now off-line and away from DeLano
Scientific (which will be closed) until January 7th.

Everyone please have a wonderful holiday and a Happy New Year!

Cheers,
Warren

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

Avram,

You use the sphere_scale setting:

i.e.  set sphere_scale, 0.2

Best,
Ken


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]On Behalf Of
sl...@ma...
Sent: Friday, December 19, 2003 12:40 PM
To: pym...@li...
Subject: [PyMOL] Another question


Hi all,

another question.  Does anyone know how to make spheres smaller.  I=20
would like to make the ball and stick looking residues like those in=20
Molscript

thank you

Avram
--=20
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104

L:215-898-3496


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Hi all,

another question.  Does anyone know how to make spheres smaller.  I 
would like to make the ball and stick looking residues like those in 
Molscript

thank you

Avram
-- 
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104

L:215-898-3496

>
>Hi,
>
>I would like to know how to insert a movie into PowerPoint (for Mac 
>OS X).  Should I firt convert it into an animated .gif in another 
>program like flash?
>
>thanks
>
>Avram
>--
>
>Avram M. Slovic
>Biochemistry and Molecular Biophysics
>University of Pennsylvania
>420 Curie Blvd.
>1010 Stellar Chance Bldg.
>Philadelphia, PA 19104
>
>L:215-898-3496


-- 
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104

L:215-898-3496

Avram,
	
	set cartoon_highlight_color, red

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 sl...@ma...
> Sent: Friday, December 19, 2003 11:38 AM
> To: pym...@li...
> Subject: [PyMOL] Question
> 
> Hi,
> 
> does anyone know how to color the inside of helices a different color
> than the outsides?
> 
> thanks
> 
> Avram
> --
> Avram M. Slovic
> Biochemistry and Molecular Biophysics
> University of Pennsylvania
> 420 Curie Blvd.
> 1010 Stellar Chance Bldg.
> Philadelphia, PA 19104
> 
> L:215-898-3496
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: IBM Linux Tutorials.
> Become an expert in LINUX or just sharpen your skills.  Sign up for
IBM's
> Free Linux Tutorials.  Learn everything from the bash shell to sys
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

=20
Hi Avram

This is possible in cartoon mode in the newer versions of PyMOL (i don't =
remember exactly from which). You have to select "highlight color" in =
the cartoon menu. The default color is grey, but can be changed by

set cartoon_highlight_color, <color_name>, <object_name>


Cheers,

Esben


-----Original Message-----
From: pym...@li...
To: pym...@li...
Sent: 19-12-03 20:37
Subject: [PyMOL] Question

Hi,

does anyone know how to color the inside of helices a different color=20
than the outsides?

thanks

Avram
--=20
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104

L:215-898-3496


-------------------------------------------------------
This SF.net email is sponsored by: IBM Linux Tutorials.
Become an expert in LINUX or just sharpen your skills.  Sign up for
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admin.
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_______________________________________________
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PyM...@li...
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Hi,

does anyone know how to color the inside of helices a different color 
than the outsides?

thanks

Avram
-- 
Avram M. Slovic
Biochemistry and Molecular Biophysics
University of Pennsylvania
420 Curie Blvd.
1010 Stellar Chance Bldg.
Philadelphia, PA 19104

L:215-898-3496

Todd Geders  said:

>Hello all,
>
>Here is a simple script that automates the electrostatic potential
>surface generation using Gromacs, MEAD, and Pymol for visualization.
>It's exclusively based off of the post by Esben Peter Friis:
>It requires you to massage your pdb file a bit, but it gets the job
>done.  Please glance at the comments in the script to see what I mean.

Thanks Todd for the script. I installed Gromacs 3.2 beta, MEAD 2.2.3 on Mac
OS 10.3.
The only change is that the $PDB.mdp file has to contain:

cpp = /usr/bin/cpp

to specify the cpp location in OS X.
Run the script, seems to work.

Now the question is how do I go about validating the results?
I tried to compare one image I get with the one published for 1ALK.pdb but
there were some differences :-(.

Would anyone in the list be willing to send me the files for one of their
proteins, so I can re-run the calculations and compare what I get?

Thanks

Michele Fuortes


-- 


--
Michele Fuortes, M.D., Ph.D.
Assistant Professor
Departments of Surgery and of Cell and Developmental Biology
Cornell University  - Weill Medical College
E-mail: mfu...@me...

David,

	For settings such as cartoon_color, surface_color, mesh_color,
the default value is -1.

set cartoon_color, -1

or

set cartoon_color, -1, object-name

will restore the color.

Thanks for pointing out that:

set cartoon_color, default

doesn't work!

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax=A0=A0 (650)-593-4020=20
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of David A.
Horita
Sent: Thursday, December 18, 2003 10:50 AM
To: pym...@li...
Subject: [PyMOL] unsetting cartoon_colors

Hi all,
I have a collection of molecules and want to color a particular helix
(in cartoon mode) a specific color different from other helices.=A0
Unfortunately, I had previously set cartoon_color from "default" to
another color, so now specifying a color for that helix (or even "color
red, ss h") has no impact.=A0 (it does change the color of the Calpha, =
but
not the cartoon itself).=A0=20
So, the question is, how do I unset the cartoon_color variable (without
wiping out my scene)?=A0 The variable setting comes with the .pse file,
"set cartoon_color, default" gives an error about not knowing what color
default is.
Thanks,
Dave Horita
=A0
-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:=A0 dh...@wf...
web:=A0 http://www.wfubmc.edu/biochem/faculty/Horita/
=A0

Hi all,
I have a collection of molecules and want to color a particular helix =
(in cartoon mode) a specific color different from other helices.  =
Unfortunately, I had previously set cartoon_color from "default" to =
another color, so now specifying a color for that helix (or even "color =
red, ss h") has no impact.  (it does change the color of the Calpha, but =
not the cartoon itself). =20
So, the question is, how do I unset the cartoon_color variable (without =
wiping out my scene)?  The variable setting comes with the .pse file, =
"set cartoon_color, default" gives an error about not knowing what color =
default is.
Thanks,
Dave Horita
=20
-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:  dh...@wf...
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
=20

Chris,
 
I hereby nominate the Targus PAUM01U as the official 3-button mouse for
PyMOL users on the go.
 
http://www.targus.com/us/product_details.asp?sku=PAUM01U
 
They might be too small for some, but they work great for me, at home
and on the road!
 
(plus, they color-coordinate with Ti PowerBooks)
 
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-----
 
Sent: Thursday, December 18, 2003 5:45 AM
To: wa...@de...
Subject: pymol
 
Hi,
I plan to update the website (http://www.macinchem.fsnet.co.uk) over the
Christmas Break and one question I'm often asked is which 3-button mouse
should I use for PYMOL under MacOSX?
Any suggestions?
Thanks
Chris

Roger,
 
            The problem with computing electrostatic maps in PyMOL
currently is that the Coulomb equation assumes a uniform dielectric and
thus doesn't give you correct potentials for macromolecules.  It is much
better to use an external tool such as Grasp, MEAD, APBS, or Delphi,
which can apply a different dielectric constant to the inside of the
protein than to the surrounding solvent.
 
            Yes, PyMOL can compute a Coulombic map using the approach
you've outlined if partial charges have been assigned - but there isn't
a good way to do that in PyMOL just yet.
 
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 Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
To: pym...@li...
Subject: [PyMOL] Display of electrostatic potential surfaces
 
Dear PyMOL users,
 
I would like to generate a figure of my protein where the surface
electrostatic potential is displayed. PyMOL now comes with a demo
function for display of such a surface. However, when I apply the
commands used in this demo, i.e.
 
cmd.set("coulomb_dielectric",80.0)
         cmd.map_new("e_pot","coulomb",1.0,"pept",5)
         cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
         cmd.set("surface_color","e_lvl","pept")
         cmd.refresh()
 
to the model from my pdb file, I get a uniformly blue surface. I believe
this must be due to the lack of assignment of partial/formal charges to
the atoms in the pdb file. So, my questions are:
 
1. Is it possible to automatically assign the correct charges to atoms
within PyMOL
2. If not, is there a program that will do this and if so can the output
from this program be understood by PyMOL in some way.
 
Thanks for your help
 
Roger
 
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge

Dear PyMOL users,

I would like to generate a figure of my protein where the surface =
electrostatic potential is displayed. PyMOL now comes with a demo =
function for display of such a surface. However, when I apply the =
commands used in this demo, i.e.

cmd.set("coulomb_dielectric",80.0)
         cmd.map_new("e_pot","coulomb",1.0,"pept",5)
         cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
         cmd.set("surface_color","e_lvl","pept")
         cmd.refresh()

to the model from my pdb file, I get a uniformly blue surface. I believe =
this must be due to the lack of assignment of partial/formal charges to =
the atoms in the pdb file. So, my questions are:

1. Is it possible to automatically assign the correct charges to atoms =
within PyMOL
2. If not, is there a program that will do this and if so can the output =
from this program be understood by PyMOL in some way.

Thanks for your help

Roger

--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge

> > What's the problem? Both PyMOL and APBS are licensed under the GPL so I
> > see no problems there.
>
> Well, pymol isn't obviously. Note to self: Don't post about licensing
> stuff after an evening of mulled wine.

I've had an evening of nice port .. we'll see how a port-influenced
evening compares to a mulled-wine-influenced evening :).

> Still, as long as the pymol license is GPL-compatible (which I believe
> it is, but I'm no lawyer), and the additional code is licensed under the
> same license, it should be alright, as I understand it.

The potential problem is this:  once I get this working, I want to give it
to PyMOL.  That way, I don't have to care about maintainance :).  If I'm
going to give it to PyMOL, I think it needs to use the PyMOL license, not
the GPL.  The license thing is probably not a big deal anyway.  On the one
hand, I'm not sure that anything I've done is actually forced to be GPL'd.
On the other hand, it would probably take Warren all of an hour to
re-create everything I've done.  It took me a while because in addition to
writing something that parses DX files, I had to figure out some of the
PyMOL internals.  And I'm slow :).  Playing around with PyMOL is
definately fun, though.

-michael

On Thu, Dec 18, 2003 at 12:26:48AM +0100, Michael Banck wrote:
> On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote:
> > I've gotten the code much closer to working.  Also, I think it's factored
> > well enough that most of it should be non-GPL-contaminated.  After I
> > actually get it working completely, I'll email the APBS folks to see if
> > they care about licensing issues.
> 
> What's the problem? Both PyMOL and APBS are licensed under the GPL so I
> see no problems there. 

Well, pymol isn't obviously. Note to self: Don't post about licensing
stuff after an evening of mulled wine.

Still, as long as the pymol license is GPL-compatible (which I believe
it is, but I'm no lawyer), and the additional code is licensed under the
same license, it should be alright, as I understand it.


sorry,

Michael

On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote:
> I've gotten the code much closer to working.  Also, I think it's factored
> well enough that most of it should be non-GPL-contaminated.  After I
> actually get it working completely, I'll email the APBS folks to see if
> they care about licensing issues.

What's the problem? Both PyMOL and APBS are licensed under the GPL so I
see no problems there. 

Do you imply that you want to license your own code under a
non-GPL-compatible license? Why?


Michael

Hi again,

I've gotten the code much closer to working.  Also, I think it's factored
well enough that most of it should be non-GPL-contaminated.  After I
actually get it working completely, I'll email the APBS folks to see if
they care about licensing issues.

Right now, I can generate isomeshes and isosurfaces for methanol that look
reasonable (yay!).  But I can't get the surface coloring to work.  If I do
this:

load methanol.pdb
show surface, methanol
run cleanerDxMap.py # loads up my APBS-generated map
ramp_new e_lvl, map, [-10,0.00,10]
set surface_color, e_lvl, methanol
isosurf surfneg, map, -0.1
isomesh meshpos, map, 0.1
color red, surfneg
color blue, meshpos

I get a good looking mesh, a good looking isosurface, and a completely
white surface around methanol.  dragging the limits on the map around to
really small things or really large things doesn't seem to help either.
Any quick guesses?

In case you have a little bit of spare time, I have two dumb sounding
questions:

1) What exactly is supposed to go into ObjectMapState->Dim?

At first, I thought it was just a list of three integers giving the map
dimensions (in grid points), but that doesn't seem to be the answer.  When
I take a map that PyMOL generates for me (e.g. with
cmd.map_new("map","gaussian","0.1","methanol")) and print it out as a
Python list (using ObjectMapAsPyList, etc.), I get different results each
time the program is run.

2) What exactly is supposed to go into ObjectMapState->Field->Points?

I think it's just the x,y,z coordinates of the points starting at
minCorner and working up through maxCorner by incrementing z then y then x
([x1,y1,z1,x1,y1,z2,...].  But, when I first tried to set points myself, I
got a few things wrong .. it looks like n_dim is supposed to be 4.  I had
guessed 3.  It also looks like Dim should be four ints, the grid
dimensions followed by the number 3.  Finally, it looks like stride should
be the normal stride followed by the base_size.  What am I missing here?
Why is points a four-dimensional thing while data is a three-dimensional
thing?

thanks,

-michael


--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

On Thu, 11 Dec 2003, Warren L. DeLano wrote:

> Michael,
>
> 	Impressive!  I think you're one of the few people to delve into
> PyMOL's source like this.
>
> 	Obviously I'd be the best person to look at your code, but I'm
> crunched right now getting ready for this upcoming trip.  Also, if the
> code is GPL-contaminated, then it can't be useful in the main version,
> but perhaps we can rewrite this cleanly later on.  I can probably help
> you in January.  What you've written sounds right...
>
> 	One thing I'd suggest for debugging in the meantime is that you
> use the isomesh or isosurface routines to explore what data is ending up
> in the Map, before trying to use the color ramps.  There may also be
> some code in the chempy brick stuff which could serve as an example for
> populating the list.
>
> Cheers,
> Warren
>
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
>
>

* Michael Bovee <mb...@uv...> [2003-12-16 14:27] wrote:

> Hmm. When I try this I get a syntax error:
> __________________________________________________
> PyMOL>load EcHRSade.pdb
>  Executive: object "EcHRSade" created.
> PyMOL>hide
> PyMOL>show cartoon
> PyMOL>dss EcHRSade
> Traceback (most recent call last):
>   File "/sw/lib/pymol/modules/pymol/parser.py", line 251, in parse
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
>   File "<string>", line 1
>      dss EcHRSade
>                 ^
>  SyntaxError: invalid syntax
> _________________________________________________
> 
> I also get the error if I type on the command line  "dss EcHRSade.pdb"
> 
> Apparently pymol's dss works for others? Maybe a problem in the fink 
> package, or on my particular system?
> I'm running the current fink package, 0.90-2, compiled from source on 
> my PBG3(Lombard/Bronze).

I think this is the problem.  The dss command was introduced in version
0.91.  I think you need to upgrade.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

On Wed, 2003-12-17 at 17:39, Scott Classen wrote:
> Hi Ann,
> you can set the radius of the "water" probe used to construct the=20
> surface by setting solvent_radius to something smaller than 1.4. You=20
> can either look in the pulldown menus for the settings panel to adjust=20
> the value in a GUI or type:
>=20

Scott,

I think that Ann wants a sphere radius larger than 1.4, since she is
looking for a less detailed surface... reducing the probe radius will
increase the amount of detail, or roughness (tending towards the
vdw surface, for radius=3D0.0)

Cheers,
Paulo


> set solvent_radius, 1.2        in the text window.
>=20
> Good Luck
> Scott
>=20
> On Dec 16, 2003, at 3:05 PM, Ann Mullin wrote:
>=20
> > Hello,
> >
> > I have been using PyMol for a few months now, and I am wondering if I=20
> > can adjust the radius about which the surface is calculated.   I have=20
> > a very large protein (28,000 atoms) to model, and I would like to be=20
> > able to create a more evenly rounded surface.  Not "realistic"=20
> > perhaps, but easier for students to see the larger view than marveling=20
> > at all the nooks and crannies.  All suggestions greatly appreciated.
> >
> > Ann
> >
> >
> > Ann Mullin
> > Cell and Molecular Biology Dept.
> > Tulane University
> > New Orleans, LA 70118-5698
> > 504-865-6742 (Ph)
> > 504-865-6785 (FAX)
> > am...@tu...
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Scott Classen, Ph.D.
>    ACS Postdoctoral Fellow
>    Department of Molecular & Cell Biology
>    University of California, Berkeley
>    237 Hildebrand Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--=20
Paulo Martel
Dept. de Qu=EDmica e Bioqu=EDmica
Faculdade de Ci=EAncias e Tecnologia
Universidade do Algarve
Campus de Gambelas, 8000-117 FARO
Tel: 289800900 Ext.7402