RE: [PyMOL] fink install fail: pymol-0.86-4

2003-03-18 Thread DeLano, Warren

It looks to me like you are missing Numeric Python.  Either you need to 
remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy 
installed.  There is likely a Fink package which contains it, but I suspect 
this dependency may have been missed in the creation of the Fink PyMOL package.

A quick workaround would be to remove the _PYMOL_NUMPY define from the 
PyMOL Rules.make file.


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: Kevin Gardner []
 Sent: Tuesday, March 18, 2003 10:59 AM
 Subject: [PyMOL] fink install fail: pymol-0.86-4
 Hi all:
  I'll continue on a thread from a couple of weeks ago, re: failed
 fink-based installs of pymol over the past month or so.  Here's the
 machine setup:
   - attempting to install pymol-0.86-4 onto OS 10.2.4
   - python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs
   (2.2.4) all installed
   - running Apple's X11 (v0.2 and now 0.3) w/SDK installed,
   other X programs compiling OK
 Output from the build attached below --- anyone have any insights
 cd pyopengl;make
 cc -ffast-math -no-cpp-precomp -g -I/sw/include 
 -DHAVE_ARRAYOBJECT_H -c _glu_nummodule.c -DPythonTypes
 In file included from _glu_nummodule.c:8:
 _glumodule.c: In function `py_glu_NewTess':
 _glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from 
 incompatible pointer type
 _glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from 
 incompatible pointer type
 _glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from 
 incompatible pointer type
 _glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from 
 incompatible pointer type
 _glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from 
 incompatible pointer type
 In file included from _glu_nummodule.c:8:
 _glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory
 _glumodule.c: In function `py_glu_Build2DMipmaps':
 _glumodule.c:723: `PyArrayObject' undeclared (first use in 
 this function)
 _glumodule.c:723: (Each undeclared identifier is reported only once
 _glumodule.c:723: for each function it appears in.)
 _glumodule.c:723: `ap' undeclared (first use in this function)
 _glumodule.c:741: parse error before ')' token
 _glumodule.c:744: parse error before ')' token
 make[2]: *** [_glu_nummodule.o] Error 1
 make[1]: *** [make-pyopengl] Error 2
 make: *** [.contrib] Error 2
 ### execution of make failed, exit code 2
 Failed: compiling pymol-0.86-4 failed
 Kevin Gardner, Ph.D.
 Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
 214-648-8916/FAX: -8947

This email is sponsored by: Does your code think in ink? 
You could win a Tablet PC. Get a free Tablet PC hat just for playing. 
What are you waiting for?
PyMOL-users mailing list

RE: [PyMOL] Transparent cartoons?

2003-03-18 Thread DeLano, Warren

Not currently.  To the rest of the list:  How important is this to 
people?  Please send me an email directly if you think it would be an important 
feature to add.


Warren 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: Fred Berkovitch []
 Sent: Monday, March 17, 2003 6:41 PM
 Subject: [PyMOL] Transparent cartoons?
 Hello everyone,
 Can pymol make transparent cartoons?  If so, how?
 This email is sponsored by:Crypto Challenge is now open! 
 Get cracking and register here for some mind boggling fun and 
 the chance of winning an Apple iPod:
 PyMOL-users mailing list

RE: [PyMOL] different transparencies

2003-03-16 Thread DeLano, Warren
CC'd to list for future reference...


For mixed colors, you need to use the same trick (separate objects). 
However, if you want the spheres to have a uniform color, in which case you can 
set sphere_color,white etc., without having to create separate objects.

PyMOL's internal raytracer isn't likely to support perspective any time 
soon.  Instead, I recommend using PovRay.


 Subject: Re: [PyMOL] different transparencies
 DeLano, Warren wrote:
 Because of the way settings work in PyMOL, you will need to 
 split your spheres into different objects in order to get 
 this to work.
 Try the following script:
 load $PYMOL_PATH/test/dat/pept.pdb
 create cpy,pept
 show sph,pept and name ca
 show sph,cpy and name n
 set sphere_transparency,0.5,pept
 Hi Warren.
 Thank you for hint. Excuse me I reply directly, but I think 
 you are the 
 best information source in this field. Could you hint me also how to 
 hack if I want to have different color for sphere and sticks 
 to the same atom (I want to use transparent sphere colored by element 
 and black sticks).
 I wonder if built-in raytracer can render in perspective mode in near 
 Michal Bozon
 I would like to have some spheres transparent, but some 
 spheres leave 
 opaque. Or to have spheres with different transparencies. Is 
 it possible?
 Michal Bozon

[PyMOL] A New Phase for PyMOL

2003-03-16 Thread DeLano, Warren
Dear PyMOL Users and Friends,

It is with great excitement and anticipation that I announce a new 
phase for PyMOL:  Beginning April 3rd, 2003, I will be committed FULL-TIME to 
the development, documentation, and support of this Open-Source package through 
my limited liability company, DeLano Scientific LLC.

This step is made possible through financial sponsorship received from 
a small group of PyMOL users during the past 18 months.  Thank you very much 
for that.  Your backing has given me the courage to launch even in these 
uncertain times.  Don't let terrorism, recession, war, or epidemics dissuade 
you -- you only get one life in which to pursue your dreams!

Fortunately, my five-year relationship with Sunesis Pharmaceuticals 
continues on good terms, and the company will remain an active test site for 
PyMOL though I will no longer be an employee.  All of us owe Sunesis a debt of 
gratitude for nurturing the development of this package over the past several 

PyMOL now enters a critical time.  We absolutely must secure additional 
funding in order to sustain our activities.  While we hold out hope for a large 
influx from big pharma, so far it has not yet materialized.  Nevertheless, 
because we are starting out small and efficient, we can succeed this year 
mainly on grass-roots academic and small-company sponsorship if each of you 
takes the initiative within your organization to support PyMOL.

Thus, I urge every user to advocate for purchase of a PyMOL license and 
maintenance subscription for their group now that the package will be supported 
with rapidly improving documentation, responsive feedback, and regular updates. 
 If you sponsored the project in 2002, then please consider renewing your 
maintenance subscription in 2003.

Though PyMOL will always be unrestricted Open-Source software, DeLano 
Scientific will also be rewarding sponsors with extra perks known as Incentive 
Products.  These will soon include an expanded manual and protein morphing 
capability, and will eventually enable electrostatic calculations, sequence 
editing, direct movie output, a molecular force-field, and on-site training.  

Please understand that my aim is to keep the package as open as 
possible while adopting a reliable strategy for paying the bills.  Without 
incentives, we find that only about 5% of users contribute.  If PyMOL is to 
eventually surpass the capabilities of traditional commercial products, we need 
to secure sponsorship from a majority of users.  Hence this compromise.

More details will follow in coming months.  If you wish to know more 
about DeLano Scientific and our software philosophy, then please follow this 

Warren L. DeLano, Ph.D.

RE: [PyMOL] select residues 4 angstrom away from the center atom or residue

2003-03-14 Thread DeLano, Warren

For example: to create a selection near145 consisting of all atoms within 4 A 
of residue 145:

select near145, all within 4 of 145/ 

And to select complete residues:

select near145, byres ( all within 4 of 145/ )


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: eric hu []
 Sent: Friday, March 14, 2003 10:39 AM
 To: pymol
 Subject: [PyMOL] select residues 4 angstrom away from the 
 center atom or
 Hi, I wonder if pymol can do this kind of selection.
 Do you Yahoo!?
 Yahoo! Web Hosting - establish your business online
 This email is sponsored by:Crypto Challenge is now open! 
 Get cracking and register here for some mind boggling fun and 
 the chance of winning an Apple iPod:
 PyMOL-users mailing list

RE: [PyMOL] Pymol and Autodock

2003-02-06 Thread DeLano, Warren
SD is a file format for small molecule ligands based around the MDL MOL file 
(CTAB core).

easy to parse
supported by most cheminformatics packages
captures valence, stereochem, charge
2D or 3D
more extensible than PDB (arbitrary tags)

999 atom limit (only useful for small molecules!)
  no standard conventions for storing of atom names or types.
fixed field lengths


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: Alan Wilter Sousa da Silva []
 Sent: Thursday, February 06, 2003 7:41 AM
 To: DeLano, Warren
 Cc: Chris; PyMOL-users
 Subject: Re: [PyMOL] Pymol and Autodock
 On Thu, 6 Feb 2003, Warren L. DeLano wrote:
  Read-in performace would be better if you could convert your
  multiligand PDB file to an SD file.
 Sorry, what's SD?
 Alan Wilter S. da Silva
  Laboratório de Física Biológica
   Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
 Rio de Janeiro, Brasil

RE: [PyMOL] non-related question related: electrostatics

2003-01-28 Thread DeLano, Warren

(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 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 []
 Sent: Tuesday, January 28, 2003 3:14 PM
 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 
 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
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] q: discrete colors and adjacent cartoon segments

2003-01-28 Thread DeLano, Warren

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 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: Bartholomeus Kuettner []
 Sent: Tuesday, January 28, 2003 3:06 PM
 Subject: [PyMOL] q: discrete colors and adjacent cartoon segments
 Dear PyMol users,
 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 
 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!
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] stop an accidental or problematic ray trace

2003-01-28 Thread DeLano, Warren

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).


(Hmm...A save session button might be nice...)
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: Anthony Duff []
 Sent: Tuesday, January 28, 2003 4:29 PM
 Subject: [PyMOL] stop an accidental or problematic ray trace
 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
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] Bug in selections

2003-01-23 Thread DeLano, Warren

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 = (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))


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: Schubert, Carsten []
Sent: Thursday, January 23, 2003 12:41 PM
Subject: [PyMOL] Bug in selections

there is a problem in pymol 0.86 under W2K using a long list of residues in a 
When I use: 
select pocket = (P_338437 and (resi 
pymol generates an error and exits. 
Splitting the selection into 2 parts prevents the crash: 
select p1 = (P_338437 and (resi 
select pocket = (p1 or (P_338437 and (resi 95,96,97,99,100,103)) 
Is there a maximum number of elements in a selection statement? 
BTW the script worked fine in the previous release, 0.82 I guess? 
Any thoughts? 


RE: [PyMOL] Separate surfaces

2003-01-20 Thread DeLano, Warren

It look to me like you've found a bug in PyMOL with the manual 
approach.  What's happening is that the result of a subsequent ignore command 
isn't updating the surface which was created before it.  The scripted behavior 
is correct, since all geometric objects should reflect the current state of the 
atom flags.

The trivial fix to this kind of problem is to split all of the 
molecules into different objects and the create the surfaces independently.  In 
this case, use three objects instead of two.  That way you can ignore the flag 
ignore.. command and only show surfaces on the proteins.

Also note that if you're planning to move objects with surfaces 
attached, use the object parameter in the translate command.  Otherwise, 
PyMOL will have to recalculate the surface for each frame.

   translate [1,0,0],object='A+amp'



Also note that

  reset object='A+amp' 

will restore the object's original position.

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: Jacob Corn []
 Sent: Monday, January 20, 2003 1:36 PM
 Subject: [PyMOL] Separate surfaces
 Hi all,
 It's possible that I've run into a bug/undocumented feature, but I'd 
 like to see if anyone has a solution to the following problem.
 I'm working on a movie script that will (in part) make two separate 
 surfaces for each subunit in a dimer (excluding a drug bound between 
 the subunits), then split the monomers apart and zoom into a drug 
 binding site. However, I'm running into some problems when I try to 
 create the separate surfaces.
 In plain english, what the script does is create two objects, one 
 containing one subunit (B), and the other containing the 
 other subunit 
 AND the drug (A) (when I split the monomers apart I want the drug to 
 follow one monomer). I then calculate the surface for subunit B, flag 
 everything that's not subunit A as ignore, then calculate the surface 
 for subunit A.
 If I input each line separately, the script works perfectly and I get 
 two separate surfaces around each subunit and no surface around the 
 drug. But if I run the script from the PyMOL command line or 
 the whole script at once into the command line, only subunit 
 A shows a 
 surface. The drug (correctly) does not have a surface, but (from the 
 output in the terminal) it looks like PyMOL isn't even calculating a 
 surface for subunit B.
 Any ideas would be greatly appreciated.
 Below are the relevant lines of the script:
 ## make all of the objects we'll need
 cmd.create(A+amp+drug,a// or l/1/ or d//)
 cmd.create(B+amp,b// or l/2/),d//),d// or l/1/)
 ## color it up
 cmd.color(orange,A+amp+drug and A+amp)
 ## let's show separate surfaces for each subunit,B+amp)
 cmd.flag(ignore,not A+amp,set)
 Many thanks,
 This SF.NET email is sponsored by: FREE  SSL Guide from Thawte
 are you planning your Web Server Security? Click here to get a FREE
 Thawte SSL guide and find the answers to all your  SSL 
 security issues.
 PyMOL-users mailing list

RE: [PyMOL] new user

2003-01-14 Thread DeLano, Warren
 From: Nukri Sanishvili []

 There is a new thing (I'm pretty sure it's a bug, not a 
 feature) in 0.86:

 When I Tab for command completion, the command ends with a 
 comma when in
 fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set

Actually, that is a feature.  Slowly, the PyMOL command language is becoming 
more consistent (and more Python like).

set name,value

   is preferred over

set name=value

Since it follows the convention that arguments to PyMOL keywords are 
separated by commas.   Nevertheless, I am a strong proponent of backwards 
compatibility.  set parameter=value will continue to function for years to 
come so that old scripts will not break.  

 Print quality doesn't seem to be as high as the image on the 
 display. Do I
 need to feed the PyMol output into something else first?

Increase the resolution:

ray 2000,1500

 Can (how) I annotate the pictures in PyMol? If it's not there 
 yet, I hope
 it'll be soon as annotation is an indivisible right for any 
 figure to have.

Sorry, your figures will continue to be oppressed with versions 0.86.  
Liberation will come in due time.


RE: [PyMOL] 1pit.pdb

2003-01-12 Thread DeLano, Warren

What are all those extra Q atoms in the pdb file?  They look to me like 
compromise/placeholder coordinates for NMR-equivalent hydrogens...or something 
like that.

To get a reasonable picture, you can get rid of the extra bonds with 

   unbond elem q*,all

or just nuke the Q atoms altogether

   remove q*


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: Jack Howarth []
 Sent: Sunday, January 12, 2003 6:17 PM
 Subject: [PyMOL] 1pit.pdb
 Under linux does anyone else see the following? If one
 loads in the 1pit.pdb from the MOLMOL data files, the
 resulting structure seems to have extra bonds drawn in the
 side chains. For example phe's seem to have all the opposing
 carbons in the rings interconnected through the center of
 the ring. Thanks in advance for any hints on what is causing
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] measuring distances

2003-01-08 Thread DeLano, Warren

Use Python (and the run command with .py files).

from pymol import cmd

You could measure the whole protein this way by putting a loop around the 
distance command:

from pymol import cmd
atom = cmd.get_model(mol1ha).atom
for i in range(len(atom)-1):
   sele1 = 'mol1///%s/HA'%atom[i].resi
   sele2 = 'mol1///%s/HA'%atom[i+1].resi
   f.write(%14s %14s %8.3f\n%(sele1,sele2,dst))

The output dist.txt would then look like:

   mol1///9/HA   mol1///10/HA4.833
  mol1///10/HA   mol1///11/HA4.933
  mol1///11/HA   mol1///12/HA4.813



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: Tara Sprules []
 Sent: Wednesday, January 08, 2003 3:20 PM
 Subject: [PyMOL] measuring distances
 I have a file which measures a bunch of distances between 
 atoms (of the
 form distance (mol1///25/ha), (mol1///26/ha)), and rather 
 than having to
 look at the results on the screen I'd like to have the values output
 to a text file. Is it possible to do this?
 Tara Sprules
 Post-Doctoral Fellow
 Department of Chemistry
 University of Alberta
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] Rolling your own functions in PyMol

2003-01-07 Thread DeLano, Warren

You're looking for the PyMOL API function extend:

from pymol import cmd

Would then permit the following:

ramp_colors chain A

See help extend for more info...


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: Stephen Graham []
 Sent: Tuesday, January 07, 2003 4:14 PM
 Subject: [PyMOL] Rolling your own functions in PyMol
 Hi All,
 I am a recent subscriber to the list, so apologies if this 
 question has
 been answered before.  I am interested in finding out how you can add
 your own functions to PyMol such that they may be 
 transparently called
 from inside PyMol's shell.  The the basic question is How do 
 I register
 PyMol names for home-grown functions so that they can be used like the
 functions in the util module.  A more detailed example of what I am
 after is below.  Also, are there any warehouses or collections of
 home-grown functions to which I could submit functions I 
 write and from
 which I could gain examples from other users?
 == More detailed description of my problem ==
 I have written a function to ramp coloring of a backbone 
 between two or
 more arbitrary colors (it is really a generalization of the code in
 util.rainbow).  I have imported the code using the general 
 Python import
   import ramp_chain
 Now, let's say that I have a selection object defined as:
   select A,(chain A)
 Were I using the rainbow command I would be able to issue the command:
   util.rainbow A
 Which follows the general rules of command line parsing.  
 in my case issuing the command:
   ramp_chain.ramp_colors A
 gives the error:
   Syntax error: unexpected EOF (and there is an arrow under the letter
 I *can* call the command using the syntax:
   ramp_chain.ramp_colors( chain A )
 but this syntax is not optimal - I would like to be able to use my
 already defined selections.
 Stephen Graham
 PhD candidate and nasty sysadmin
 Crystallography Group
 School of Molecular and Microbial Biosciences
 Building G08
 University of Sydney
 New South Wales, 2006
 Ph: +61 2 9351 8197
 Fax: +61 2 9351 4726
 This SF.NET email is sponsored by:
 SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
 PyMOL-users mailing list

RE: [PyMOL] Zooming in animations

2002-12-02 Thread DeLano, Warren

If you are talking about a controlled zoom into a specific active site 
region, there isn't any automated way to do this.  Peter's movie.zoom routine 
can help with a general zoom.  Try this:

fragment arg
mset 1 x100
movie.zoom 1,100,1,0
mappend 1:move z,-100


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: Chris Arthur []
Sent: Monday, December 02, 2002 5:20 AM
To: pymol-users
Subject: [PyMOL] Zooming in animations

Hi Guys
Sorry if this question has been asked before but does anyone know a way to zoom 
in on an area as an animation (eg an active site or interface). 
Thanks in advance

RE: [PyMOL] Pymol ignores SCALE records in PDB files

2002-11-27 Thread DeLano, Warren

Thank you for bringing this issue to my attention.

I can confirm that PyMOL doesn't currently read SCALE records. In order 
to generate correct crystal symmetry, it requires the input PDB coordinates to 
be  properly oriented and translated with respect to the crystal lattice origin 
and axes.  However, I think this is the default case with most of the standard 
refinement programs.  At the very least, PyMOL should print a warning if it 
finds a SCALE record!

I'll see if we can't get SCALE handling in before the next release.


 -Original Message-
 From: Keith Refson []
 Sent: Wednesday, November 27, 2002 7:02 AM
 Subject: [PyMOL] Pymol ignores SCALE records in PDB files
 Just to repeat the subject, it appears that pymol takes no account of
 the SCALE records in a PDB file.
 The built in assumptions of the orientation of the unit cell therefore
 gives an erroneous relationship between the unit cell and the atomic
 co-ordinates.  The attached file demonstrates the problem.
 Show-Cell puts the long dimension of the cell perpendicular to the
 line of the atoms, rather than collinear with them as it ought to be.
 More seriously then, symexp gives a completely wrong expansion.
 CRYST15.0245.0245.024  39.69  39.69  39.69 P 1
 SCALE1  0.338511  0.00  0.0721210.0
 SCALE2 -0.169255  0.293159  0.0721210.0
 SCALE3 -0.169255 -0.293159  0.0721210.0
 HETATM1  H00 NON A   1   0.000   0.000   6.933  1.00  
 0.00   H
 HETATM2  F00 NON A   1   0.000   0.000   5.792  1.00  
 0.00   F
 HETATM3  F00 NON A   1   0.000   0.000   8.073  1.00  
 0.00   F
 HETATM4 Na00 NON A   1   0.000   0.000   0.000  1.00  
 0.00  Na
 TER   4  NON A   1
 Keith Refson
 Dr Keith Refson, 
 Building R3
 Rutherford Appleton Laboratory
 Oxfordshire OX11 0QX
 T: 01235 778023   K.Refson@
 F: 01235 445720
 This email is sponsored by: Get the new Palm Tungsten T 
 handheld. Power  Color in a compact size!
 PyMOL-users mailing list

RE: [PyMOL] Color plotting of electron density contours?

2002-11-12 Thread DeLano, Warren

There has been some discussion of this desirable feature, but it doesn't 
currently exist.


 -Original Message-
 From: []
 Sent: Tuesday, November 12, 2002 1:27 PM
 Subject: [PyMOL] Color plotting of electron density contours?
 Hi Folks:
 Is there a way to display a cross-section of electron density  
 (false)-color-coded for electron density?  In other words, I 
 would like 
 to produce a 2-D plot that looks like a contour map (eg: 
 output of CCP4 
 npo) but color-coded with respect to electron density.  A 
 continuum, if 
 possible, would actually be better than a series of contour lines.
 Has this by any chance been implemented in pymol or anywhere?
 Many thanks,
 Bill Scott
 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
 phone:  +1-831-459-5367 (office)
 +1-831-459-5292 (lab)
 fax: +1-831-4593139  (fax)
 This email is sponsored by: 
 To learn the basics of securing your web site with SSL, 
 click here to get a FREE TRIAL of a Thawte Server Certificate:
 PyMOL-users mailing list

RE: [PyMOL] help with surface parameters

2002-11-11 Thread DeLano, Warren

 From: Scott Classen []
 Hello fellow PyMOLers,
   Is the surface in PyMOL a solvent accessible surface or 
 a molecular 
 surface? It looks like a solvent accessible surface to me. Is 
 there any 
 way to change the radius of the water probe that is used to 
 create the 

PyMOL's default surface is a water contact surface (approximates a Connolly 

I noticed that there are a few surface settings, but I can't 
 figure out what effects they are having on the displayed surface. Can 
 anybody shed light on these commands? What are their default 

You can use the settings editor to get the default (except if you're using the 
native OSX version on a mac).

 What are the high and low values they can take?

These settings haven't yet been documented, but they will be in an upcoming 
version of the manual.  

   I would like to create a fairly tight molecular surface and I just 
 can't figure it out. ANy help would be appreciated.

show surface
set surface_quality=1
set solvent_radius=0.8

WARNING: PyMOL may crash if solvent_radius is too low.  If it does, try 
incrementing it by 0.1 until it stabilizes.


RE: [PyMOL] Current settings list in Pymol OSX

2002-10-30 Thread DeLano, Warren
This is undocumented:

To get a list of settings:

from pymol import setting
print setting.get_name_list()

To get the current value of a setting:

print setting.get_setting_text(bg_rgb)
print setting.get_setting_text(gamma)

To get a list of names with values:

print map(lambda x:[x,setting.get_setting_text(x)],setting.get_name_list())



-Original Message-
From: Kelley Moremen []
Sent: Wednesday, October 30, 2002 10:13 AM
Subject: [PyMOL] Current settings list in Pymol OSX

Dear Pymolers,

Since the Mac OSX version of Pymol does not have a menu interface that has a 
pull-down menu to view and alter the settings, is there any way to display and 
alter the full set of settings from the command line?  I keep forgetting what 
the relevant command line syntax is for changing the settings commands (there 
is only a partial list in the manual) and a global list (as in the pull-down 
menu) is a great reminder, but alas the menu interface is not yet there in the 
Mac OSX version.

Thanks for your help.


Dr. Kelley Moremen 
Associate Professor 
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology 
University of Georgia, Athens, GA 30602-7229 
Office (706) 542-1705Fax: (706) 542-1759
(send email with large attachments to:

RE: [PyMOL] making a two step movie in pymol

2002-10-30 Thread DeLano, Warren
mset 1 x360
movie.roll 1,180,1,axis=y
movie.roll 181,360,1,axis=x

 -Original Message-
 From: Craig Smith []
 Sent: Wednesday, October 30, 2002 11:43 AM
 Subject: [PyMOL] making a two step movie in pymol
 How do I create a movie in pymol in which I rotate a molecule 
 about the 
 y-axis 360 deg and then immediately do a 360 deg rotation about the 
 x-axis?  I couldn't figure it out from published examples.
 Thanks in advance
 Craig L. Smith, Ph. D.
 Molecular Microbiology
 Washington University School of Medicine
 660 South Euclid Box 8230
 Voice: (314) 362-9054
 Fax: (314) 362-1232
 This email is sponsored by: Influence the future 
 of Java(TM) technology. Join the Java Community 
 Process(SM) (JCP(SM)) program now.
 PyMOL-users mailing list

RE: [PyMOL] PyMol Manual

2002-10-28 Thread DeLano, Warren

I fully agree with your assessment that PyMOL is currently unable to reach 
its potential due to a number of factors, including poor documentation. 

Nevertheless, I do have a defined plan for eliminating these deficits.  It 
involves securing funding to hire people under contract to document, support, 
and develop PyMOL on an ongoing basis.  While I am grateful for the continued 
assistance of PyMOL users on numerous minor tasks, it is not reasonable to 
expect anyone to prepare a complete well-written manual or to perform other 
major tasks without some form of compensation.  Also, PyMOL is still immature 
enough in certain areas that a full manual really can't be constructed until 
the 1.0 features are settled upon (soon hopefully!).

Understanding this situation, several large pharmaceutical companies and 
many smaller entities have lent support to PyMOL development through donations 
and license purchases.  At present the flux is low, but we are getting to a 
point where some real headway can be made.  The forthcoming Incentive PyMOL 
(iPyMOL) add-on will hopefully increase the flux by providing a specific 
reward to those who fund the PyMOL development effort.  

I know it may sound like PyMOL/iPyMOL is becoming commercial gray-ware, but 
that's not it at all.  I haven't devoted thousands of hours to this project 
just to see it end up as yet another expensive, lousy, inflexible, and 
closed-source commercial tool.  PyMOL will remain a vital open-source project, 
and iPyMOL will exist solely to accelerate PyMOL's growth and guarantee its 
long-term health.  Nurturing PyMOL and similar efforts to fruition on such 
terms is central to my career vision -- it's what I stand for in this industry.

I believe that well-supported, well-documented, and well-maintained 
open-source software will be a superior research product to what is currently 
offered by the major scientific software vendors.  My hope is that scientists 
in industry and academia will eventually come to appreciate this, and then 
choose to make creation of such software economically viable through funding of 
balanced approaches such as the one I am taking with PyMOL.

Free software is great once it exists, but there are far too few developers 
in this field to expect the kinds of dramatic successes achieved by the Linux, 
GNU, and BSD communities.  If open-source/free-software is going to have a 
large impact on molecular modeling, it will need direct support from users, 
universities, governments, and for-profit companies.  If really good 
open-source tools were available and able to meet the needs of research, would 
you be willing to pay reasonable amounts of money for their development, 
maintenance, and support?  I hope so.

Thus, pharmaceutical companies like EMD/Lexigen/Merck can choose to 
continue to spend millions of dollars on traditional closed-source packages 
with no hope of a reprieve, or they can choose to funnel a small fraction of 
that money into efforts like PyMOL.  Over the long term, open-source packages 
offer vendor-independence, cost-effectiveness, flexibility, opportunities for 
innovation, and support for broad sharing of information and technology.  These 
are all key ingredients in scientific progress, both within a single 
organization and across the industry.  

Realistically, it will take a year or more before PyMOL can fulfill the 
potential you described.  How soon this happens will depend in part on whether 
people like yourself are content to merely gripe about the status quo, or 
whether you are prepared to commit resources towards improving it.


Warren L. DeLano, Ph.D.
PyMOL Creator 
Founder, DeLano Scientific

-Original Message-
From: []
Sent: Monday, October 28, 2002 10:33 AM
Subject: [PyMOL] PyMol Manual

Fellow PyMol Users 

Although I like using PyMol, I would like to submit a gripe about the severe 
lack of a decent PyMol manual. 

A deeper description of the program's features is required if people are 
seriously going to use PyMol for tricky things beyond simple visualization 
(simple visualization programs are ten-a-penny and PyMol could be so much more) 

Particularly lacking are details of structural editing (mutation, bond 
rotation, cut-and-paste etc.), interfaces (if any exist) to routines for enegy 
minimization and a detailed description of the Python command line interface 
with examples of scripting and how to extend PyMol's capabilities. 

By neglecting to adequately document what may be a really useful program, the 
PyMol user community might fail to attract the kind of user base and support 
that it deserves and that it needs to ensure its success. 

A good, clear and well-thought out manual really helps to make a case for using 
a particular piece of software (and it might also lower the odds of PyMol 
having to join the gray 

RE: [PyMOL] distance parameters

2002-10-23 Thread DeLano, Warren
 From: Jules Jacobsen []
 you can change most of the parameters using set dash_n where 
 n= length,
 width, gap, radius. Unfortunately dash_color doesn't exist.
...but you can change the color of a distance object

color red,dist01


RE: [PyMOL] CMYK colors

2002-10-22 Thread DeLano, Warren
Thanks for the suggestion?

For now, why not just redefine the existing colors? 

No need for a leading underscore...

set_color green= [0.00 , 0.53 , 0.22]


Note that there are default atom colors such as carbon, nitrogen, oxygen, 
hydrogen, sulfur, etc. which should also be redefined.

set_color carbon= [0.00 , 0.53 , 0.22]



 -Original Message-
 From: Gil Prive []
 Sent: Friday, October 18, 2002 1:38 PM
 Subject: [PyMOL] CMYK colors
 This is not directly PyMOL specific, but it addresses a 
 problem I think 
 a lot of us have encountered in preparing hardcopy outputs.
 Some RGB triplets do have equivalents in CMYK space, and as a 
 result, a 
 figure that looks great on a screen can come out with unpredictable 
 colors when printed.
 Most applications do a good job with RGB-to-CMYK conversions 
 for photos, 
 but do not do such a good job with graphics that use pure primary 
 colors.  For example, reds are generally OK, but pure blues 
 and greens 
 do not translate very well.
 Here are some RGB values that are within the CMYK gamut  (i.e. are 
 #optimized rgb values for cmyk output:
 set_color _dblue= [0.05 , 0.19 , 0.57]
 set_color _blue=  [0.02 , 0.50 , 0.72]
 set_color _mblue= [0.5  , 0.7  , 0.9 ]
 set_color _lblue= [0.86 , 1.00 , 1.00]
 set_color _green= [0.00 , 0.53 , 0.22]
 set_color _lgreen=[0.50 , 0.78 , 0.50]
 set_color _yellow=[0.95 , 0.78 , 0.00]
 set_color _orange=[1.00 , 0.40 , 0.0 ]
 # these are trivial
 set_color _red=   [1.00 , 0.00 , 0.00]
 set_color _mred=  [1.00 , 0.40 , 0.40]
 set_color _lred=  [1.00 , 0.80 , 0.80]
 set_color _vlred= [1.00 , 0.90 , 0.90]
 set_color _white= [1.00 , 1.00 , 1.00]
 set_color _vlgray=[0.95 , 0.95 , 0.95]
 set_color _lgray= [0.90 , 0.90 , 0.90]
 set_color _gray=  [0.70 , 0.70 , 0.70]
 set_color _dgray= [0.50 , 0.50 , 0.50]
 set_color _vdgray=[0.30 , 0.30 , 0.30]
 set_color _black= [0.00 , 0.00 , 0.00]
 There may be a more elegant way to do this (specific to the OS and 
 post-PyMOL application), but this is a simple solution.
 It would be useful to specify a CMYK mode in PyMOL, so that 
 the color 
 palate uses RGB colors that have good CMYK equivalents.  This would 
 simplify color selection when preparing hardcopy figures.
 With apologies to color-matching gurus,
 Gil Privé
 Ontario Cancer Institute
 University of Toronto
 This email is sponsored by:
 Access Your PC Securely with GoToMyPC. Try Free Now
 PyMOL-users mailing list

RE: [PyMOL] Stereographics CrystalEyes problem

2002-10-08 Thread DeLano, Warren
Yep, we ran into the same problem with our ESGI emitters and FireGL2 cards -- 
we ended up having to buy new StereoGraphics (E-2) emitters for the Linux 
machines  (~$200).
part # SV-008-A-PC-E2 


 -Original Message-
 From: Viktor Hornak []
 Sent: Tuesday, October 08, 2002 2:19 PM
 To: Schubert, Carsten
 Cc: pymol-users
 Subject: Re: [PyMOL] Stereographics CrystalEyes problem
 your guess sounds very likely to me. Unfortunately, we only 
 have ESGI 
 emitters so I cannot confirm it for sure (but I bet you're right).
 Thanks a lot for the tip.
 Schubert, Carsten wrote:
  just a wild guess, but in order to get stereo to work on my 
 PC (under 
  W2K) with a Oxygen GVX card I had to use a ENT emitter from 
  Stereographics. As far as I recall the regular emitters used on the 
  SGI's, type ESGI, did not work.
  Hope it helps.
  -Original Message-
  From: Viktor Hornak []
  Sent: Tuesday, October 08, 2002 15:45
  To: pymol-users
  Subject: [PyMOL] Stereographics CrystalEyes problem
  I followed the discussion on 3D stereo support in PyMOL and saw that
  many people were able to get PyMOL in stereo with FireGL or Nvidia
  cards. Finally I got the chance to try it out myself with a 
  Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the 
 latest nvidia
  drivers (1.0-3123). There were no problems to get 
 accelerated X up with
  blazingly fast PyMOL rendering. So next, I tried to get 
 stereo working.
  I am using Stereographics emitter and CrystalEyes which 
 I've been using
  with our SGIs (so that I know they are functional; in fact 
 PyMOL works
  in stereo on our SGIs without a problem). I plugged the 
 emmiter into the
  DIN on my Quadro4 card, put   Option Stereo 3   into my
  XF86Config-4, restarted X and hoped that things will just work.
  According to XFree log file, X was really initiated in 
 stereo mode. The
  emmiter light turned on when I started PyMOL. I switched to 'quad
  buffered stereo' and the molecule getss rendered in stereo 
 but when I
  look at it with CrystalEyes glasses nothing changes. I 
 still see double
  rendered image on the screen, which means that the emmiter does not
  synchronize glasses correctly (or at all).
  I tried to change some options in XF86Config-4 but nothing 
 helped, so I
  was wondering if someone experienced the same problem. Do 
  emmiter and CrystalEyes glasses work with Quadro4 at all? 
 Do I need to
  get a different emmiter or glasses? Any help appreciated...
 This email is sponsored by:ThinkGeek
 Welcome to geek heaven.
 PyMOL-users mailing list

[PyMOL] RE: pyMol help (Ball Sticks)

2002-09-30 Thread DeLano, Warren
From: George Nicola

I've tried several settings and commands but cannot figure out how to make 
a simple ball-and-stick representation of a molecule.  Can it be done in 


Yes, but it is non-obvious:

hide lines
show sticks
show spheres
set stick_radius=0.1
set sphere_scale=0.25

You can change the two numbers above to fit preferences.


RE: [PyMOL] moving one segment relative to the rest

2002-09-30 Thread DeLano, Warren

The easiest way to do this is to split the objects and then use the rotate 

# save as a .pml file...

load 1FJ1.pdb

# split PDB file

create anti=(chain F) 
create fab=(chain A,B)

# delete original object

delete 1FJ1

# color objects

color green,fab
color pink,anti

# color interface

select inter = (byres ((fab within 5 of anti)\
   or (anti within 5 of fab)))

color yellow,inter

# splay apart

origin fab
rotate y,60,fab
origin anti
rotate y,-60, anti

# zoom interface region

zoom inter
show sph,inter
disable inter

-Original Message-
From: Shohei Koide []
Sent: Monday, September 30, 2002 12:14 PM
Subject: [PyMOL] moving one segment relative to the rest


I am wondering if one can move one segment (in my case, an antigen 
protein) relative to the rest of the complex (antibody) using PyMOL. 
So far I have only been able to translate/rotate the entire complex. 
I would like to manually undock the complex for an illustration 


Shohei Koide

This email is sponsored by:ThinkGeek
Welcome to geek heaven.
PyMOL-users mailing list

RE: [PyMOL] pair_fit crashes

2002-09-26 Thread DeLano, Warren
Hi Jeremy,

If the proteins have significant homology, then you can use the align command:

align prot1ca,prot2

which will perform a sequence alignment of prot1 against prot2, and then an 
optimizing fit using the CA positions.  I'm not sure if the help text for align 
got into 0.82, but the next version will definitely have it.

PyMOL's command length is limit to about 1000 characters, which is probably 
what is causing pair_fit to crash.  However, ideally it should complain 
gracefully instead of crashing, so if you have a sample script  input PDB 
files which cause it to crash, please send them to me as attachments.

As far as script options go, you've pointed out a hole which I had forgotten 
about, but Robert's suggestion on defining a function call in the script is 
definitely the way to go for now.


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: Jeremy Craven []
Sent: Thursday, September 26, 2002 2:00 AM
Subject: [PyMOL] pair_fit crashes

I have been trying to write a script to overlay two arbitrary proteins via my 
own alignment and the 'pair_fit' command. 
1) After running into the problem I described below I looked through the 
pymol-users mailing list as hard as I could and found a statment that such 
arbitrary alignment should be in pymol anyhow from vsn 0.80.  I am using 0.82 
but cannot find it. Is it there ? 
2) Anyhow, (and assuming that I might want to do alignments my own way anyhow), 
I created a script which read in an alignment and created a big long pair_fit 
command of the form  
pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr and 
resi 192 and name ca),(bs and resi 175 and name ca),  etc 
The script then executed this string with 
If I restricted this to about 10 atom pairs it worked fine.  If I allow more 
atoms it crashes the program.  On linux it gave segmentation violation.  On 
irix it gave bus error.  On irix it gave another message that implied that 
maybe the selections had got truncated.  On linux it got as far as giving a 
sensible 'ExecutiveRMS' message (including a value for the rmsd and the number 
of atoms) and then froze and eventually core dumped. It therefore seems that 
the long selection has been accepted properly, but may it corrupts something 
else as a side effect ? 
Any ideas anyone ??  I wondered about doing all the selections invidually into 
named selections and then create a shorter pair_fit command, but decided I 
would ask here first. 
A second little quesion is how do you send command line arguments to a pymol 
python script. 
If I say 
PyMOL   run abcdef 
it says 
Traceback (most recent call last): 
  File /usr/lib/python1.5/site-packages/pymol/modules/pymol/, line 
186, in parse 
IOError: [Errno 2] No such file or directory 
whereas really does exist, and run works fine. 
Otherwise pymol is a great joy to have discovered in the last month or so, and 
a project that I hope I can support (e.g. by contributing scripts like this one 
once I can get it to work properly ...) 

Dr C. Jeremy Craven
Department of Molecular Biology and Biotechnology
University of Sheffield, 
Firth Court, Western Bank
S10 2TN Sheffield UK


Phone:   x24323 
From outside Sheffield:  0114 222 4323
From outside UK: +44 114 2224323
Fax: 0114 272 8697


RE: [PyMOL] electron density maps

2002-09-20 Thread DeLano, Warren

isomesh msh1, map1, 1.5, myobject, carve=2.1

The postfix carve=2.1 will trim density which is more than 2.1 A from 

You may want to play around with the exact cutoff...


 -Original Message-
 From: Scott Classen []
 Sent: Friday, September 20, 2002 3:11 PM
 Subject: [PyMOL] electron density maps
 Hello fellow PyMOL users,
   I am trying to display a ccp4 map over just a ligand. I have 
 successfully read in the map and displayed it around the ligand with:
 isomesh msh1, map1, 1.5, myobject
 but the map has bits and peices of the surrounding sidechains.
 Is there a way to only display the map around my ligand?
Scott Classen
University of California, Berkeley
Department of Molecular  Cell Biology
229 Stanley Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290
 This email is sponsored by:ThinkGeek
 Welcome to geek heaven.
 PyMOL-users mailing list

RE: [PyMOL] Re: Amber

2002-09-09 Thread DeLano, Warren

None of the official releases have Amber trajectory support (although 
the mac 0.84 beta may have an early version of this code).  I'm planning on 
another release near the end of September.

If you can build from the CVS repository, then you can use the code today:

(1) make sure that your trajectory and topology files have the same prefix and 
end in .top and .trj respectively.  Also make sure that your topology exactly 
corresponds to the trajectory file (you may need to create a new topology file 
if you've deleted some atoms from the trajectory).

(2) Now load them:

load_traj parm.trj

help load_traj

has some additional options, such as start, stop, average, interval, 

So long as trajectories are generated from the same topology, you can 
concatentate them as follows:

load_traj part1.trj,parm
load_tram part2.trj,parm
load_traj part3.trj,parm

For now, you'll probably want to preprocess your trajectory using ptraj in 
order to center, average, and perhaps to remove waters.  And you'll need to 
create a new topology file reflecting any atom deletions.  Tom Cheatham and I 
are talking about trying to fold a copy of ptraj into PyMOL, but don't have any 
definite plans yet.


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] Pymol slow on a mac G4 with os 10.1

2002-08-23 Thread DeLano, Warren
Yes, the Fink and GNU/Darwin versions of PyMOL are unaccelerated.  As far as I 
know, the only way to get access to hardware is to call Apple's 
platform-specific OpenGL libraries from within a platform-specific window.  

I am still working on the native OSX port, but with competition from all the 
other PyMOL priorities: such as new features, bug-fixes, and support, not to 
mention my own career and personal life, it is taking far longer to complete 
than I anticipated.  

There was an incomplete test version available with acceleration, but OS 10.2 
has reportedly broken it.

If you can put up with software rendering, then X-windows based Fink or 
GNU/Darwin versions are fine.  But if you want fast PyMOL, then an x86-based PC 
with Windows or Linux is the only alternative (we're talking about a 10-50X 
performance difference of hardware over software -- huge!).  Plus, PC's can do 
stereo -- Macs can't.

If you need fast 3D graphics on a Mac, I'd encourage you to look around for 
other 3D viewers for at least the next couple months.  VMD reportedly has a 
native version...though I haven't tried it myself.


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: Russell Poyner []
 Sent: Friday, August 23, 2002 7:56 AM
 Subject: [PyMOL] Pymol slow on a mac G4 with os 10.1
 The machine is a newish G4 733Mhz 256K ram with a radeon 7500 
 card.  I have 
 installed the Fink version of pymol with the Fink supplied 
 Xfree.  It works 
 but is noticably slower than pymol on my 500 Mhz K6/lintel 
 box, also with a 
 radeon 7500 and Xig xserver.
 It would seem that the mac installation is not benefitting 
 from the graphics 
 hardware despite claims of full acceleration in the xserver.  
 If there is a 
 trick here that I am missing please let me know.
 Russell Poyner
 This email is sponsored by: OSDN - Tired of that same old
 cell phone?  Get a new here for FREE!
 PyMOL-users mailing list

RE: [PyMOL] byres, around, expand etc

2002-08-13 Thread DeLano, Warren

search for SELE_ARD_ and SELE_EXP_ in SelectorModulate1 in 

and SELE_BYR1 in SelectorLogic1

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: Michael Tallhamer []
 Sent: Tuesday, August 13, 2002 6:49 PM
 Subject: [PyMOL] byres, around, expand etc
 I would like to take a look at the code for these selection keywords:
 (byres, around, expand ... etc)
 Does anyone know where to find it?
 Michael Tallhamer
 Undergraduate Researcher
 Cleveland State University
 MSN Photos is the easiest way to share and print your photos:
 This email is sponsored by: Dice - The leading online job board
 for high-tech professionals. Search and apply for tech jobs today!
 PyMOL-users mailing list

RE: [PyMOL] How to ouput a PDB file with transformed coordinates?

2002-08-08 Thread DeLano, Warren
No, not a stupid question.  PyMOL doesn't currently provide a means for doing 
this -- I'll put it on the list...


 -Original Message-
 From: Luca Jovine []
 Sent: Thursday, August 08, 2002 4:41 PM
 To: Mailing List PyMol
 Subject: [PyMOL] How to ouput a PDB file with transformed coordinates?
 Hello PyMolers,
 This is probably a really stupid question, but, is there a 
 simple way to 
 create a PDB file with *transformed* coordinates? The save command 
 always seems to save the original coordinates, even after 
 altering the 
 view with set_view etc...
 I apologize in advance if this is obvious,
 Thanks 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
 This email is sponsored by:ThinkGeek
 Welcome to geek heaven.
 PyMOL-users mailing list

RE: [PyMOL] Problem with Seleno-Cysteine

2002-08-06 Thread DeLano, Warren
alter eys/,type='ATOM'

The problem is that, by default, PyMOL doesn't create ribbons for HETATMs 
(typically ligands and solvent).  With the above command, you're converting 
selenocysteine residues into regular atoms and sorting them into place so that 
they can be included in the ribbon.


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: []
 Sent: Tuesday, August 06, 2002 7:43 AM
 Subject: [PyMOL] Problem with Seleno-Cysteine
 Hi everybody
 I have the structure of a Molybdo-CODH (CO-Dehydrogenase), 
 which contains a
 Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb)
 The residue b/388 is denoted as EYS in the pdb file.
 In the cartoon representation, pymol does not display this 
 part of the backbone
 (I get a hole in the cartoon structure).
 I can display this residue using show sticks, resi 388, and 
 I can pick every
 single atom, even the selenium.
 Any idea how I can display the backbone without break?
 Internet et mail gratuit AltaVista
 This email is sponsored by:ThinkGeek
 Welcome to geek heaven.
 PyMOL-users mailing list

RE: [PyMOL] molecular sculpting

2002-07-18 Thread DeLano, Warren
Molecular sculpting works like a real-time energy minimizer, except that it 
isn't minimizing the energy.  Instead, its just trying to return local atomic 
geometries (bonds, angles, chirality, planarity) to the configuration the 
molecules possess when they were first loaded into PyMOL.  

To actually use this feature:

1. load a PDB file

2. configure the mouse for editing (Mouse menu)
   or click in the mouse/key matrix box

3. select auto-sculpting from the Sculpting menu

4. select Sculpting from the Wizard menu

5. ctrl-middle-click on any atom in your protein to activate sculpting
   the green part will be free to move
   the cyan part will be a fixed cushion to provide context
   the grey part will be excluded

6. now perform any conformational editing operation in the green region
   such as: 

 ctrl-left-click-and-drag on an atom

 ctrl-right-click on a bond, then ctrl-left-click-and-drag about that

You can adjust the radius and cushion using the blue pop-up menus.

Right now I'm not sure the sculpting feature is more than entertainment, but my 
expectation is that it will become part of PyMOL's crystallographic model 
building system in the future.


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: []
Sent: Thursday, July 18, 2002 4:04 AM
Subject: [PyMOL] molecular sculpting

I would like to understand the molecular sculpting possibilities of pymol 
but haven't been able to figure it out yet.  When using the wizard, the 
first request is to click and atom but how to proceed from there? 

I have used the bit of script provided on the web page and deformed 
the benzene ring but have not been clever enough to see the possibilities 
from that. 

Could anyone provide just enough of a step-by-step push-this, click-that lead 
into the 
molecular sculpting to get me started?


RE: [PyMOL] pymol without GL

2002-07-17 Thread DeLano, Warren
Not right now...

In order to build PyMOL without linking to real GL libraries, you'd either need 
a fake copy of the GL API, or #define out all of the gl calls in PyMOL (many 
hours of work).


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: Nathaniel Echols []
 Sent: Tuesday, July 16, 2002 12:09 PM
 Subject: [PyMOL] pymol without GL
 quick question: I'm trying to do batch jobs on a server.  Obviously,
 there's no X or OpenGL installed.  Is there any way to build 
 PyMOL without
 any graphical frontend, and just use it as a raytracer?  I 
 don't want to
 go through the trouble of adding in these libraries...
 This email is sponsored by: Jabber - The world's 
 fastest growing 
 real-time communications platform! Don't just IM. Build it in!
 PyMOL-users mailing list

RE: [PyMOL] How to run PyMol from within Python?

2002-07-16 Thread DeLano, Warren
 So there is no way to run and control PyMol from within 
 another python program?

If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you 
can launch PyMOL from an external Python program as shown in 

However, this is not recommended because the PyMOL launch sequence is not 
fixed.  If you do use it, be prepared to deal with changes down the road. 

 The reason for asking is that we are working on a python platform to 
 run and evaluate protein-protein docking calculations. It would be a 
 nice feature to be able to call up interaction surfaces and 
 protein-protein clusters for display  in PyMol and then interact with 
 them from within our program.

 As things are now I'm forced to treat PyMol as I would treat any 
 molecular graphics program, that is write macros macros for it. This 
 is of course much less convenient and less flexible compared to 
 running PyMol from within our python code.

 Has anyone been able to run and quit PyMol from within python without 
 killing the interpreter? Is it possible? How?

The underlying source of the limitation here is that the GLUT and Tcl/Tk 
libraries which PyMOL uses do not support repeated set-up/take-down -- they are 
both static global systems which steal threads and never return.  Thus, while 
PyMOL is not inherently limited in this fashion, these building blocks which it 
employs are.  Eventually there will be versions of PyMOL which are both GLUT 
and TCL/Tk independent -- but not today.

Instead, I recommend using some kind of inter-process communication along with 
object serialization to pass data from your program into PyMOL.  Python makes 
this relatively easy, but you are looking at a little bit of development.

Sorry the news isn't better!


RE: [PyMOL] Re: movie -script - conversion from .png to .tga

2002-07-15 Thread DeLano, Warren

I think that the line may have been wrapped in your copy of the input file. Try 
making sure that entire Python in the script file appears on a single line -- 
then it should work.


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: []
Sent: Monday, July 15, 2002 10:05 AM
Subject: [PyMOL] Re: movie -script - conversion from .png to .tga

I am trying to run the mkmov1.pml script from the Pymol page. 
I am stopped at the line 

/for i in glob(png/*):os.system(convert +i+  re.sub(png, tga, 

I get the errors: 
Traceback (innermost last):
 File /apps/pymol/modules/pymol/, line 98, in parse
 File string, line 1
for i in glob(png/*): os.system(convert +i+
SyntaxError: invalid token
Traceback (innermost last):
 File /apps/pymol/modules/pymol/, line 234, in parse
 File string, line 1
SyntaxError: invalid syntax 

Without knowing python, I haven't been able to figure out what is wrong 
with the input line.  Can anyone help? 


RE: [PyMOL] color gradient

2002-07-11 Thread DeLano, Warren

It would take a little Python programming, but modules/pymol/ 
has the rainbow command which can be modified so as to give a more restricted 
gradient than the current rainbow.


load prot.pdb

(or just select the rainbow option on the color pop-up menu on prot)


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: jeff chao []
Sent: Thursday, July 11, 2002 2:40 PM
Subject: [PyMOL] color gradient

i would like to make a color gradient (something like purple-cyan) from N to C.
is there an easy way to do this?  thanks, jeff

Jeffrey A. Chao

The Scripps Research Institute  PHONE: (858)784-8743
Molecular Biology MB 33 FAX: (858)784-2903
10550 N. Torrey Pines Road  E-MAIL:
La Jolla, CA  92037  USA


RE: [PyMOL] How to run PyMol from within Python?

2002-07-09 Thread DeLano, Warren
 From: Johan Leckner []
 I'm having problems running PyMol from within another Python program.

This is not the recommended way to run PyMOL and may lead to problems.  You can 
run Python programs within PyMOL as follows:

from the command-line:

pymol # synchronous, in PyMOL module
pymol -r  # synchronous in __main__ module
pymol -l  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

run synchronous in pymol module
run,main   # synchronous in __main__ module

spawn asychronous in a new module
spawn,global # asychronous in the PyMOL module
spawn,main   # asychronous in the __main__ module


help launching
help run
help spawn

 Following the examples in /pymol/examples/devel I have been able to 
 launch and controll PyMOL. The problem occur when I try to quit PyMol 
 (version. 0.82) however I do it I end up with a fault terminating my 
 Python interpreter.
 Under Redhat 7.1/Python 2.1 i get a segmentation fault and under 
 MacOS 10.1.5/Python 2.2.1 I get a Python bus error. I get the same 
 result both when quitting from the gui or within python with the 
 command cmd.quit()
 How can I quit PyMol properly?

I know for a fact that the Mac take-down process is currently flawed, and 
frequently gives a bus error.  Because it only happens after you quit the 
program, its a low priority issue...

Not sure about Redhat.



RE: [PyMOL] Update to ScriptBox 0.3 for PyMOL

2002-06-20 Thread DeLano, Warren
 From: Kristian Rother []
 As suggested by Warren, i have made some improvements to the 
 which should integrate better into PyMOL now,

Thanks Kristian!

 On my page, there is also a 'quick and dirty' hack for PyMOL. allows to execute PyMOL commands from a shell. It 
 starts its 
 own thread and reads lines from a text file. This doesn't 
 work well, but 
 it works.

 Does anyone have a better idea to do this?

Try launching PyMOL with the -p option.  PyMOL will then accept commands on 
standard input using a separate thread, in a manner similar to what you 

See 'help launching' for other command line options.


RE: [PyMOL] Colors and ray-tracing

2002-05-28 Thread DeLano, Warren
My guess is that you may still be showing sticks in the original object, 
instead of just cartoons.  If you have the same overlapping representation in 
two objects, it isn't predictable which will show up in the ray-tracer, and you 
can get exactly this behavior, where you see one color in OpenGL and a 
different one in the raytracer.

Here is the general sequence of steps you'll want to follow to insure success:

load prot.pdb
create cpy,prot
show cartoon,prot
show sticks,cpy
color red,prot
color green,cpy

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: Peter Stogios []
 Sent: Tuesday, May 28, 2002 9:08 AM
 Subject: [PyMOL] Colors and ray-tracing
 This topic was touched on before but I'm still having 
 problems with it.
 Somebody asked how to color sticks differently from cartoons 
 and Warren
 explained that this can be done by creating duplicate 
 objects.  I managed
 to accomplish that, but when I ray-trace the image the 
 cartoon takes the
 same color as the stick does.  As soon as I move the 
 ray-traced image, it
 restores back to the different colors, as I want them.
 For example, I colored the cartoons in one object green, 
 while I showed
 only sticks in the duplicate object and colored a specific 
 residue stick
 blue.  When I ray-trace the image, the cartoon at that residue turns
 green, instead of staying blue.
 Is this a bug or how can I get around this?  Thanks in advance.
 Peter Stogios
 Dept. of Medical Biophysics, Univ. of Toronto
 Don't miss the 2002 Sprint PCS Application Developer's Conference
 August 25-28 in Las Vegas --
 PyMOL-users mailing list

RE: [PyMOL] problem importing pymol.cmd module

2002-05-06 Thread DeLano, Warren

   A present, you can't simply import the PyMOL program as a module.  You 
need to use PyMOL as your Python interpreter.

You can use Run from the File menu or the run command from within PyMOL.

PyMOLcd c:\some_directory

Since you are under windows, you can use the DOS/Win command shell:

C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe

# command-line only scripts

C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe -qc

- Warren

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: Sorich, Michael Joseph - SORMJ001 

Subject: [PyMOL] problem importing pymol.cmd module

I have just started to use PyMol. I wish link some scripts I have written in 
python with PyMol using PyMol’s API. From what I understand, all I need to do 
is import the module pymol.cmd and call the functions contained within.
However, when I attempt to import this module, I get the following error:
 from pymol import cmd
Traceback (most recent call last):
  File pyshell#0, line 1, in ?
from pymol import cmd
  File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\, 
line 137, in ?
import _cmd
ImportError: No module named _cmd
Where have I gone wrong? Any help would be appreciated.

RE: [PyMOL] Linux install problem

2002-05-03 Thread DeLano, Warren

   That is an unusual error.  I suspect it has something to do with your 
symbolic links, which isn't the most reliable way to solve the dependency 
problem.  Instead, delete those symlinks, and modify Rules.make to seek out the 
system libraries in the usual location.  Rules.linux-rh7x should be your 
starting point for Rules.make.


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: Gareth Stockwell []
 Sent: Friday, May 03, 2002 4:00 AM
 Subject: [PyMOL] Linux install problem
 I am having a problem installing PyMol 0.80 on my (Redhat 
 7.1) Linux box.
 I already have Tcl, Tk, Python 2.1, zlib and libpng so I just 
 made libglut 
 from the ext-0.79 package.
   cd $PYMOL_PATH/ext
   ./ glut-linux
 The GL libraries are in strange places on my system, so I made the 
 following links:
   ln -s /usr/lib/ $PYMOL_PATH/ext/lib/
   ln -s /usr/lib/ $PYMOL_PATH/ext/lib/
   ln -s /usr/X11R6/lib/modules/extensions/libGLcore.a \
 Then I built the PyMol program
   cd $PYMOL_PATH/pymol
   vi Rules.make
 The 'make' succeeds, but when I execute, I get
 Traceback (most recent call last):
 line 19, in ?
 import pymol
 line 137, in ?
 import _cmd
 ImportError: /usr/X11R6/lib/ shared object not open
 This shared object file exists - is there any reason why this 
 error should 
 P.S. I don't have root access on this system
  Gareth Stockwell
  PhD student, Thornton Group
  EMBL - European Bioinformatics Institute
  Wellcome Trust Genome Campus
  Cambridge CB10 1SD
  Tel 01223 492548

RE: [PyMOL] Let's Introduce Your Company To China Government

2002-05-03 Thread DeLano, Warren
 From: Marc Saric []

 2. Let's Introduce Your Company To China Government 
   ^ ^ ^ ^
 Shouldn't that have been filtered out?

Absolutely.  After digging into the settings, I found that SourceForge doesn't 
protect these lists by default (grumble), but I changed the settings so only 
list members will be able to post from now on.  Contact me directly if you have 
any trouble posting.  We lost about 5 subscribers from that PRC spam. 

- Warren

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] easy (?) question

2002-05-01 Thread DeLano, Warren
 From: Byron DeLaBarre []
 Anyone out there know how to prevent bonding of adjacent but 
 unconnected atoms in pymol?

Two step process:

1. edit the PDB file and replace ATOM   with HETATM
2. after the HETATM's add a single record CONECT following by nothing but a 
new-line.  This will signal PyMOL to expect explicit connectivity (of which 
there will be none).  In the future, if you need to specify connectivity 
explicitly, this is how you do it using a PDB file (CONECT records followed by 
connectivity info)

Note if you need to surface hetatms, set surface_mode=1 or alter 
(all),type='ATOM' followed by sort and rebuild.  Same for goes for meshes.

 And along those lines, anyone had success with showing a 
 Calpha trace?  I
 tried once but couldn't figure out how to get pymol to connect the
 individual Calpha atoms.  I think this must be easy to do  
 but I couldn't
 work it out at the time.

So long as the N and C atoms are also present, the ribbon representation can do 
this.  It looks for CA atoms three bonds apart to form the trace.   To get a 
linear C-alpha trace (no smoothing), set ribbon_sampling=1


RE: [PyMOL] H-bonds too thick

2002-04-10 Thread DeLano, Warren
 From: Mario Sanchez []

 I am drawing hydrogen bonds using command dist, but the rayied image
 has a too thick line to these interactions. I was not able to find the
 command to set the thickness of it, but I hope someone 
 (DeLano?) will be
 able to help me.

You can generally tweak fix hese kinds of issues using one of PyMOL's many 
settings -- most of them have verbose names.  Try Edit All under the settings 
menu for a complete list.  In this case:

set dash_radius=0.10

- Warren

Warren L. DeLano, Ph.D.

RE: [PyMOL] multiple MODEL files

2002-03-25 Thread DeLano, Warren
 From: Eckhart Guthöhrlein 

 I'm trying to use pymol for the display of pdb files 
 containing multiple 
 models using the MODEL card. Indeed, pymol reads in all 
 models in the file.
 Currently, I'm able to switch between them using the frame 
 command. Is 
 there a different way to do this? Something like next_model or 
 prev_model or show_model ...?
 Furthermore, I tried to use the selection command to access models.
The model operation in the selection command allows you to select objects by 
number -- not models in the sense of multi-model PDB files.  The first PDB file 
you load is model 1, the second is model 2, etc.  Sorry for the confusion.  
Model was a bad choice in terminology and should be replaced with an object 
operator instead.  However, the chemical python package uses model instead of 
object, so it's probably a hopeless case.

PyMOL treats multi-model PDB files like trajectories, in that each model is one 
state of the trajectory.  You can display them as a series of frames as you 
were doing.  You can use the left and right arrow keys to iterate through, or 
the forward and back commands, or press the play button.  You can use mset to 
display states in a different order, etc. 

 color red,(model 10)
 leads to
 SelectorSelect1-Error: Invalid Model
   PyMOL: abrupt program termination

That's a flat-out bug.  Thanks for finding it.  

 although model 10 exists and has been read in, as shown before by the 

As I indicated above, model/object 10 doesn't actually exist, but PyMOL 
certainly shouldn't crash...I'll fix that.

 How to access models in an atom selection?

You can't address atoms individually in one model or another without breaking 
them into separate objects.  You can do this using a Python loop and use the 
create command after loading the model file.

When you create an atom selection, you are essentially selecting all states of 
those atoms.  However, many commands take a state argument, which is the 
1-based index for which state you wish to operate on for the atom selection.  
This is what allows you to change the conformations of atoms in a particular 
state, for instance.  NOTE the PyMOL's atom selections can span any number of 

 Another question: Is there a way to list details about the currently 
 available objects? Like sequence, secondary structure, how many 
 models/chains/ etc.? And the current properties like colour, 
 charge etc. 
 of an atom selection? I just browsed the manual very quickly, 
 so sorry 
 if I overlooked the information.

The manual stinks.  Some volunteer with more time than myself needs to team up 
with me to create a decent manual -- but one can't complain too much about free 
software.  I can think of more than one company that will sell you an expensive 
closed-source license similar packages, and still not provide you with a decent 
manual.  If you prefer DeLano Scientific's open-source approach, then be sure 
to support it with effort or funding.

The key commands are alter, alter_state, iterate, and label -- and they 
represent the heart of PyMOL's built-in atom property manipulation capability.  
However, there are a bunch of other commands for manipulating coordinates and 

iterate (all),print name
iterate (all),print color
iterate (all),print partial_charge
iterate (name ca),print resn,resi,s

alter (all),vdw=vdw*0.5
alter (all),resi=int(resi)+10
alter (chain E),chain='C'

alter_state 1,(all),x=x+2.0

label (name ca),resi

label (all),name
label (all),%1.2f%vdw

In all cases, a Python expression is evaluated for each atom in the selection.

See help iterate, etc., but note that the docs are incomplete.  To see all 
the properties which can be printed or altered, load a model and then try:

iterate (index 1),print locals().keys()

Note that you can also obtain and manipulate a complete copy of any model (erg, 
object) at the Python level, using Python code like:

from pymol import cmd

m = cmd.get_model('old')


RE: [PyMOL] RNA and Pseudo-atom Models

2002-02-28 Thread DeLano, Warren
Busy day on the list : ) I'll take this one...

 From: Albion Baucom []

Nice to hear from you Albion, glad to see you're finally getting a
chance to try the package.

 I want to make high resolution, smooth (high frame rate) 
 playing movies of
 the Ribosome. 

Great -- PyMOL should be up to the task provided that you've got a fast
machine with tons of RAM.

 Ideally I would like to move seperate objects 
 in the view
 separeately, that is have things dock in the movies. I dont know if
 PyMol will do this yet ...

Yes, it can do this using the translate, origin, and rotate commands.
Unfortunately the docs are incomplete, so I recommend you take a look at
the Python code in modules/pymol/ (rotate, translate) and (origin) for the specific calling conventions.  

def rotate(axis='x',angle=0.0,selection=all,
def translate(vector=[0.0,0.0,0.0],selection=all,
def origin(selection=(all),object=None,position=None):

Here's a key bit of information for these commands:  If you pass the
object name using 'object=...', then you'll translate the entire object
matrix.  If instead you pass in a selection with object still equal to
NULL, then you'll translate the atom coordinates within the object.  

This functionality is still primitive, but I think it will do the around with them for a while, see if you can get them to do
what you need.

 Now, the rRNA I have is phosphorus atom only, with some 
 allatom proteins
 some CA-only proteins.

Ugh -- this is something PyMOL doesn't yet handle well, and you're the
third person to draw my attention to this in the last couple weeks!
 PyMol opens the psueudo-atom rRNA as a cloud of atoms, 
 presumably because
 it does not know how to bond these files. That is my first 
 question. How,
 and what do I modify (bond definition file) to make it bond 
 the adjacent
 atoms of the phosphorus only backbone? 

There is no bond definition file (yet -- this will be changed in the
future).  Except for HETATMS, PyMOL connects atoms based on proximity,
not dictionary lookups.  The quick-and-dirty solution is to add explicit
CONECT records for the atoms into the PDB file for the phosphates.
 My second question for now is once I bond it, will Pymol be 
 able to render
 a cartoon using the P atoms to interpolate?

Nope, PyMOL won't be fooled by such trickery.  It will only draw ribbons
between phosphates separated by six bonds (i.e. in real nucleic acids).
Minor code changes will be required to accomplish what you're looking
for. You might be able to comment-out the line in RepCartoon.c, but I
haven't tested the idea. 

Look for:

 My only workaround ideas now are to take the pseudo-atom 
 model, use CNS
 (generate.inp) to build in the rest of the bases, use that to generate
 the cartoon, and undisplay the stick representation (which of 
 course will
 have completely bogus conformations). Im not sure what biases 
 the built in
 bases will impose on the cartoon if PyMol uses them to interpolate the

Unfortunately for now you'll have to provide full coordinates in order
to get ribbons.  This is probably a decent way to go.

 At some point I would like to draw pseudo-bonds between base-paired
 pseudo-atoms, but I will see if I can do the above before that.

Such bonds can be drawn using the dist command.


RE: [PyMOL] using external python interpreter to control pymol ??

2002-02-19 Thread DeLano, Warren
NOTE: the following is unix-specific.

This is a common problem with PyMOL.  Right now it is impossible (in
practice) to use PyMOL as merely an imported module within an external
interpreter (i.e. without using instead of python to
invoke the interpreter).  This will be fixed in a later version.

For example:

python END
from pymol import cmd

...will fail.

For now, you need to use the script to launch your Python
interpreter if you are going to use PyMOL.

Normal commands are interpreted first by PyMOL and then passed to Python
if PyMOL doesn't recognize the command.  You can skip PyMOL evaluation
with a preceeding /, which is almost equivalent to typing the same
command (without a preceeding slash) in a Python interpreter:

print hello
/print hello

However, you can run native Python script in external using the run


...which is almost equivalent to typing:


...on the unix or windows command shell, or by issuing


...from within an existing Python interpreter.


The key difference between 

python on command line # on commmand line
run   # in PyMOL

is that default evaluation in PyMOL currently takes place in the pymol
module, not __main__.  Right now there is no easy way to start a
process in the __main__ module.  I will remedy this in the next public
release, and probably make __main__ the default namespace for the run
command (so long as that doesn't break anything).

You can however, force evaluation of your script to occur in its own


...or in a local namespace:


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

 From: Ingo Dramburg []
 I want to include my own modules into PyMOL for visualization
 If I try to use the pymol.cmd module to control a running
 PyMOL process from an external python interpreter
 I always get a segmentation fault. (SuSE 7.2, Python 2.0)
 Everything else works fine.
  from pymol import cmd
 segmentaion fault
 Is it possible to do such things in general or is it possible
 to switch to a 'native' python mode in the PyMOL window to enter 
 python commands directly :-). 
 The next question is how can I pass selections from PyMOL to external 
 scripts to do calculations that are not supported by PyMOL 
 and later back to
 PyMOL for visualization.
 Thanks you for any help,
 Ingo Dramburg 
 Institute of Pharmaceutical Chemistry
 Philipps-University Marburg
 Marbacher Weg 6, D 35032 Marburg, Germany
 Tel. + 49 6421 282 1313
 Fax  + 49 6421 282 8994
 PyMOL-users mailing list

RE: [PyMOL] Installing from source on a linux box

2002-02-04 Thread DeLano, Warren

   Try checking out a new copy of the source code from the current CVS
repository -- the Makefiles have been simplified somewhat, so
compilation under Linux may go easier.  You should only need to change
the Python version in one place : )

Read INSTALL.linux-rh7x


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: Michael George Lerner []
 Sent: Monday, January 28, 2002 1:44 PM
 Subject: [PyMOL] Installing from source on a linux box
 I have PyMol up and running on my windows partition .. the 
 was super easy.  Now, I want to set it up on my Linux 
 partition.  I have
 Mandrake 8.1 installed, which means that my default python 
 version is 2.1.
 It also means that many things (Numeric, zlib, etc..) are 
 for me.
 So, I downloaded the PyMol sources and tried to install it.  In the
 external packages bit, it looked like the only thing I need 
 is glut.  So,
 I changed the setenv BASE line in to point to the 
 right place
 (/home/mglerner/src/pymol/ext in my case) and changed the setenv
 PYMOL_TARGETS line to say glut-linux and did ./  I also
 tried ./ glut-linux for variety .. both seemed to work.
 Then I went up a directory into the main pymol directory.  I 
 then moved
 Rules.linux to Rules.make and edited it.  There were many instances of
 -lpython1.5 .. I changed all of them to -lpython2.1.  It was 
 still having
 some trouble finding libpython2.1, so I added 
 to the LIB_DIRS line.  After typing make, things get pretty 
 far, but it
 doesn't get far enough.  I wasn't sure how many of the error 
 messages to
 include, but I've tacked on the last screen or so of output 
 at the end of
 this message.
 There were some things that made me think that various parts 
 of this build
 process were really looking for python sources in the ext 
 directory, so I
 placed a copy of the python 2.1 sources there just in case.  It didn't
 seem to help.
 Sorry if this is a dumb question,
 -- begin output from make --
 make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
 rm -f *.o *~
 rm -f *.a tags TAGS config.c Makefile.pre python sedscript
 rm -f *.so *.sl so_locations
 VERSION=`../../ext/bin/python -c import sys; print 
 sys.version[:3]`; \
 installdir=`../../ext/bin/python -c import sys; print sys.prefix`; \
 exec_installdir=`../../ext/bin/python -c import sys; print
 sys.exec_prefix`; \make -f ./ VPATH=. srcdir=. \
 installdir=$installdir \
 exec_installdir=$exec_installdir \
 /bin/sh: ../../ext/bin/python: No such file or directory
 /bin/sh: ../../ext/bin/python: No such file or directory
 /bin/sh: ../../ext/bin/python: No such file or directory
 make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
 make[3]: *** No rule to make target 
 `/lib/python/config/Makefile', needed
 by `sedscript'.  Stop.
 make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
 make[2]: *** [boot] Error 2
 make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
 make[1]: *** [make-modules] Error 2
 make[1]: Leaving directory `/home/mglerner/src/pymol/contrib'
 make: *** [.contrib] Error 2
 -- end output from make --
 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
|   / \ | mler...@umich
 PyMOL-users mailing list

RE: [PyMOL] ray doubts

2002-01-18 Thread DeLano, Warren

  Yes, ray makes a huge difference in quality.  You get true specular
reflections (not just OpenGL interpolations), you get perfectly round
spheres, you get shadows, you get clean transparent surfaces (without
artifacts), and you get better depth-cue fogging (although with light
backgrounds you'll probably want to set ray_trace_fog to 0).

  It renders all objects in the scene except for labels (which it is
incapable of handling at present).

  Yes, you need to render (ray-trace) again after the image is rotated.
(If you rotate an object, the shadows move).  

  Most of the figures you see in the top journals are generated using
Molscript and Raster3D (or PovScript and PovRay) using a process very
similar to the ray command.  PyMOL simply makes creation of such
figures much easier since you only need one program and you get to
preview the exact image before-hand (set orthoscopic=0 to get a
pixel-for-pixel match between OpenGL and the ray tracer).


Warren L. DeLano, Ph.D.

 From: Ricardo Aparicio []
 Dear PyMol users,
 as stated in the manual, command
  ray creates a ray traced image of the current frame. This
can take some time (up to several minutes, depending on image
 My question is:
 - is it necessary? Does it make great difference in the final 
 quality of
 figures published (in the case of a paper)?
 - does it renderize(?) all the active objects in the screen?
 - after finished ray process, if the image is rotated, is it necessary
 to renderize again (I think no, just to confirm)
 Many thanks,
 Ricardo Aparicio
 PhD Student - USP 
 Sao Paulo - Brazil
 PyMOL-users mailing list

RE: [PyMOL] pymol on SGI

2001-12-18 Thread DeLano, Warren

   I think your problem is one of two possibilities: either your
LD_LIBRARY_PATH is not being set correctly by, or your shared object isn't valid.  

You might try using linking against a static Python library as described

Good luck!

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: Danny G Smith []
 Sent: Tuesday, December 18, 2001 12:52 PM
 Subject: [PyMOL] pymol on SGI
 I have complied pymol-0_73, with ext-0_51, useing the following in the ext subdirectory.  When I try to run I get
 the following message:
 omega[272]:/misc/local/src/pymol/pymol % ./
 Traceback (innermost last):
   File /misc/local/src/pymol/pymol/modules/, 
 line 6, in
 import pymol
 /misc/local/src/pymol/pymol/modules/pymol/, line 24,
 in ?
 import _cmd
 ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
 Fatal Error: Cannot Successfully map soname '' 
 under any
 of the filenames
 omega[273]:/misc/local/src/pymol/pymol %
 Any help would be appreciated.
 # in ext directory
 # Build script for making PyMOL External dependencies
 # (can't do this stuff in a makefile cause we need to define
 #  some important environmental variables)
 #- Paths -
 # --- Base
 #setenv BASE /home/local/export/ext
 setenv BASE /misc/local/src/pymol/pymol/ext
 #- Targets 
 # -- Linux with just Tcl/Tk
 # setenv PYMOL_TARGETS tcl tk zlib python distutils numpy 
 pmw png-linux
 # -- Linux with Tcl/Tk and wxPython
 # setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw 
 glut-linux glib gtk wxgtk wxpython
 # -- SGI/IRIX with just Tcl/Tk
 # setenv PYMOL_TARGETS tcl tk zlib python distutils numpy 
 pmw png-irix
 # -- SGI/IRIX with Tcl/Tk and wxPython
 setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw png-irix
 glut-irix glib gtk wxgtk wxpython
 #- For creation of a shared python library --
 # --- Linux
 #setenv LDALLFLAGS --whole-archive
 # --- SGI/IRIX
 setenv LDALLFLAGS -n32 -all
 #- Misc --
 # --- SGI/IRIX
 setenv SGI_ABI -n32
 setenv MAKE gmake
 setenv CXX CC
 # --- Linux
 #setenv MAKE make
 #- Path pre-emption critical for building gtk/wx -
 setenv PATH ${BASE}/bin:$PATH
 setenv LD_LIBRARY_PATH ${BASE}/lib
 #- Build 
 $MAKE -f $1
 Danny G Smith  
 UNIX Systems Administrator
 Crystallography Dept Oklahoma Medical Research Foundation
 phone 271-8954 fax 271-7953
 UNIX air conditioned environment, keep the windows closed
 PyMOL-users mailing list

RE: [PyMOL] CSD .dat files

2001-12-14 Thread DeLano, Warren

   .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/  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.


Warren L. DeLano, Ph.D.

 From: Ross, Charles []
 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?
 Charles Ross
 Department of Structural Biology
 St. Jude Children's Research Hospital
 PyMOL-users mailing list

[PyMOL] Learning Python for PyMOL

2001-12-10 Thread DeLano, Warren
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

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.

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

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.


-- 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))

-- END .emacs excerpt

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 
 Sent: Monday, December 10, 2001 7:40 AM
 To: Glen L. Prosise
 Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux)
 Last night I posted binaries of PyMOL 0.73 for Windows and 
 Linux to the
 downloads page. 
 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.  
 PyMOL-users mailing list