pymol-users Mailing List for PyMOL Molecular Graphics System

	
I will be giving a talk at Stanford on PyMOL and Open-Source this
Wednesday, as part of the Computer Systems Laboratory Colloquium.  This
is a high-profile seminar series, which this year inludes leaders
from Microsoft, Intel, CNN, IBM, VA Linux (now VA Software) and a
variety of major universities.  It should be very encouraging to everyone
involved that the PyMOL phenomenon has been deemed important enough
to merit coverage in such a venue. 

If you are fortunate enough to live in the SF Bay Area, then please
consider attending.  Otherwise, be sure to check out the streaming version
on the web, which should become available shortly after the talk.

"Creating Open-Source Tools for Drug Discovery:   
 How Free Software Might Save Your Life"

4:15PM, Wednesday, April 3, 2002 
NEC Auditorium, Gates Computer Science Building B03

http://www.stanford.edu/class/ee380/Abstracts/020403.html

Cheers, 
Warren

Updated Abstract:

Biology and medicine are being revolutionized by technological advances
such as the human genome project, DNA chips, proteomics, automated
synthesis, and high-throughput screening technologies.  As a result,
modern research is becoming profoundly information-driven and heavily
software-dependent.  However, many key software tools for analyzing
biological and chemical information are not widely accessible because of
continued adherence to traditional, restrictive approaches to software
development and distribution.

In order for biomedicial science to progress at an optimal pace, we must
adopt a new paradigm for creation and dissemination of core computational
technologies.  During the past decade, while chemists and biologists were
busy developing new experimental methods, computer scientists invented
powerful new software technologies that will enable a more
research-oriented approach to biomedical software.  Specifically,
collaborative internet development tools and modular dynamically-linked
programming languages make open-source development a realistic and
superior means by which scientists can create interoperable tools and
share them in true academic spirit.  The internet provides the foundation
for formation of global communities around specific projects, and thanks
to the proliferation of high-bandwidth connections, distribution costs
have been reduced to near zero.

The PyMOL molecular graphics system is a concrete and successful example
of this new paradigm for scientific software development.  Here I explore
how PyMOL will specifically help to spread the open-source vision, and how
open-source developers may be able to eventually assemble a complete
platform for biomedical science through sponsored development of
critical components.  Also addressed are some of the economic issues
surrounding open-source development, and the important role to be played
by independent open-source software publishers. 

On Tue, 26 Mar 2002, Nat Echols wrote:

> Is there any way to color by secondary structure?  I know of other

It's a snap:

# first, load a structure with defined SS

load $PYMOL_PATH/test/dat/1tii.pdb
hide
show cartoon

# now color

color green
color red,ss h
color yellow,ss l
set cartoon_discrete_colors=1

NOTE: the last command turns off color annoying color blending between
secondary structure elements.

Cheers,
Warren

Is there any way to color by secondary structure?  I know of other
programs that do this (Molmol, for example- though its colors are
hideous); I'd be happy using a scripted solution if that's easiest.  I'm
guessing there's some easy way to loop through residues or atoms and
determine what their structure assignment is, but I never figured out how
to access this info.

If there isn't anything that'll do this, perhaps I'll just write it.

-Nat

Potential OSX PyMOL Users

I made a mistake yesterday when I stated that the demo requires a G4.  =
At least one fast G3 has been able to run the demonstration.  If there =
are other users out there with G3-based macs, feel free to respond to my =
inquiry regarding pre-release testing (but do please still indicate your =
CPU and graphics hardware).  Backwards compatability with older hardware =
is worth exploring, but don't expect great performance.

-Warren
wa...@de...

> From: Eckhart Guth=F6hrlein=20

> I'm trying to use pymol for the display of pdb files=20
> containing multiple=20
> models using the MODEL card. Indeed, pymol reads in all=20
> models in the file.
> Currently, I'm able to switch between them using the frame=20
> command. Is=20
> there a different way to do this? Something like next_model or=20
> prev_model or show_model ...?
> Furthermore, I tried to use the selection command to access models.
=20
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)
>=20
> leads to
>=20
> SelectorSelect1-Error: Invalid Model
>   PyMOL: abrupt program termination

That's a flat-out bug.  Thanks for finding it. =20

> although model 10 exists and has been read in, as shown before by the=20
> message

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 objects...

> Another question: Is there a way to list details about the currently=20
> available objects? Like sequence, secondary structure, how many=20
> models/chains/ etc.? And the current properties like colour,=20
> charge etc.=20
> of an atom selection? I just browsed the manual very quickly,=20
> so sorry=20
> 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 geometries.

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

alter (all),vdw=3Dvdw*0.5
alter (all),resi=3Dint(resi)+10
alter (chain E),chain=3D'C'

alter_state 1,(all),x=3Dx+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 =3D cmd.get_model('old')
m.atom[0].name=3D'C1'
cmd.load_model(m,'new')

Cheers,
Warren

Hi all,

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.

color red,(model 10)

leads to

SelectorSelect1-Error: Invalid Model
  PyMOL: abrupt program termination

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

ObjectMolReadPDBStr: read MODEL 10

How to access models in an atom selection?

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.

I'm using pymol 0.78 running under IRIX 6.5.

Eckhart

Friends,

I need some volunteers to test a pre-release OSX port on their Mac =
hardware.  This is to determine whether or not the core module is stable =
across a range of hardware systems.  The native port typically offers =
10-50X better OpenGL performance than existing versions.

If you want be a tester, then please respond to me directly with an =
exact description of your hardware, including the type of graphics card =
you have. =20

You will need a G4 based machine with a graphics accelerator card (most =
Macs have one).  MacOSX 10.1.x is likely required.  Most importantly, =
you will need a fast internet connection (T1/Cable/1.5Mb DSL) capable of =
downloading a ***50 MB*** disk image.=20

Note that this early port does NOT contain any menus or buttons other =
than those which exist inside the OpenGL window.  Thus, although the =
port is fully functional for graphics, editing, scripting, and =
rendering, the external GUI features are nonexistent.  You will need to =
use the command line (pwd, cd, ls, & load) to navigate the file system =
and open files.

The native port is completely separate from GNU/Darwin and will not =
conflict if you have the GNU/Darwin version of PyMOL installed.

Cheers,
Warren

Hello there,
I am trying to install pymol under red hat 7.2 using
the rpm file and I have the message:
'libGLcore.so.1   is needed by
pymol-0.78-3.rh72.py21n'

this library it is in /usr/lib, so what's wrong?
Hugo

__________________________________________________
Do You Yahoo!?
Yahoo! Movies - coverage of the 74th Academy Awards®
http://movies.yahoo.com/

On Fri, 22 Mar 2002, Mario Sanchez wrote:
> I am trying to find some program like Chemdraw or ACD chemscketch to
> Linux. I already find some, but all not so good like these.

Mario-

I know of three: chemtool, gchempaint, and xdrawchem:

http://www.uni-ulm.de/~s_tvolk/chemtool.html.
http://jean.brefort.free.fr/info/en/gcp/index.html
http://www.prism.gatech.edu/~gte067k/xdrawchem/

Maybe SAL or gnome.org will have others.

Ciao,
-- 
Reece Hart, http://www.in-machina.com/~reece/, GPG:0x25EC91A0

Sorry 'couse it is not a directly related question.
I am trying to find some program like Chemdraw or ACD chemscketch to
Linux. I already find some, but all not so good like these.
Can anyone give me some tip?

Thank you in advance.
--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

Dear Folks (perhaps especially Warren!),

I'm trying to write a script for python that happens to use the
Computational Crystallography Toolbox (cctbx) and its python interface.
I keep getting dumped out of pymol with no error message whatsoever.

The script, test_cell.py, is an abbreviated script to try to sort out
the problem when I was running something larger. All it contains is

	#### test_cell.py
	from cctbx import uctbx, sgtbx
	a =3D 31.1
	b =3D 52.5
	c =3D 85.3
	alpha =3D 90.
	beta =3D 100.
	gamma =3D 90.
	sg =3D 'P21'
	Unitcell_obj =3D uctbx.UnitCell((a,b,c,alpha,beta,gamma))

Here is an exact transcript from the terminal window:

   % pymol
  =20
    PyMOL(TM) Molecular Graphics System, Version 0.78.
    Copyright (C) 1998-2002 by DeLano Scientific.
    All Rights Reserved.
   =20
       Created by Warren L. DeLano, Ph.D.=20
   =20
       Other Major Authors and Contributors:
  =20
          Ralf W. Grosse-Kunstleve, Ph.D.
   =20
       This software is open source and freely available.
       Updates can be found at "http://www.pymol.org".
   =20
       Is PyMOL a free and open-source project worthy of your support?
  =20
       Then visit the home page to learn what you can do to contribute!
  =20
       Also, please cite PyMOL in publications and presentations:
  =20
          Warren L. DeLano "The PyMOL Molecular Graphics System."
          DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
  =20
       Enter "help release" for release notes (PLEASE READ!).
       Enter "help commands" for a list of commands.
       Enter "help <command-name>" for information on a specific command.
  =20
    Hit ESC anytime to toggle between text and graphics.
  =20
    OpenGL based graphics front end:
     GL_VENDOR: NVIDIA Corporation
     GL_RENDERER: RIVA TNT2/PCI/SSE
     GL_VERSION: 1.3.0
   PyMOL>set bg_rgb, .5 .5 .5
    Setting: bg_rgb set to [ 0.50000, 0.50000, 0.50000 ].
   PyMOL>viewport 800, 600
   PyMOL>set cgo_line_radius, 0.05
    Setting: cgo_line_radius set to 0.05000.
   PyMOL>set line_width, 2
    Setting: line_width set to 2.00000.
   PyMOL>set cgo_line_width, 2
    Setting: cgo_line_width set to 2.00000.
   PyMOL>run test_cell.py

   [134]%

The '134' in brackets above is the value of the $status variable that
gets set by the shell on the exit from pymol.  (This is the only clue
to the problem that I can think of, but I don't know what it means.)

I have verified that the unwanted exit happens when the 'Unitcell_obj'=20
instance gets created in the line:

   Unitcell_obj =3D uctbx.UnitCell((a,b,c,alpha,beta,gamma))

by typing it alone (with it commented out of the script). I've tried a
different call to the sgtbx class:

   sgsymb =3D sgtbx.SpaceGroupSymbols(sg)

and it has exactly the same effect.

Anybody have a clue that they'd like to share, or some other test that
could be done for debugging purposes?

Cheers,
Robert
--=20
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Thanks to all who replied.  I was going by the html manual, which said
that pymol only reads XPLOR/CNS maps.  I know that the manual is
out-of-date --- I should have dug harder. 

Thanks,

Ben

I believe pymol reads ccp4 maps...  at least, it did a few months ago :)
To do the conversion off-line, you'd have to install ccp4, then you
could use 
something like xdlmapman.  

phx.


> -----Original Message-----
> From: Ben Cornett [mailto:ac...@em...]
> Sent: Wednesday, March 20, 2002 12:48 PM
> To: pym...@li...
> Subject: [PyMOL] ccp4 map?
> 
> 
> Can anyone offer some advice on how to convert a ccp4 map to an XPLOR
> map for import into pymol?  I know next to nothing about
> crystallography, so perhaps the question is not even meaningful.
> 
> Thanks,
> 
> Ben
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


----------
This message contains confidential information and is intended only for
the individual named. If you are not the named addressee you should not
disseminate, distribute or copy this e-mail. Please notify the sender
immediately by e-mail if you have received this e-mail by mistake and
delete this e-mail from your system. E-mail transmission cannot be
guaranteed to be secure or error-free as information could be
intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
contain viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this message, which arise as a
result of e-mail transmission. If verification is required please
request a hard-copy version. 

Can anyone offer some advice on how to convert a ccp4 map to an XPLOR
map for import into pymol?  I know next to nothing about
crystallography, so perhaps the question is not even meaningful.

Thanks,

Ben

> From: Mirek Cygler [mailto:mir...@br...]

> 	I wonder if there is a command equivalent to "turn" in=20
> molscript? I would
> like to show a cartoon view of my molecule with some=20
> sidechains. When I use
> "show cartoon" and include a selection of sidechains, they=20
> appear far from
> the backbone worm.

Turn off "smooth loops" and "flat sheets" using the cartoon menu or the
commands

set cartoon_smooth_loops=3D0
set cartoon_flat_sheets=3D0

> 	Can I change the name of the object after loading the=20
> molecule into PyMol?

No, but you can create an identical copy and delete the original.

load test1.pdb
create test2=3Dtest1
delete test1

> When I save the molecule can I also save the secondary=20
> structure assignments
> with it?=20

I wish...this is on the "to do" list.

> Is there a facility within PyMol to detect secondary=20
> structure
> automatically?

Sort of.  util.ss make an attempt at it, but the algorithm in
unvalidated (something I just cooked up one morning).  For publication,
I encourage users to obtain secondary structure assignment via an
accepted algorithm.

load test1.pdb
util.ss test1
show cartoon

- Warren

Hello,
	I wonder if there is a command equivalent to "turn" in molscript? I would
like to show a cartoon view of my molecule with some sidechains. When I use
"show cartoon" and include a selection of sidechains, they appear far from
the backbone worm.
	Cheers,

                                                Mirek

Hi,
	Can I change the name of the object after loading the molecule into PyMol?
When I save the molecule can I also save the secondary structure assignments
with it? Is there a facility within PyMol to detect secondary structure
automatically?
	Thanks for your help,

                                                Mirek

Mario,
> From: Mario Sanchez [mailto:sa...@if...]

> I have some questions using pymol and I wonder if someone can give me
> some help.
>=20
> At first I would like to know if there are any way to define=20
> more colors
> than that appearing in the menu. Is there some kind of "rgb"=20
> definition,
> for exemple?

the "set_color" command:

set_color khaki,[0.95,0.9,0.7]

> I also tried to change the colors of the sticks only, without success.
> When I chance the colors of the atoms in side chains it works, but
> changing color of carbon alpha causes change in cartoon too.=20
> Is there a
> way to do it?

Not with a single object, but remember that it is trivial to make copies
of objects in PyMOL which are shown using different representations and
coloring schemes.

In this case, create a copy of the object, then show the ribbon on the
original with one color scheme, and then show the sticks on the copy:

load orig.pdb
create cpy,(orig)
hide
show cartoon,orig
show sticks,cpy

You can now color the two independently.

> Finally I didn't find a way to put labels in residues -- like Tyr-25
> beside a tyrosine -- and to make "ray" of it.=20

You got me there: vectorized labels are on the TO DO list, but for now
you'll need to add labels manually.  The normal labels won't work
because they are rasterized into the OpenGL buffer...

Cheers,
Warren

I have some questions using pymol and I wonder if someone can give me
some help.

At first I would like to know if there are any way to define more colors
than that appearing in the menu. Is there some kind of "rgb" definition,
for exemple?
I also tried to change the colors of the sticks only, without success.
When I chance the colors of the atoms in side chains it works, but
changing color of carbon alpha causes change in cartoon too. Is there a
way to do it?
Finally I didn't find a way to put labels in residues -- like Tyr-25
beside a tyrosine -- and to make "ray" of it.=20

I will appreciate very much any suggestion.

--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

Here is what is going on: PyMOL's atom selection mechanism has a set of
keywords (name,resi,chain,model,etc), which includes "b" and "q" --
B-factor and occupancy.   An object named "b" gets confused with the
"b" keyword.  Normally you are able to simply use an object name in a
selection, but with a object named "b", you'll need to prefix
it with the "model" keyword to make it clear what you're asking for...

load b.pdb

# ambiguous:
color red,(b)

# unambiguous:
color red,(model b)

It is an embarassing design deficiency, but most of the time, the
convenience of not using the "model" keyword is probably worth
it.  However, PyMOL should probably inform you if/when there is a
name-space conflict like this : )

Cheers,
Warren

On Wed, 13 Mar 2002, Robert Campbell wrote:

> 
> Lari Lehti? <le...@ma...> [2002-03-13 08:40] wrote:
> > Just a funny thing...
> > 
> > If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
> > an error:
> > 
> > Selector-Error: Misplaced ).
> > Selector-Error: Malformed selection.
> > ( ( ( byres ( b )<--
> > 
> > If I rename the file and load it, coloring works fine.
> > 
> 
> I noticed the same problem if I had read in any file name, but created a
> selection named "b".  I don't do that now!  :)  I guess "b" must be some
> other predefined object?
> 
> Cheers,
> Robert
> 

Lari Lehti? <le...@ma...> [2002-03-13 08:40] wrote:
> Just a funny thing...
> 
> If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
> an error:
> 
> Selector-Error: Misplaced ).
> Selector-Error: Malformed selection.
> ( ( ( byres ( b )<--
> 
> If I rename the file and load it, coloring works fine.
> 

I noticed the same problem if I had read in any file name, but created a
selection named "b".  I don't do that now!  :)  I guess "b" must be some
other predefined object?

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Just a funny thing...

If I try to color my cartoon with rainbow. The file name can't be b.pdb. I get
an error:

Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ( ( byres ( b )<--

If I rename the file and load it, coloring works fine.

-Lari-

On Mon, Mar 11, 2002 at 10:47:17AM -0800, DeLano, Warren wrote:
[..]
> # Python code for reading an SD file with
> # identifier as separate SD field 'MOLID' 
[..]

Brilliant, now I only have to generate some environment around. Thanks!

Szilva

By default, PyMOL creates single bonds when joining fragments.  To
change a bond valence, CTRL-right click on the bond to select it.  You
should see a "ring" about the bond.  Then press CTRL-W to cycle through
the possible bond valences: single, double, triple.

Note that it is essentially impossible right now to build complex
molecules in PyMOL without using some external molecular minimization
and mechanics program, since the "molecular sculpting" feature can only
maintain pre-existing atomic geometries. =20

For coarse modeling of protein-ligand interactions, I tend to use PyMOL
to draw the initial covalent structures, use MacroModel to perform
energy minimization, and then return the structure to PyMOL for purposes
modeling the complex.

- Warren

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



> -----Original Message-----
> From: Guillaume Michaud [mailto:r1...@em...]
> Sent: Monday, March 11, 2002 12:43 PM
> To: pym...@li...
> Subject: [PyMOL] Create a double bond
>=20
>=20
> PLEASE WRITE BACK TO=20
> rp...@ma...
>=20
> Hi,
>=20
> I was just wondering how to create a=20
> double bond between two atoms (for=20
> example between a carbon and an oxygen=20
> or C=3DC).
>=20
> Thankx
> r1ck5p
> --=20
>=20
> _______________________________________________
> Sign-up for your own FREE Personalized E-mail at Email.com
> http://www.email.com/?sr=3Dsignup
>=20
> Travelocity.com is giving away two million travel miles.
> http://ad.doubleclick.net/clk;3969773;6991039;g?http://svc.tra
velocity.com/promos/millionmiles_main/0,,TRAVELOCITY,00.html



_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

PLEASE WRITE BACK TO 
rp...@ma...

Hi,

I was just wondering how to create a 
double bond between two atoms (for 
example between a carbon and an oxygen 
or C=C).

Thankx
r1ck5p
-- 

_______________________________________________
Sign-up for your own FREE Personalized E-mail at Email.com
http://www.email.com/?sr=signup

Travelocity.com is giving away two million travel miles.
http://ad.doubleclick.net/clk;3969773;6991039;g?http://svc.travelocity.com/promos/millionmiles_main/0,,TRAVELOCITY,00.html