pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] H-bonds too thick

[DeLano, W. <wa...@su...>]

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

> 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=20
> (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=3D0.10
ray=20

- Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

[PyMOL] H-bonds too thick

[Mario S. <sa...@if...>]

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.

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

[PyMOL] RE: question: how to save unfinished job

[DeLano, W. <wa...@su...>]

=20
From: Yunfeng Hu [mailto:yu...@uc...]

>I've tried a couple graphic programs and find that pymol is very
> powerful. I wonder how I can save the unfinished job and work
> on it next time I open pymol. Thanks!

Yunfeng,

    Session save/restore isn't yet possible with PyMOL, but it is =
planned.  For now, just open a "Log" file which records your actions =
(File menu).  You can then Run or Resume the log file to pick up where =
you left off, and you can edit the log file using a text editor.

- Warren

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20

[PyMOL] Release v0.80 (Windows only for now)

[Warren L. D. <wa...@su...>]

Sorry about the two-month release drought -- the native OSX port has been
chewing up most of my development time lately.

I just posted a Windows build of PyMOL v0.80 along with a source tarball.  

NOTE: This release is not well tested [ that's your job! :-) ], so please
be cautious when upgrading, particularly if you are counting on PyMOL to
function on critical tasks.  I'll post binaries for other platforms
after giving this release a week or two to shake out.

v0.80 is mainly a bug-fix release, but it has few nice new features:

- "align" command attempts automated sequence and refined structure
  alignment.  Be sure to let me know what kind of mileage you get out of
  this highly experimental feature.  "help align" for info.

- optional flat-capped cylindrical helices in cartoon ribbons

- "command-name ?" will display the command's arguments -- this may help
  with undocumented commands, or jostle your memory on occasion...

- better handling of three-atom waters found in some PDB files along
  with improved connectivity for other hydrogens (fewer extra bonds).

- molecular sculpting now does a reasonable job with -CN and -C#C- 

- menu option for "white background" 

- ray-tracable 3D text accessible to developers using the CGO module
  (if you know Python, feel free to consult me on usage)

- many minor bug-fixes

Remember, new releases don't just happen spontaneously.  If PyMOL is
meeting an important need of yours, then you should protect your
interests by supporting the project with direct effort or funding  
( http://www.pymol.org/donate.html ). 

Cheers,
Warren

RE: [PyMOL] Cell

[DeLano, W. <wa...@su...>]

# load a molecule with crystal data

load $PYMOL_PATH/test/dat/1tii.pdb,mol1

# show cell

show cell,mol1

# zoom out

zoom all,30

# change object color using explicit name (changes cell too)

color red,mol1

# now restore atom coloring (doesn't change cell)

util.cbag mol1

# for OpenGL rendering

set cgo_line_width=3D3

# or for raytracing...

set cgo_line_radius=3D0.4

ray

# - Warren


> -----Original Message-----
> From: Mario Sanchez [mailto:sa...@if...]
> Sent: Monday, April 08, 2002 1:24 PM
> To: pymol list
> Subject: [PyMOL] Cell
>=20
>=20
> I would like to know if anyone knows how to set up cell thickness and
> color. I am trying to generate a picture of a packing and I would like
> to show the unit cell in a white background.
> Thanks.
> --=20
> Mario Sanches,  PhD Student
> Protein Crystallography Group
> S=E3o Paulo University, S=E3o Carlos Physics Institute
> Phone:  +55 (16) 273 9868
> sa...@if...
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Cell

[Mario S. <sa...@if...>]

I would like to know if anyone knows how to set up cell thickness and
color. I am trying to generate a picture of a packing and I would like
to show the unit cell in a white background.
Thanks.
--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

[PyMOL] Cell

[Mario S. <sa...@if...>]

I would like to know if anyone knows how to set up cell thickness and
color. I am trying to generate a picture of a packing and I would like
to show the unit cell in a white background.
Thanks.
--=20
Mario Sanches,  PhD Student
Protein Crystallography Group
S=E3o Paulo University, S=E3o Carlos Physics Institute
Phone:  +55 (16) 273 9868
sa...@if...

RE: [PyMOL] e-density around atoms

[DeLano, W. <wa...@su...>]

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

> I am trying to draw an eletronic density around some specific atoms
> only, but pymol always draw a box in the region. I am using the
> following comand:
>=20
> isomesh den, map21, 1.0, (c;A & i;12 & !n;n,o,ca,cb |  c;A & i;89 &
> !n;n,o,ca,cb | c;E & i;327), 0.4=20

Sorry, the manual is out of date on this topic.  You'll need to use =
"carve=3D" when specifying the buffer around the atoms.

Also, hierarchical atom selections are a bit cleaner for big =
expressions...

> Is there a way to draw the density only around the selected atoms
> without defining this box?

isomesh den, map21, 1.0, (A/12/n,o,ca,cb | A/89/ & !*/n,o,ca,cb | E/327/ =
), carve=3D2.1
=20
- Warren=20

[PyMOL] e-density around atoms

[Mario S. <sa...@if...>]

Hi all

I am trying to draw an eletronic density around some specific atoms
only, but pymol always draw a box in the region. I am using the
following comand:

##########
isomesh den, map21, 1.0, (c;A & i;12 & !n;n,o,ca,cb |  c;A & i;89 &
!n;n,o,ca,cb | c;E & i;327), 0.4=20
##########

The problem is that the e-density for aa E327, for exemple, is cutted
due the box.
Is there a way to draw the density only around the selected atoms
without defining this box?

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

RE: [PyMOL] Making PNG files of protein surfaces

[DeLano, W. <wa...@su...>]

> 1. Is there any way of getting rid of the shadows when ray-tracing a
> picture (I have tried turning off the "specular reflections"=20
> setting but
> that doesn't seem to help)?

set reflect=3D0
set direct=3D0.7

> 2. I would also like to export non-ray-traced images. However, when I
> write PNG files from these images, they are speckled (there=20
> is a grid of
> small white dots superimposed on the image). I don't have this problem
> when writing out ray-traced figures, so I assume that there is nothing
> strange about the programs that I'm using to read the png files. Also,
> the white dots only lie over the surface. There is also an=20
> inhibitor in
> these figures and it looks fine.

Sounds like a bug, either in PyMOL, your OpenGL renderer, or your PNG =
viewer.  What version of PyMOL are you using?  Have you tried another =
PNG viewer?  What OS and hardware are you using?   I have seem similar =
problems on SGIs...
=20
[You may want to email me with your follow-up so that other's aren't =
spammed with the technical details].

Warren

[PyMOL] Making PNG files of protein surfaces

[Somoza, J. <Joh...@ce...>]

Hi,

I am trying to make figures of protein surfaces using pymol, and I have
two questions:

1. Is there any way of getting rid of the shadows when ray-tracing a
picture (I have tried turning off the "specular reflections" setting but
that doesn't seem to help)?

2. I would also like to export non-ray-traced images. However, when I
write PNG files from these images, they are speckled (there is a grid of
small white dots superimposed on the image). I don't have this problem
when writing out ray-traced figures, so I assume that there is nothing
strange about the programs that I'm using to read the png files. Also,
the white dots only lie over the surface. There is also an inhibitor in
these figures and it looks fine.

Has anyone out there had experience with either of these situations?

Thanks!!

John

[PyMOL] Talk at Stanford

[Warren L. D. <wa...@su...>]

	
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. 

Re: [PyMOL] ss coloring

[Warren L. D. <wa...@su...>]

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

[PyMOL] ss coloring

[Nat E. <nat...@ya...>]

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

[PyMOL] OSX port on G3 macs

[DeLano, W. <wa...@su...>]

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...im

RE: [PyMOL] multiple MODEL files

[DeLano, W. <wa...@su...>]

> 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

[PyMOL] multiple MODEL files

[<eck...@un...>]

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

[PyMOL] Testing Native OSX Port

[DeLano, W. <wa...@su...>]

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

[PyMOL] install problem in linux

[Hugo A. <haz...@ya...>]

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/

Re: [PyMOL] 2D scketch

[<re...@in...>]

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

[PyMOL] 2D scketch

[Mario S. <sa...@if...>]

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...

[PyMOL] Error when running python script that uses cctbx

[Robert C. <rl...@k2...>]

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

Re: [PyMOL] ccp4 map?

[Ben C. <ac...@em...>]

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

RE: [PyMOL] ccp4 map?

[Frank V. <Fra...@sy...>]

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
>


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[PyMOL] ccp4 map?

[Ben C. <ac...@em...>]

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