pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] stereo pictures

[Ricardo A. <apa...@if...>]

Dear users,


I am running PyMol in a PIII500 without any stereo hardware and I would
like your help to solve these 2 questions:



1) what is the effect of command "stereo" in PyMol? Does it makes a
confuse screen (like in O when one is not using stereo glasses)? If so,
there is no sense in capture the image from the screen with png command.


2) how to make stereo figures using PyMol. If necessary we have SGIs
with stereo here.



Thank you very much,


Ricardo Aparicio
PhD student, USP
Sao Paulo
Brazil

[PyMOL] how to load dssp into pymol

[Tommy W. <che...@im...>]

How do I get pymol to read in my dssp output so that I can view it as a 
cartoon?

Re: [PyMOL] PyMol module _cmd version

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

On Sun, 20 Jan 2002, Ricardo Aparicio wrote:

> I am using PyMol version 0.68 and it is very very slow the control of
> graphical interface.
> I've got the following error when starting the program and I would like
> to know if this slow response is a consequence of it:
> 
> WARNING: Python C API version mismatch for module _cmd:
>   This Python has API version 1009, module _cmd has version 1007.

You'll get this error if the "Python.h" header file you built PyMOL with
is different from the one corresponding to the Python library you're
using.  The message is usually harmless.  

PyMOL will seem slow unless you have a hardware graphics accelerator, with
suitable drivers (under Linux).  PyMOL does not perform at all well using
software OpenGL (Mesa) because it does not use display lists.

- Warren

Re: [PyMOL] transparency question

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

On Sun, 20 Jan 2002, Ricardo Aparicio wrote:

> Thank you all for reply my ray question. Just for information, using the
> default parameters (without clues from "help faster"), an image of a map
> plus a cartoon took 30 min. to be rendered in a PIII500 MHz:
> " Ray: total rendering time: 1820.91 sec. = 2.0 frames per hour."

Wow, that is slow.  Increasing hash_max can help, but certain
geometries will always give PyMOL trouble.  One alternative is to upgrade
to 0.73 and then use PovRay to do the rendering.   PovRay is smarter about
handling tough scenes efficiently.  How many geometric primitives are
trying to render?

> I am using a mask from NCSMASK (with a very fine grid) converted to ccp4
> map and loaded in PyMol.
> I would like very much to compare more than 1 mask but it is necessary
> to make them transparent.

If you can't see through your meshes then these are extremely dense --
which probably explains why raytracing and openGL are dog slow -- I've
never loaded maps that tight into PyMOL.  Is there any way you can
resample them to a more reasonable level before loading them into PyMOL?

> As stated in the "help transparency",
> 
> " Transparency is currently managed by setting either the global
> transparency variable or one attached to an individual molecule object.
>    set transparency=0.5        # makes all surfaces 50%
> transparent             "
> 
> But using transparency=0.5 I can't see any results on the masks.
> 
> Please, if you can help me once more, 
> 
> 1- Is it map considered a "surface" by PyMol??  I think not, that is the
> reason by which transparency doesn't have any effect in the mask.

Molecule and isosurface meshs are not considered surfaces in this
context.  By "all surfaces" I was referring to the surfaces
representation in all molecules.

> 2- Is it possible to obtain a "surface" from a map? I think not, just to
> confirm.

Not yet, but that is planned.

> PS: 
> 1) The "surface" command in PyMol didn't give a nice surface as the
> number of atoms model per unit of volume is low.

That is the expected behavior.  A surface with holes big enough for waters
to penetrate should look like swiss cheese : ).

> 2) I always can make the mask with a coarser grid to get "transparency"
> but I wouldn't like in view of the rough surface obtained in this way.

There should be a reasonable middle-ground between a mesh which is so fine
that it is opaque and a mesh which is so coarse that it appears rough.

> 3) Sorry but because manual is not very complete (I know about
> development problems) and I don't have experience in this area, I need
> to ask what could be considered "silly" questions.

Your questions aren't silly.  Particularly since your are clearly trying
to use PyMOL for a task I didn't originally envision.  That's great, but
understand it may or may not be up to the task (I hope it is).

Regarding the manual, please don't lose the proper perspective:  this
software is free and created 100% in my spare time.  That a manual exists
at all is a remarkable thing!  Preparing good documentation takes more
time than does development, and I don't get the benefit from creating a
manual that I do from adding a new feature to the program.  

My hope is that users will starting supporting PyMOL on a regular
basis and will thus provide the resources for improved documentation and
other enhancements.  

- Warren

[PyMOL] PyMol module _cmd version

[Ricardo A. <apa...@if...>]

I am using PyMol version 0.68 and it is very very slow the control of
graphical interface.
I've got the following error when starting the program and I would like
to know if this slow response is a consequence of it:

WARNING: Python C API version mismatch for module _cmd:
  This Python has API version 1009, module _cmd has version 1007.


Where can I get the correct "module_cmd" ?? I am using Linux Mandrake
8.0 on a PIII500 MHz.

Does this problem could be solved installing new PyMol version?

Thank you again,

Ricardo Aparicio
PhD Student

[PyMOL] transparency question

[Ricardo A. <apa...@if...>]

Hi again.

Thank you all for reply my ray question. Just for information, using the
default parameters (without clues from "help faster"), an image of a map
plus a cartoon took 30 min. to be rendered in a PIII500 MHz:
" Ray: total rendering time: 1820.91 sec. = 2.0 frames per hour."

I am using a mask from NCSMASK (with a very fine grid) converted to ccp4
map and loaded in PyMol.
I would like very much to compare more than 1 mask but it is necessary
to make them transparent.

As stated in the "help transparency",

" Transparency is currently managed by setting either the global
transparency variable or one attached to an individual molecule object.
   set transparency=0.5        # makes all surfaces 50%
transparent             "

But using transparency=0.5 I can't see any results on the masks.

Please, if you can help me once more, 

1- Is it map considered a "surface" by PyMol??  I think not, that is the
reason by which transparency doesn't have any effect in the mask.

2- Is it possible to obtain a "surface" from a map? I think not, just to
confirm.



Thank you very much,


Ricardo Aparicio
PhD Student - USP
Sao Paulo - Brazil


PS: 
1) The "surface" command in PyMol didn't give a nice surface as the
number of atoms model per unit of volume is low.

2) I always can make the mask with a coarser grid to get "transparency"
but I wouldn't like in view of the rough surface obtained in this way.

3) Sorry but because manual is not very complete (I know about
development problems) and I don't have experience in this area, I need
to ask what could be considered "silly" questions.

[PyMOL] PyMol dosen't find Tcl

[W. <re...@wu...>]

Hi,

where can i set the path to the tcl-directory. PyMol looks for tcl in a=20
false directory.

Thanks,
Ren=E9

[PyMOL] Re: "ray" doubts

[Andrey K. <ak...@kd...>]

Ricardo,

"RA" == Ricardo Aparicio wrote:

 RA> - is it necessary? Does it make great difference in the final quality of
 RA> figures published (in the case of a paper)?

Yes, ray-traced images have much better quality than simple and fast 
render for interactive use.

 RA> - does it renderize(?) all the active objects in the screen?
(render)

 RA> - after finished ray process, if the image is rotated, is it necessary
 RA> to renderize again (I think no, just to confirm)

Yes, it has to be rendered again.

The idea is to select the projection you want to be printed out, render it
and use the resulting image file in your publication.

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] "ray" doubts

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

Ricardo,

  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). =20

  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=3D0 to get a
pixel-for-pixel match between OpenGL and the ray tracer).

 =20
Cheers,
Warren


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

> From: Ricardo Aparicio [mailto:apa...@if...]
>=20
> Dear PyMol users,
>=20
> as stated in the manual, command
>=20
>  "ray" creates a ray traced image of the current frame. This
>    can take some time (up to several minutes, depending on image
>    complexity).
>=20
> My question is:
>=20
> - is it necessary? Does it make great difference in the final=20
> quality of
> figures published (in the case of a paper)?
>=20
> - does it renderize(?) all the active objects in the screen?
>=20
> - after finished ray process, if the image is rotated, is it necessary
> to renderize again (I think no, just to confirm)
>=20
>=20
> Many thanks,
>=20
>=20
> Ricardo Aparicio
> PhD Student - USP=20
> Sao Paulo - Brazil
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] "ray" doubts

[Ricardo A. <apa...@if...>]

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
   complexity).

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

RE: [PyMOL] scripts and movies

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

> From: Scott Dixon [mailto:sc...@me...]

> > By the way, it is important to understand the disntinction=20
> between PyMOL's
> > scripts and Python programs you run your PyMOL -- PyMOL scripts are
> > basically just a linear series of PyMOL commands.  For anything more
> > sophisticated, use straight Python.

> Understood.  BTW, one way to get part of the benefit of arguments to
> PyMOL scripts is to use named selections and to load molecules into
> specific object names (like say, "ligand").  Then your=20
> scripts can work
> on the standard names and be more widely reusable.  But I take your
> point about Python being much more versatile.

Yes, you can certainly use program state as a means of conveying
information, and you can even use global python variables in this manner
even when operating inside of PyMOL command scripts: =20

/obj1=3D"hi"
@ex1.pml

# where ex1.pml contains...

reset
/cmd.zoom(obj1)
/cmd.show("spheres",obj1)

NOTE: a forward slash can be used to explicitly include a line of Python
in a PyMOL script.  Normally it isn't required (since PyMOL commands
fall back on Python "eval"), but it is more efficient because is
bypasses normal parsing.

Again, I view these approaches as best for limited -- real Python
scripts gives you so much more, with very little added burden.

Cheers,
Warren
=20

Re: [PyMOL] scripts and movies

[Scott D. <sc...@me...>]

Hi, Warren-
On Mon, 2002-01-14 at 01:53, Warren L. DeLano wrote:
> > First of all, Warren, thanks for an impressive program.  A couple of
> > questions as I begin to get into it:
> 
> Thanks for the kind words!
> 
> > I'm probably missing something obvious, but I don't see it in the
> > documentation.  Is it possible to send arguments to scripts (either the
> > .pml script or Python scripts)?  It would seem like that would make them
> > much more versatile.
> 
> Hmm...script arguments aren't exactly present, but there is a more
> powerful solution: use Python functions to extend the PyMOL command
> language.  Any functions defined in Python script can then be called from
> PyMOL (interatively or otherwise)
> 
> By the way, it is important to understand the disntinction between PyMOL's
> scripts and Python programs you run your PyMOL -- PyMOL scripts are
> basically just a linear series of PyMOL commands.  For anything more
> sophisticated, use straight Python.
Understood.  BTW, one way to get part of the benefit of arguments to
PyMOL scripts is to use named selections and to load molecules into
specific object names (like say, "ligand").  Then your scripts can work
on the standard names and be more widely reusable.  But I take your
point about Python being much more versatile.
> 
> To achieve what you're looking for, create "test.py" with the following
> function (foo here for example)
> 
> from pymol import cmd
> def foo(arg1,arg2):
>    print arg1,arg2
> cmd.extend("foo",foo)
> 
> Once you run the above script in PyMOL "run test.py", you will then be
> able to type "foo 1,2" to invoke the foo command with arguments.
Perfect.  That is what I needed to know.
> 
> > Second question:  How would one write a Python script which went through
> > each frame of a movie and modified some aspect of the structure (like
> > the molecule name for example)?
> 
> There are a couple of ways to do this.  One would be to pull the object
> into the Python layer (cmd.get_model), change it, and then load in back in
> to PyMOL (cmd.load_model).  The advantage of this approach is that you can
> directly manipulate the molecule, bond, and atom objects.  The
> disadvantage is poor performance for large molecules (probably fine for
> organics though).
> 
> Other approaches vary depending on what you want to change.  Titles can be
> changed with "set_title", (which revealed a couple of minor bugs when I
> tried it just now, arrgh).  Atomic properities can be modified using
> "alter".  Atoms and bonds can be moved, created, or deleted using the
> editor functions, but which may not yet me sufficiently documented.
> 
> No matter what you're changing, you'll need to apply changes to molecular
> "states".  Just use a 1-based loop over each state, and pass this integer
> into the state argument (where required).  Example:
> 
> dock_score = [ -24.0, -9.5, -2.0 ]
> obj = "foo1" # your object name
> for a in xrange(1,4):
>    cmd.set_title(obj,a,str(dock_score[a-1]))
Exactly what I wanted.  Thanks.
Scott

Re: [PyMOL] scripts and movies

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

> First of all, Warren, thanks for an impressive program.  A couple of
> questions as I begin to get into it:

Thanks for the kind words!

> I'm probably missing something obvious, but I don't see it in the
> documentation.  Is it possible to send arguments to scripts (either the
> .pml script or Python scripts)?  It would seem like that would make them
> much more versatile.

Hmm...script arguments aren't exactly present, but there is a more
powerful solution: use Python functions to extend the PyMOL command
language.  Any functions defined in Python script can then be called from
PyMOL (interatively or otherwise)

By the way, it is important to understand the disntinction between PyMOL's
scripts and Python programs you run your PyMOL -- PyMOL scripts are
basically just a linear series of PyMOL commands.  For anything more
sophisticated, use straight Python.

To achieve what you're looking for, create "test.py" with the following
function (foo here for example)

from pymol import cmd
def foo(arg1,arg2):
   print arg1,arg2
cmd.extend("foo",foo)

Once you run the above script in PyMOL "run test.py", you will then be
able to type "foo 1,2" to invoke the foo command with arguments.

> Second question:  How would one write a Python script which went through
> each frame of a movie and modified some aspect of the structure (like
> the molecule name for example)?

There are a couple of ways to do this.  One would be to pull the object
into the Python layer (cmd.get_model), change it, and then load in back in
to PyMOL (cmd.load_model).  The advantage of this approach is that you can
directly manipulate the molecule, bond, and atom objects.  The
disadvantage is poor performance for large molecules (probably fine for
organics though).

Other approaches vary depending on what you want to change.  Titles can be
changed with "set_title", (which revealed a couple of minor bugs when I
tried it just now, arrgh).  Atomic properities can be modified using
"alter".  Atoms and bonds can be moved, created, or deleted using the
editor functions, but which may not yet me sufficiently documented.

No matter what you're changing, you'll need to apply changes to molecular
"states".  Just use a 1-based loop over each state, and pass this integer
into the state argument (where required).  Example:

dock_score = [ -24.0, -9.5, -2.0 ]
obj = "foo1" # your object name
for a in xrange(1,4):
   cmd.set_title(obj,a,str(dock_score[a-1]))

etc.

Cheers,
Warren

[PyMOL] scripts and movies

[Scott D. <sc...@me...>]

Hi,
First of all, Warren, thanks for an impressive program.  A couple of
questions as I begin to get into it:
I'm probably missing something obvious, but I don't see it in the
documentation.  Is it possible to send arguments to scripts (either the
.pml script or Python scripts)?  It would seem like that would make them
much more versatile.
Second question:  How would one write a Python script which went through
each frame of a movie and modified some aspect of the structure (like
the molecule name for example)?
Thanks,
Scott

Re: [PyMOL] Support for Python 1.5.2?

[ezra p. <epe...@ME...>]

As long as you update the external source package (and all
dependencies) to python 2, I have no objection. I feel that pymol is a
moving target and if you need the latest and greatest tools, use them.
My only concern is performance. If moving to python 2 has a
performance hit, then I would be concerned.

For my compilations, I treat pymol as a separate beast - which includes
python in it's own little tree - so a new version of python is no problem.

       Ezra

[PyMOL] Support for Python 1.5.2?

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

A Quick PyMOL User survey:

Is anyone still depending on PyMOL's ability to support Python 1.5.2?
If I don't hear any objections, then I will only support Python versions
2.1 and above for future releases...

If you do have an objection, then please give me a roough time estimate
as when you'd be willing to migrate to version 2.1 so that I can plan
accordingly.

To avoid extraneous list traffic, please reply directly to=20

   wa...@de...
      or
   wa...@su...

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

[PyMOL] PyMOL tips (was: Re: GNU-Darwin and Fink)

[proclus r. <pr...@in...>]

> Maybe the path where pymol expects other 
> packages is hardcoded into its source?

GNU-Darwin has a unique PyMOL installation method, but it follows
standards, and I'm expecting that
it will be adopted by the other distributions eventually.  The pymol
executable is actually a shell script (pymol.com) that is installed in
/usr/local/bin. 
I believe that you can edit this script to change the PYTHON_PATH
variable to the Fink installation path.  

If you really want to use Python from the Fink with PyMOL, then you might
consider copying this file to your home directory and editing it there, so
that it
does not get overwritten when you upgrade PyMOL.  

> 
> I also had to install py-pmw with pkg_add and I then moved it to the 
> site-packages directory from python.

I'd be surprised if the Fink
doesn't provide Megawidgets ;-}.  Sorry, but I also find all of this a
little
amusing, because it seems like alot of work to use the Fink in this case,
when
GNU-Darwin was truly built as a PyMOL installer.  You should note
that the PyMOL developer, Warren Delano, intends to base his OSX
development efforts on some of the GNU-Darwin tools.  The situation is
somewhat
similar with CCP4, Raster3D, and many other major projects as well.

http://www.ccp4.ac.uk/problems/ccp4onMacs.html
http://www.ccp4.ac.uk/ccb/
http://www.bmsc.washington.edu/raster3d/r3d_FAQ.html#PC

Although GNU-Darwin is a free software distribution, it was founded to
build the infrastructure for molecular graphics and crystallographic
computing.  

http://www.newsforge.com/article.pl?sid=00/12/01/2028254&mode=thread
http://www.gnu.org/brave-gnu-world/issue-25.en.html

PyMOL provided the impetus for GNU-Darwin to go Beta so that users would
have a user friendly way to install PyMOL.  I believe that our distribution
will emerge as the primary free software distribution for biotechnology in
general, and PyMOL support will be a crucial part of that emergence.  I
have the utmost respect for the Fink project and their free software
offerings, but it will never meet the standards that we have set in this
arena, which is mission-critical for GNU-Darwin.  The Fink has nothing like
this...

http://gnu-darwin.sourceforge.net/gdc/mol.html

or this,

http://gnu-darwin.sourceforge.net/art.html

or this,

http://gnu-darwin.sourceforge.net/gdc/ccp4.html

and it probably never will.  (Heh, I bet there will be Fink PyMOL and
Megawidgets right away now! ;-).

> Finally, I installed povray with Fink, 
> if I give the command 'ray' in pymol it works.

Here again is a problem.  ray by itself invokes PyMOL's own internal
rendering
engine.  You need to add an argument to ray to invoke POV-ray as an
external rendering engine.  PyMOL-0.7.3 is requred for this.  Type "help
ray".  I believe that PyMOL looks for x-povray in the PATH variable, so
that the Fink's non-standard installation directory should not matter in
this case.

Sorry, if this seems tedious.  I really love the Fink as a fellow free
software project, although I do not use it myself for anything.  GNU-Darwin
is sufficient without the Fink.  TDC is sufficient.   It gets tiresome
answering questions about the Fink all the time, and I do not believe that
the others on the GNU-Darwin list are interested.  The GNU-Darwin
infrastructure was built expressly for projects like PyMOL.  If you want to
use GNU-Darwin PyMOL, then I highly recommend using the GNU-Darwin packages
that were built to support it (instead of the Fink).  

Be sure to consult the PyMOL documentation.  Warren has done an
excellent job with the PyMOL website.  I printed out a color copy of the
manual.
It's so beautiful.

http://pymol.sourceforge.net/

Regards,
Michael L. Love
MacCHESS
Cornell University
http://www.gnu-darwin.org/


-- 
Visit proclus realm! http://proclus.tripod.com/
-----BEGIN GEEK CODE BLOCK-----
Version: 3.1
GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O
M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++
h--- r+++ y++++
------END GEEK CODE BLOCK------

[PyMOL] PyMOL in 2002

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

Dear PyMOL Users:

   Happy New Year!  2001 was a great year for PyMOL, with the following
developments: cartoon ribbons, improved rendering quality, transparency,
CCP4 maps, concise atom selections, increased stability, bug fixes, and
many other minor improvements.  According to SourceForge's updated
statistics, PyMOL has accumulated about 75,000 web-page hits, 15,000
file downloads, and 72 subscribers to the mailing list.  Hooray!

   Given this wonderful response, I intend to continue developing PyMOL as
a hobby in 2002 under the same unrestricted software license.  Some of my
goals include:  updated documentation, tutorials, a better user interface
and API, an improved builder with structure clean-up, MOL2 file support,
electrostatic potential display, generalized volumetric rendering, a
native OSX version, and an ActiveX control (to replace Chime).  

   Although PyMOL is free and unrestricted, the reality of software
development is that it takes substantial time and money.  If you
haven't yet considered whether it would be in your interest to support
PyMOL with a monetary donation, then please do so today!  DeLano
Scientific can now take donations via credit card or check, or we can even
sell your company or institution a standard software license -- whatever
is most convenient.
   
   Details at http://www.pymol.org/donate.html 

   Even if you are cash-poor, there are many others ways in which you
can advance the PyMOL vision.  See the "contribute" section of the
home page for more information on what you can do.

   As an individual scientist, I am striving to make the PyMOL vision a
reality, but it will not happen unless many other scientists join me in
this quest.  As of today, only 2 parties have made donations, and 3 more
have made pledges.  Less than ten people have directly contributed to 
development.  This is a good start, but let us turn this promising little
snowball into a roaring avalanche which validates the PyMOL approach for
developing free and unrestricted research software.

   Join me in taking a stand against outrageously expensive commercial
research tools.  Working together as individual scientists, we can create
free and unrestricted alternatives.  Please support PyMOL today!

   Cheers,

   Warren L. DeLano, Ph.D.
   PyMOL Creator
   DeLano Scientific
   San Carlos, CA, USA

RE: [PyMOL] secondary structure and many more questions

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

That's the spirit Jason -- don't hold back with those questions!

> From: Jason Yano [mailto:jk...@br...]

> 1) Is there a way to find out what secondary strucuture has been=20
> assigned by the automatic algorythem?
> I assume there must be a python command that will dump the=20
> output of the=20
> utility to the screen or to a file.

util.ss
iterate (name ca),print resn,resi,chain,ss

# or to a file (using the persistent global object "stored")

stored.file =3D open("secondary.txt","w")
iterate (name ca),stored.file.write("%s %s %s
%s\n"%(resn,resi,chain,ss))
stored.file.close()

# but remember, that SS algorithm is bogus -- it was cooked up in a few
hours based on what I thought "looked right".=20

> 2) Is there any information available for any of the other=20
> util programs?

The menu module makes use of the util module, so you will see some
example code there.  So far there isn't much else in the way of
documention.=20
=20
> 3) Is it possible to color the chain by B-factor?

# yes, but it's weak.=20

color br0
color br1,(b>5)
color br2,(b>10)
color br3,(b>15)
color br4,(b>20)
color br5,(b>25)
color br6,(b>30)
color br7,(b>35)
color br8,(b>40)
color br9,(b>45)

# You can create a python loop which does the same thing.

# Try colors, s000, s001, ... up through s999 for more subtle shading.
=20
> 4) I have a heme moiety, I can get the program to display the=20
> FE atom,=20
> but I'm not sure how to increase the sphere size of the atom=20
> so that I=20
> can exagerate it, it is possibe? something close to the set=20
> atomradius=20
> command in molscript.

alter (elem fe),vdw =3D 4.0
rebuild

# should work, but just in case you might need to use the
# atom name (whatever it is)

alter (name fe),vdw =3D 4.0
rebuild

> 5) For some strange reason it recognizes the Nitrogens on the heme=20
> differently and colors some of them blue and others pink. I tried to=20
> manually set it like I could for the Fe, but I think that I am not=20
> getting the atom type/name correct. Is there a list of atom names?

PyMOL is probably getting confused.  Please send a copy of the PDB file
to warren@delanoscientific to debug.

> 6) Is there a way to make a C-alpha trace? other than ribbons=20
> something=20
> that will draw straight bonds between C-alpha's?

#ala midas "chain" command?

set ribbon_sampling=3D1
show ribbon

> 7)  Is it possible to change the color of the mesh (not the isomesh)=20
> relatve to helix color ie what are the command line commands. I have=20
> tied color red, mesh and that didn't seem to work, same=20
> question for the=20
> surfaces as well.

set mesh_color=3Dblue
set surface_color=3Dgreen

> 8) Is it possible to have a "ball and stick" representation?

yes, but right now is it kludgy...you will need to create multiple
copies of an object if you want to simultaneously adjust vdw and show
surfaces.

alter (all),vdw=3Dvdw*0.25
set stick_radius=3D0.15
rebuild

> 9) What is the command to output a pov ray file?

You'll need to use Python for this.

cmd.get_povray() returns a tuple of two strings (header and data).
Write these to a  file in order to get a povray input file.
=20
> 10) How do you get two color helicies, ie the equivalent to=20
> planecolour2=20
> in molescript?

sorry can't do this, but 8.5 out of 10 aint bad ; ) PyMOL's secondary
structures are unicolor for now.

> So far the program is running great. The stereo works very=20
> well for me.=20
> I have it running on a dual AMD athlon 1.4GHz, with an Oxygen GVX1=20
> graphics card and 1 gig of  DDR ram under the Windows 2000 pro OS.

I envy you.  That's pretty much the machine I'd like to buy except that
I'd run Linux on it at +200 mhz.  Athlon's are definitely the way to go
-- Python really flies on them.

- Warren

[PyMOL] secondary structure and many more questions

[Jason Y. <jk...@br...>]

Hello All,
    I had a few questions:

1) Is there a way to find out what secondary strucuture has been 
assigned by the automatic algorythem?
I assume there must be a python command that will dump the output of the 
utility to the screen or to a file.


2) Is there any information available for any of the other util programs?

3) Is it possible to color the chain by B-factor?

4) I have a heme moiety, I can get the program to display the FE atom, 
but I'm not sure how to increase the sphere size of the atom so that I 
can exagerate it, it is possibe? something close to the set atomradius 
command in molscript.

5) For some strange reason it recognizes the Nitrogens on the heme 
differently and colors some of them blue and others pink. I tried to 
manually set it like I could for the Fe, but I think that I am not 
getting the atom type/name correct. Is there a list of atom names?

6) Is there a way to make a C-alpha trace? other than ribbons something 
that will draw straight bonds between C-alpha's?

7)  Is it possible to change the color of the mesh (not the isomesh) 
relatve to helix color ie what are the command line commands. I have 
tied color red, mesh and that didn't seem to work, same question for the 
surfaces as well.

8) Is it possible to have a "ball and stick" representation?

9) What is the command to output a pov ray file?

10) How do you get two color helicies, ie the equivalent to planecolour2 
in molescript?


So far the program is running great. The stereo works very well for me. 
I have it running on a dual AMD athlon 1.4GHz, with an Oxygen GVX1 
graphics card and 1 gig of  DDR ram under the Windows 2000 pro OS.


Thanks,


Jason Yano

RE: [PyMOL] pymol on SGI

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

Danny,

   I think your problem is one of two possibilities: either your
LD_LIBRARY_PATH is not being set correctly by pymol.com, or your
python1.5.so shared object isn't valid. =20

You might try using linking against a static Python library as described
in http://pymol.sourceforge.net/workarounds.html

Good luck!
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: Danny G Smith [mailto:dg...@om...]
> Sent: Tuesday, December 18, 2001 12:52 PM
> To: pym...@li...
> Subject: [PyMOL] pymol on SGI
>=20
>=20
> I have complied pymol-0_73, with ext-0_51, useing the following
> build.com in the ext subdirectory.  When I try to run pymol.com I get
> the following message:
>=20
> omega[272]:/misc/local/src/pymol/pymol % ./pymol.com
> Traceback (innermost last):
>   File "/misc/local/src/pymol/pymol/modules/launch_pymol.py",=20
> line 6, in
> ?
>     import pymol
>   File=20
> "/misc/local/src/pymol/pymol/modules/pymol/__init__.py", line 24,
> in ?
>     import _cmd
> ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
> Fatal Error: Cannot Successfully map soname 'libpython1.5.so'=20
> under any
> of the filenames
> /usr/local/lib/libpython1.5.so:/usr/lib32/libpython1.5.so:/usr
> /lib32/internal/libpython1.5.so:/lib32/libpython1.5.so:/opt/li
> b32/libpython1.5.so:
> omega[273]:/misc/local/src/pymol/pymol %
>=20
>=20
> Any help would be appreciated.
>=20
>=20
> # build.com in ext directory
> #!/bin/csh
> #
> #---------------------------------------------------------------------
> # 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=20
> -------------------------------------------------------------
> # -- Linux with just Tcl/Tk
> # setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy=20
> pmw png-linux
> glut-linux"
> #
> # -- Linux with Tcl/Tk and wxPython
> # setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw=20
> png-linux
> glut-linux glib gtk wxgtk wxpython"
> #
> # -- SGI/IRIX with just Tcl/Tk
> # setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy=20
> pmw png-irix
> glut-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=20
> --------------------------------------------------------------
> $MAKE -f Makefile.in $1
>=20
>=20
>=20
>=20
> --=20
> thanks,
> Danny G Smith =20
>=20
> UNIX Systems Administrator
> Crystallography Dept Oklahoma Medical Research Foundation
> phone 271-8954 fax 271-7953
>=20
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
> UNIX air conditioned environment, keep the windows closed
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] pymol on SGI

[Danny G S. <dg...@om...>]

I have complied pymol-0_73, with ext-0_51, useing the following
build.com in the ext subdirectory.  When I try to run pymol.com I get
the following message:

omega[272]:/misc/local/src/pymol/pymol % ./pymol.com
Traceback (innermost last):
  File "/misc/local/src/pymol/pymol/modules/launch_pymol.py", line 6, in
?
    import pymol
  File "/misc/local/src/pymol/pymol/modules/pymol/__init__.py", line 24,
in ?
    import _cmd
ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
Fatal Error: Cannot Successfully map soname 'libpython1.5.so' under any
of the filenames
/usr/local/lib/libpython1.5.so:/usr/lib32/libpython1.5.so:/usr/lib32/internal/libpython1.5.so:/lib32/libpython1.5.so:/opt/lib32/libpython1.5.so:
omega[273]:/misc/local/src/pymol/pymol %


Any help would be appreciated.


# build.com in ext directory
#!/bin/csh
#
#---------------------------------------------------------------------
# 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
glut-linux"
#
# -- Linux with Tcl/Tk and wxPython
# setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw png-linux
glut-linux glib gtk wxgtk wxpython"
#
# -- SGI/IRIX with just Tcl/Tk
# setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy pmw png-irix
glut-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 Makefile.in $1




-- 
thanks,
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

RE: [PyMOL] resolution of th eimage

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

> From: Mirek Cygler [mailto:mir...@br...]
>=20
> 	I am trying my first steps with PyMOL. I have tried to=20
> display a XPLOR map.
> It worked well but the isomesh command displayed the entire=20
> map. How can I
> display only a part of the map (box or sphere) around a=20
> specific point (say,
> the center of the screen) if I do not have a model yet (ie, no atoms).

Mirek,

   That exactly functionality isn't yet implemented, but you can kludge
it by:

1. creating a model on the fly
2. setting the atom coordinates in the model to the location
3. creating a mesh around the model
4. and deleting the model.

The following .pml example script shows you how to get a 10 A brick
(msh1) or a sphere (msh2) about (2.0,21.0,4.0).  If you plan to use this
functionality often, you should convert the following script into a
Python function with four arguments and place its definition in your
PyMOL start-up file.  This is how you can customize PyMOL to suit your
needs...

# begin example

fragment methane,_pos
alter_state 1,(_pos),x=3D2.0;y=3D21.0;z=3D4.0
isomesh msh1,map1,1.0,(_pos),10.0
isomesh msh2,map1,1.0,(_pos),carve=3D10.0
del _pos
zoom msh1

# end example

Cheers,
Warren

cc: PyMOL mailing list

--
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



>=20

[PyMOL] Re: electron density 'surface'

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

On Sat, 15 Dec 2001, Manfred W. Baumstark wrote:

> I would like to display an electron density as a surface instead of a mesh.
> Is this somehow possible with PyMOL?
> 
> Thanks in advance for any help

This is planned but not yet possible.

Cheers,
Warren

Re: [PyMOL] resolution of th eimage

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

On Sat, 15 Dec 2001, Mirek  Cygler wrote:

> 	The images produced by PyMOL are really nice. Is there a way to define the
> resolution of the image file? Say I would like to get an image with a
> resolution of 1600 x 1200 pixels but my screen is only 1400 x 1050?

ray 1600,1200
png image.png

I've even used PyMOL to generate poster sized images at 4800 by 3600,

Warren