pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] png output

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

Jason Yano <jk...@br...> writes:

> Hi All,
> 	I just wanted to know if there was a way to include resolution
> and pixels per inch ie 150 or 300 rather than the default of 72
> pixles/inch in the .pml scritp ie
> 

Just provide `ray' with an optional width and height.

Ben

[PyMOL] png output

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

Hi All,
	I just wanted to know if there was a way to include resolution
and pixels per inch ie 150 or 300 rather than the default of 72
pixles/inch in the .pml scritp ie


[1280x1024, 150pixels/inch]
ray 

png image_name.png


Jason

RE: [PyMOL] Electrostatic potential surface?

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

> From: Eric C. Peterson [mailto:ec...@ua...]

> I am putting some figures together for an upcoming manuscript=20
> and am trying
> to figure out a few details.  Some of the things I want to do may be
> possible, some not.  Here are the questions I have:
>=20
> 1. How do you display electrostatic potential on surface displays?

Not yet directly possible, but that will change soon. The nearest thing
you can achieve is to color by charge. =20

> 2. Can the colors of individual side chains be changed=20
> without affecting the
> surface?

If you want a uniform surface color,

set surface_color, <color-name>, <object-name>

For anything complicated, just create a second copy of the object.  Show
the surface in one and sticks in the other.  Then color independently.
=20
> 3. I have tried to assign SS manually, but the cartoon skips=20
> at certain
> sections (ie alpha helices).  What can I do to fix this?

Hmm.  This should happen unless those atoms are HETATMS.  To be sure:

show cartoon
alter all,type=3D'ATOM'
rebuild

I'm a little suspicious that there might be some lingering bugs in the
ribbon code.  If you have an example PDB file and script which
reproduces the problem, please send them to me.

[PyMOL] Fe-S clusters

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

Hi All,
	I'm looking for a way to display a "ball and Stick" representation
of an Fe-S cluser, with a cartoon for the protein back bone. I can get the
spheres for the Fe-S cluster, but can't connect them. Here's the script so
far.

#Pymol script for Adx 1AYF
load C:\Documents and Settings\jkyano\My Documents\P450 pdb\1AYF_A.pdb,
ADX
bg white
### cut below here and paste into script ###
set_view (\
    -0.057087217,    0.618627429,   -0.783607304,\
     0.026588190,    0.785550535,    0.618226647,\
     0.998013437,    0.014458310,   -0.061293427,\
    -1.276597023,    0.201005965, -106.195739746,\
   -12.916477203,  -11.231512070,   -8.815745354,\
    74.405113220,  137.986404419,    0.000000000 )
### cut above here and paste into script ###
util.ss
color slate, ADX
hide everything, ADX
show cartoon, ADX
select fes =(resid 109)
show sphere, fes
color yellow, fes
alter (name s1), vdw=.75
alter (name s2), vdw=.75
rebuild
sel elem fe
color marine, fe

Thanks for the help,



Jason

[PyMOL] PyMOL-x86

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

Announcing PyMOL for GNU-Darwin on Intel architecture (x86)!

terminal shot
http://gnu-darwin.sourceforge.net/gdc/pymol.x86.png
sample graphic
http://gnu-darwin.sourceforge.net/gdc/pymol2.x86.png
installation script (for Intel only!)
http://gnu-darwin.sourceforge.net/gdc/pymol-x86

The installation script provides ncurses-5.2.x86.tgz python-2.2_1.x86.tgz
tcl-8.3.4_3.x86.tgz
tk-8.3.4_1.x86.tgz py22-numeric-20.2.1.x86.tgz py22-tkinter-2.2.x86.tgz and
pymol-0_73_1.x86.tgz.  
For more information about the x86 platform, see the ports and
packages page for GNU-Darwin-x86.

http://gnu-darwin.sourceforge.net/x86/

PyMOL now builds automatically with the ports system, and required source code
is in CVS.

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gnu-darwin/4Darwin-x86/ports/science/pymol/

BTW. This japanese Balsa now appears to be working pretty well ;-}.  Heave Ho!

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++++ UBOULI++++$ 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] Electrostatic potential surface?

[Eric C. P. <ec...@ua...>]

First of all, I am quite impressed with this program, free or not.  I also
saw Dr. Wells speak at the Keystone conference in Breckenridge in January
where he presented some graphics using Rigimol.  Very nice.

I am putting some figures together for an upcoming manuscript and am trying
to figure out a few details.  Some of the things I want to do may be
possible, some not.  Here are the questions I have:

1. How do you display electrostatic potential on surface displays?

2. Can the colors of individual side chains be changed without affecting the
surface?

3. I have tried to assign SS manually, but the cartoon skips at certain
sections (ie alpha helices).  What can I do to fix this?

Any help is appreciated.  Thanks.


Eric Peterson
Ph.D. Candidate
Cell and Molecular Biology
19 West Avenue Annex
University of Arkansas
Fayetteville, AR 72701
(501) 575-3021
Fax (501) 575-8434

RE: [PyMOL] movie frame alterations

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

Don't you hate it when users outsmart the programmer?

This is a tough one.  The only solution I can think of is not memory
efficient, but it should work:

Load each frame of the movie into a separate segment or chain.  This
should allow you to independently address each frame...

# assume that the segment is '' (empty) in the PDB files...

load frame1.pdb,mov
alter (segi ''),segi=3D'1'
load frame2.pdb,mov
alter (segi ''),segi=3D'2'

etc.=20

You can use Python to make a loop by switching to the Python API as
follows:

from pymol import cmd
for a in range(1,30):
   cmd.load("frame%d.pdb"%a,"mov")
   cmd.alter("(segi '')","segi=3D'%d'"%a)

Then you should be able to say:

color red,/mov/1//101/ca
color red,/mov/2//101/ca
color red,/mov/3//101/ca

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: Nat [mailto:nat...@ya...]
> Sent: Wednesday, January 23, 2002 7:39 PM
> To: pym...@li...
> Subject: [PyMOL] movie frame alterations
>=20
>=20
>=20
> Is it possible to make changes to the way individual frames=20
> are rendered?
> Specifically, I'm writing a Python script (translated=20
> literally from C,
> but I'm too tired to learn the Python API right now) to evaluate bond
> "quality" and highlight the distorted regions in a frame of a protein
> morph.  However, since the distortions tend to come in the middle of a
> morph, I want to examine each frame alone and apply highlighting only
> where applicable.
>=20
> Right now, treating individual frames as part of an object (i.e. for a
> movie) means that calls like 'color red, 101/ca' are applied to every
> state.  Is there some way to only run that command on one state?  In
> simple terms, I'm trying for a movie that changes color=20
> during its course
> to indicate bond quality.  It's much easier to do this if I=20
> can use movie
> objects, especially since it would be nice to be able to run this
> interactively.  Otherwise, I'm going to just create a very=20
> long pml file
> with all the commands.
>=20
> thanks,
> Nat
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] movie frame alterations

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

Is it possible to make changes to the way individual frames are rendered?
Specifically, I'm writing a Python script (translated literally from C,
but I'm too tired to learn the Python API right now) to evaluate bond
"quality" and highlight the distorted regions in a frame of a protein
morph.  However, since the distortions tend to come in the middle of a
morph, I want to examine each frame alone and apply highlighting only
where applicable.

Right now, treating individual frames as part of an object (i.e. for a
movie) means that calls like 'color red, 101/ca' are applied to every
state.  Is there some way to only run that command on one state?  In
simple terms, I'm trying for a movie that changes color during its course
to indicate bond quality.  It's much easier to do this if I can use movie
objects, especially since it would be nice to be able to run this
interactively.  Otherwise, I'm going to just create a very long pml file
with all the commands.

thanks,
Nat

RE: [PyMOL] stereo pictures

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

> From: Ricardo Aparicio [mailto:apa...@if...]

> 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.

No, it just fails altogether.=20

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

Easy -- you do it the old fashion way:

png left.png
turn y,5
png right.png

And then use something like Photoshop or PowerPoint to combine the two
images into a single stereo-pair. =20

The above recipe gives you cross-eye.  You'll want to play with the
angle a bit and or negate it in order to do wall-eye stereo.

- Warren

[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...