pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] CA trace

[<bjo...@ka...>]

I know something similar has been answered earlier, but I can not find =
it.

How do I display CA trace of a molecule, if I only have CA-coordinates?

-- Bjorn

[PyMOL] Pymol 0.82 and Python 2.2

[Marc S. <mar...@mp...>]

> Finally, I wish to say that, I have got the 0.82 RPM already,
> but since I installed python 2.2.1, there are always warning
> when I start pymol complaining about the version of python.
> However, actually there is no problem at all running under
> python 2.2.1.

I think this is only a minor glitch, might be due to python itself, 
checking for versions. I think, for the time beeing, one could either 
install a separate Python2.1 for Pymol or just ignore the messages.

And you could recompile Pymol from source I think. In this case, it 
should not complain anymore.

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] Introductory PyMOL tutorial first draft

[<chu...@in...>]

Hello PyMOL users,

I have just started using PyMOL to visualize molecules and thought since
I'm at the beginning I could write a tutorial giving an introduction to
using PyMOL. This tutorial is directed at complete beginners so that they
can start using the software right away.

I have posted the tutorial at http://pymol_tutorial.tripod.com/ (I
apologize for the pop-ups, if someone has better hosting the page could
easily be moved).

I welcome any comments or criticism and can be reached at:
chu...@in...

Carly Huitema

RE: [PyMOL] Update to ScriptBox 0.3 for PyMOL

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

> From: Kristian Rother [mailto:kri...@be...]
>=20
> As suggested by Warren, i have made some improvements to the=20
> ScriptBox,=20
> which should integrate better into PyMOL now,

Thanks Kristian!

> On my page, there is also a 'quick and dirty' hack for PyMOL.
> FilePipe.py allows to execute PyMOL commands from a shell. It=20
> starts its=20
> own thread and reads lines from a text file. This doesn't=20
> work well, but=20
> it works.

> Does anyone have a better idea to do this?

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

See 'help launching' for other command line options.

Cheers,
Warren

Re: [PyMOL] Update to ScriptBox 0.3 for PyMOL

[Kristian R. <kri...@be...>]

Hello PyMOL users,

As suggested by Warren, i have made some improvements to the ScriptBox, 
which should integrate better into PyMOL now,

>>I have written a small program that lets you select your favorite PyMOL 
>>script from a comfortable box floating beside your PyMOL window.

The URL is still the same:

>>http://www.rubor.de/bioinf/scriptBox.html
On my page, there is also a 'quick and dirty' hack for PyMOL.
FilePipe.py allows to execute PyMOL commands from a shell. It starts its 
own thread and reads lines from a text file. This doesn't work well, but 
it works.
Does anyone have a better idea to do this?


> If you want to have both GUIs running simulaneously, then try using the
> startup directory in modules/pmg_tk (you'll need to modify ScriptBox.py
> to have an __init__ method which creates the window, but simply
> returns instead of forking a thread or calling mainloop)

Thanks, this works in fact really well.


     Kristian

[PyMOL] Re: PyMOL-users digest, Vol 1 #105 - 6 msgs

[<kk...@ga...>]

Hi, dear Pymolers,

It is great to see the cross-eye stereo support in 0.82.
I am also very much interested in knowing the new selection operators.
The documentation seems to be a little bit behind?
Actually as we play more and more with pymol,
it is easily realized that the selection functions are
important not only for making pictures,
but also for doing further research and analysis.
How can I learn more about the selection and pymol object?
For example, what are the properties of each atom or
residue that I can use?

Finally, I wish to say that, I have got the 0.82 RPM already,
but since I installed python 2.2.1, there are always warning
when I start pymol complaining about the version of python.
However, actually there is no problem at all running under
python 2.2.1.

Cheers,
K.K.Liang

[PyMOL] Another Linux Stereo configuration

[Gene C. <gc...@ci...>]

Just thought I'd let people know that I was able to get
a stereo configuration working under linux.

The details...

My setup...
    OS: RedHat 7.1
    Xserver: XiG's Summit Platinum, multi-head version 2.1-8
    Video Card: Matrox G450(I think 32 Mb RAM)
    CPU: Intel(R) Pentium(R) 4 CPU 1300MHz
    RAM: 256Mb
    Monitor: ViewSonic PS790
    Stereo Equipment: Stereographics Stereoeyes wired.
    Pymol: 0.82

Notes:
    XiG offers a demo version of the server which is
    active for 20 minutes each invocation. This gives
    you ability to experiment before deciding to buy.

    After Summit is installed, and you've started the
    new Xserver, you need to use "Xsetup" to chose
    "Stereo Mode" under the OpenGL window. I chose
    WhiteLine. Restart your X server. The glasses should
    start to shutter at this point and the program "glxinfo"
    should indicate if you have stereo capability.

    If you get core dumps when you launch OpenGL programs,
    look at:
        Is your glibc at or above version 2?
        Try removing
         /usr/X11R6/lib/X11/AcceleratedX/modules/olg_sse2.mod

    select "Quad-Buffered Stereo" from the stereo selections.

[PyMOL] PyMOL 0.82 Released

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

PyMOL 0.82 has been released, and it includes binaries for Windows, Linux,
and IRIX.  It is mostly a bug-fix release.

Please test this version with your specific tasks before upgrading all
your systems -- there is always the possibility that something which
worked in a previous version won't work in this one.  If you do encounter
problems, please let me know.

Cheers,
Warren
wa...@de...

Re: [PyMOL] PyMOL gentoo package

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

On Mon, Jun 17, 2002 at 03:43:56PM +0200, Eckhart Guth=F6hrlein wrote:
> Hi all,
>=20
> just a short notice for debian users: there is a PyMOL deb-package
> available as part of the unstable distribution.
>=20
> http://packages.debian.org/unstable/science/pymol.html
>=20
> It is currently version 0.80, but probably it will soon be updated by
> the maintainer.
>=20
> Eckhart

Also,  for those of you running Gentoo linux, I created an ebuild awhile
back for version .80.  Unfortunately, it seems to be mired in a bugzilla
backlog, but you can get it here:

http://bugs.gentoo.org/show_bug.cgi?id=3D2917

At some point, I imagine it will make its way into the main portage
tree.

Regards,


Ben

[PyMOL] PyMOL debian package

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

Hi all,

just a short notice for debian users: there is a PyMOL deb-package
available as part of the unstable distribution.

http://packages.debian.org/unstable/science/pymol.html

It is currently version 0.80, but probably it will soon be updated by
the maintainer.

Eckhart

[PyMOL] Pymol 0.82 Redhat7.2 rpm on SuSE 8.0

[Marc S. <mar...@mp...>]

Hi all,

Just to let you know that the RedHat 7.2-rpm installs on SuSE-Linux 8.0 
as well.

All you need to do is to install with "--nodeps", because it seems that 
the rpm does not find the SuSE-Python-Installation (2.2), even if it's 
there. And you need to make a link from /usr/bin/python to 
/usr/bin/python2.1 to make Pymol think it has found the right version.

Of course one could recompile from source, but...


-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

Re: [PyMOL] mesh spheres

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

Michael,

Hmm not exactly, but try this:

show mesh
set solvent_radius=0.0001
rebuild

- Warren


On Mon, 17 Jun 2002, Michael Sorich wrote:

> Hi, 
>  
> Is it possible represent a molecule as mesh atom spheres? This would be
> like the spheres representation but the spheres would have a mesh
> surface, instead of an opaque or semi-transparent surface. I am aware of
> the mesh representation. However, this follows the surface of the
> molecule rather than the surface of the atom spheres.
>  
>  
> Thanks
>  
> Michael Sorich
> PhD Student
> School of Pharmaceutical, Molecular and Biomedical Sciences
> University of South Australia
> Email: mic...@po...
>            mik...@ho...
>  
> 
> ---
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>  
> 

[PyMOL] mesh spheres

[Michael S. <mik...@ho...>]

Hi, 
 
Is it possible represent a molecule as mesh atom spheres? This would be
like the spheres representation but the spheres would have a mesh
surface, instead of an opaque or semi-transparent surface. I am aware of
the mesh representation. However, this follows the surface of the
molecule rather than the surface of the atom spheres.
 
 
Thanks
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
 

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Re: [PyMOL] Release of ScriptBox 0.2 for PyMOL

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

> I have written a small program that lets you select your favorite PyMOL 
> script from a comfortable box floating beside your PyMOL window.

Kristian, thanks for sharing! 

> ScriptBox 0.2 can be found at:
> http://www.rubor.de/bioinf/scriptBox.html
> 
> Its my first release, so the program might still have bugs.

Specifically, this script may be incompatible with the standard external
GUI since Tcl/Tk/Tkinter does not multi-thread, and currently ScriptBox
fires up its own thread.  However, if you turn off the external GUI, then
the program works fine.

pymol -x ScriptBox.py

If you want to have both GUIs running simulaneously, then try using the
startup directory in modules/pmg_tk (you'll need to modify ScriptBox.py
to have an __init__ method which creates the window, but simply
returns instead of forking a thread or calling mainloop)

[However, if you are currently using the accelerated test version on a
mac, then you can ignore my comments about the external GUI, since it
doesn't yet exist on that platform.]

> BTW, is there any collection of scripts on the internet to browse through?

Clearly there is a consensus that this needs to be done.  I can't do 
it myself, but what I can do is place high visibility links on the
PyMOL web page.  So here goes...

You'll now see a "Scripts" item on the top of http://pymol.sf.net.  This
will take you to a page of submitted links, of which we have exactly one.

Please post your scripts somewhere on the internet and then send in the
URLs!  

By the way, while I personally disfavor GPL, I respect everyone's freedom
to choose their own license for their own code.  Please understand though
that I can't add a GPL component like ScriptBox to PyMOL without 
compromising on the overall PyMOL vision.  PyMOL exists to serve ALL
scientists, institutions, and companies -- including closed-source
software companies.

However, I do encourage use of PyMOL with GPL packages such as OELib and
GROMACS, and I have no objection to people distributing PyMOL derivatives
as GPL or even closed-source, particularly if they want to prevent their
code from being swallowed by the blue vortex ; ).  As for PyMOL, well,
that contingency has been part of the experiment from day one...

Cheers,
Warren

[PyMOL] Release of ScriptBox 0.2 for PyMOL

[Kristian R. <kri...@be...>]

Hello PyMOL users,

I have written a small program that lets you select your favorite PyMOL 
script from a comfortable box floating beside your PyMOL window.

ScriptBox 0.2 can be found at:
http://www.rubor.de/bioinf/scriptBox.html

Its my first release, so the program might still have bugs.

BTW, is there any collection of scripts on the internet to browse through?


Kristian Rother

RE: [PyMOL] displaying pharmacophores

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

Building ChemPy models is a snap.  Just "run" the following Python =
program from within PyMOL.

from chempy.models import Indexed
from chempy import Bond, Atom
from whrandom import random
from pymol import cmd

model =3D Indexed()

# create some atoms

for a in range(1,11):
   at =3D Atom()
   at.name =3D "X%02d"%a
   at.coord =3D [random()*5,random()*5,random()*5]
   model.atom.append(at)

# now create some bonds

for a in range(1,10):
   bd =3D Bond()
   bd.index =3D [a-1,a] # zero-based indices!
   model.bond.append(bd)

# now load and label

cmd.load_model(model,"example")
cmd.label("example","name")

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20


-----Original Message-----
From: Sorich, Michael Joseph - SORMJ001 =
[mailto:Mic...@po...]
Sent: Thursday, June 13, 2002 11:55 PM
To: pym...@li...
Subject: [PyMOL] displaying pharmacophores


Hi,
=20
I wish to use pymol to display pharmacophores. A pharmacophore will =
basically be a set of points/spheres each colored to represent the atom =
type it represents (eg hydrophobe, neg charged atom, hydrogen bond =
donor...).=20
=20
I have been using compiled graphics objects to display the =
pharmacophores, however, it would probably be more flexible to use a =
ChemPy object to represent the pharmacophore. The pharmacophore would be =
analogous to a molecule and would contain dummy atoms (eg hydrophobe =
atom, pos charged atom...) instead of the usual atom types. Would this =
be difficult? Does anyone have documentation on ChemPy?
=20
Also, could someone point me to an example python script to make a =
simple ChemPy molecule and load it with cmd.load_model()?
=20
Thanks for you help
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
=20


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[PyMOL] displaying pharmacophores

[Sorich, M. J. - S. <Mic...@po...>]

Hi,
 
I wish to use pymol to display pharmacophores. A pharmacophore will basically
be a set of points/spheres each colored to represent the atom type it
represents (eg hydrophobe, neg charged atom, hydrogen bond donor...). 
 
I have been using compiled graphics objects to display the pharmacophores,
however, it would probably be more flexible to use a ChemPy object to represent
the pharmacophore. The pharmacophore would be analogous to a molecule and would
contain dummy atoms (eg hydrophobe atom, pos charged atom...) instead of the
usual atom types. Would this be difficult? Does anyone have documentation on
ChemPy?
 
Also, could someone point me to an example python script to make a simple
ChemPy molecule and load it with cmd.load_model()?
 
Thanks for you help
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
 

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RE: [PyMOL] Continuous surfaces?

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

There is another (until now, undocumented way):

flag ignore, not A/49-63/, set
delete indicate
show surface

Would achieve the same effect.  If the surface was already computed, =
then you'll also need to issue the command:

rebuild

Cheers,
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: Frank Vondelft [mailto:Fra...@sy...]
> Sent: Tuesday, June 11, 2002 3:18 PM
> To: Peter Stogios; pym...@li...
> Subject: RE: [PyMOL] Continuous surfaces?
>=20
>=20
> Hi Peter
>=20
> What happens is that the surface is CREATED for the whole object, but
> only DISPLAYED for the selection.  You have to make a new object, and
> then draw the surface of that:
>=20
> create newobject, (chain a AND i;49-63)
> show surface, newobject
>=20
> Cheers
> phraenquex
>=20
> > -----Original Message-----
> > From: Peter Stogios [mailto:pst...@uh...]
> > Sent: Tuesday, June 11, 2002 3:14 PM
> > To: pym...@li...
> > Subject: [PyMOL] Continuous surfaces?
> >=20
> >=20
> > I'm trying to create a surface over only a range of residues.=20
> >  I'm simply
> > typing
> >=20
> > show surface, (chain a AND i;49-63)
> >=20
> > The surface I get is not continous and full of holes.  I=20
> > can't view the
> > surface from all angles either.  When I generate a surface=20
> > over the entire
> > molecule I don't get this problem.
> >=20
> > I think it might have something to do with a "slab view" or=20
> > some kind of
> > cutaway view, but I'm not sure.  How could I create a surface=20
> > over a range
> > of residues that isn't disjointed?
> >=20
> > --=20
> > Peter Stogios
> > Dept. of Medical Biophysics, Univ. of Toronto
> >=20
> >=20
> > _______________________________________________________________
> >=20
> > Multimillion Dollar Computer Inventory
> > Live Webcast Auctions Thru Aug. 2002 -=20
> > http://www.cowanalexander.com/calendar
> >=20
> >=20
> >=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
> ----------
> This message contains confidential information and is=20
> intended only for
> the individual named. If you are not the named addressee you=20
> should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail by mistake and
> delete this e-mail from your system. E-mail transmission cannot be
> guaranteed to be secure or error-free as information could be
> intercepted, corrupted, lost, destroyed, arrive late or incomplete, or
> contain viruses. The sender therefore does not accept=20
> liability for any
> errors or omissions in the contents of this message, which arise as a
> result of e-mail transmission. If verification is required please
> request a hard-copy version.=20
>=20
> _______________________________________________________________
>=20
> Multimillion Dollar Computer Inventory
> Live Webcast Auctions Thru Aug. 2002 -=20
> http://www.cowanalexander.com/calendar
>=20
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

RE: [PyMOL] Continuous surfaces?

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

Hi Peter

What happens is that the surface is CREATED for the whole object, but
only DISPLAYED for the selection.  You have to make a new object, and
then draw the surface of that:

create newobject, (chain a AND i;49-63)
show surface, newobject

Cheers
phraenquex

> -----Original Message-----
> From: Peter Stogios [mailto:pst...@uh...]
> Sent: Tuesday, June 11, 2002 3:14 PM
> To: pym...@li...
> Subject: [PyMOL] Continuous surfaces?
> 
> 
> I'm trying to create a surface over only a range of residues. 
>  I'm simply
> typing
> 
> show surface, (chain a AND i;49-63)
> 
> The surface I get is not continous and full of holes.  I 
> can't view the
> surface from all angles either.  When I generate a surface 
> over the entire
> molecule I don't get this problem.
> 
> I think it might have something to do with a "slab view" or 
> some kind of
> cutaway view, but I'm not sure.  How could I create a surface 
> over a range
> of residues that isn't disjointed?
> 
> -- 
> Peter Stogios
> Dept. of Medical Biophysics, Univ. of Toronto
> 
> 
> _______________________________________________________________
> 
> Multimillion Dollar Computer Inventory
> Live Webcast Auctions Thru Aug. 2002 - 
> http://www.cowanalexander.com/calendar
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


----------
This message contains confidential information and is intended only for
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delete this e-mail from your system. E-mail transmission cannot be
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contain viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this message, which arise as a
result of e-mail transmission. If verification is required please
request a hard-copy version. 

[PyMOL] Continuous surfaces?

[Peter S. <pst...@uh...>]

I'm trying to create a surface over only a range of residues.  I'm simply
typing

show surface, (chain a AND i;49-63)

The surface I get is not continous and full of holes.  I can't view the
surface from all angles either.  When I generate a surface over the entire
molecule I don't get this problem.

I think it might have something to do with a "slab view" or some kind of
cutaway view, but I'm not sure.  How could I create a surface over a range
of residues that isn't disjointed?

-- 
Peter Stogios
Dept. of Medical Biophysics, Univ. of Toronto

[PyMOL] (no subject)

[Sona V. <vas...@nc...>]

Hello All,

Need your help:

I would like to overlay a cartoon representation onto a surface
representation and would like to color certain residues that show up on
the surface representation. This is what I did and recall doing awhile ago but it
isn't working now. I would appreciate knowing what i am doing wrong.

Step 1: load temp.pdb

step 2: create cpy=temp

show surf, cpy

set transparency=0.5, cpy

Then I go on to color individual residues:

select t1=(resi 42)

Now I want residue 42 to be coloured say red on the surface 1.e object
cpy. Ofcourse overlaying is not the problem.

 Thanks much,

sona

Re: [PyMOL] Saving movie

[<kk...@ga...>]

"Warren L. DeLano" wrote:
> 
> You've got choose either real-time manipulation with OpenGL-quality
> rendering or prerendered movies without manipulation.  We need another
> 100-1000 fold increase in CPU performace before real-time raytracing will
> become possible.
> 
> -Warren

Dear Warren, 

 Don't be too upset for that.
I use a P4 1.8GHz machine (512kb) with RH7.2 to run the ray tracing
and it takes about 4.5 sec - to generate each frame.
Remember that in my pdb, besides the protein which is plot as cartoon,
there are 1718 water molecules,
and very often people are showing the movie frames
in 1 frame/ 5sec pace. They could not see clearly what happens
if we play it even faster.
This is already realtime considering all these.

Anyway, good job.

Best regards,
K.K.Liang

Re: [PyMOL] Saving movie

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

On Sun, 2 Jun 2002 kk...@ga... wrote:

> Now here comes another question.
> I prepared a long movie by running the script I wrote.
> I use a very good desktop to generate the movie and
> the speed of rendering is fast.
> But if I want to demonstrate the same movie with pymol on a
> notebook, there are only 2 things that I can do (as far as I know).
> First, I can copy the pdb files as well as the script I wrote
> to the notebook.
> But when I shall demonstrate the movie, I have to render all of
> the frames again.
> That is slower in the notebook we have in the conference roon.
> Also everything has to be rendered again if I restart pymol.
> To avoid rendering again and again, I can copy the png files
> generated, and use some other program to view the movie.
> By far I did not find a good free software giving control
> on how the movie be played as easy as pymol.

If you have all the frames rendered as png files, you can use load_png to
load the frames back into PyMOL for viewing, but you will need to do the
following

1. use mset to define a movie of proper length (mset 1 x10)
2. set cache_frames=1
3. write a script or program which uses cmd.frame to got to each frame and 
   individually loads each png file into the frame cache

cmd.mset("1 x10")
cmd.set("cache_frames","1")
cmd.frame(1)
cmd.load_png("frame01.png")
cmd.frame(2)
cmd.load_png("frame02.png")
...
cmd.frame(10)
cmd.load_png("frame10.png")

However, I just usually create AVI files of rendered movies using
commercial software (Premiere).  Such movies can be loaded directly into
PowerPoint, etc.

> Besides, I can modify the view point, rotation, etc,
> during the demonstration if I usr pymol.

You can't if it is pre-rendered, as is the case with the above example.

> Is there any suggestion on the best way to play the movie?

You've got choose either real-time manipulation with OpenGL-quality
rendering or prerendered movies without manipulation.  We need another
100-1000 fold increase in CPU performace before real-time raytracing will
become possible.

-Warren

Re: [PyMOL] selection in python script

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

On Sat, 1 Jun 2002 kk...@ga... wrote:

> Dear pymolers,
> 
> I can select some residues in my protein in the command prompt
> by saying for example
>  select prot = (////VAL or ////PRO or ////GLY)

There is a more concise way to write this:

select prot, val+pro+gly/

> but now I have trouble translating this into python script.
> I tried many varieties including something like
>  cmd.select( prot, (////VAL or ////PRO or ////GLY) )
> but by far nothing works.

You need to quote your strings:

cmd.select("prot","val+pro+gly/")

- Warren

[PyMOL] Saving movie

[<kk...@ga...>]

Dear pymolers,

Yesterday I asked the question about selection.
After studying python manual I figure out what I should do.

> I can select some residues in my protein in the command prompt
> by saying for example
>  select prot = (////VAL or ////PRO or ////GLY)
> but now I have trouble translating this into python script.
> I tried many varieties including something like
>  cmd.select( prot, (////VAL or ////PRO or ////GLY) )

I wrote cmd.select( "prot", "(////VAL or ////PRO or ////GLY)" )
and I got what I want.

Now here comes another question.
I prepared a long movie by running the script I wrote.
I use a very good desktop to generate the movie and
the speed of rendering is fast.
But if I want to demonstrate the same movie with pymol on a
notebook, there are only 2 things that I can do (as far as I know).
First, I can copy the pdb files as well as the script I wrote
to the notebook.
But when I shall demonstrate the movie, I have to render all of
the frames again.
That is slower in the notebook we have in the conference roon.
Also everything has to be rendered again if I restart pymol.
To avoid rendering again and again, I can copy the png files
generated, and use some other program to view the movie.
By far I did not find a good free software giving control
on how the movie be played as easy as pymol.
Perhaps ACDSee can play the movie better but it is not free.

Besides, I can modify the view point, rotation, etc,
during the demonstration if I usr pymol.

Is there any suggestion on the best way to play the movie?

Thanks and best regards,
K.K.Liang