pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

> Just for the sake of the uninitiated ....
>=20
> What are .p1m files and how do they differ from regular .pml files. I=20
> took a quick look at Sebastians file and it looked pretty much like a=20
> regular .pml file to me.
>=20
>=20
> Cheers,
>=20

.p1m files are web oriented. With them, you can embedded whole=20
structures and PyMOL commands in one file.

You can do the same with a pml file here and a load command which loads=20
the pdb file there. But that is two files instead of only one.

>=20
>  > But, '#' doesn't work in p1m file.
>  >     Error: unrecognized keyword: #second
>  > The # line involves an error but the script goes on.
>=20
> I think indeed you found a bug with the parsing of p1m files.
> I have the same behaviour on my Linux computer.
>=20
> Nice choice of colors by the way.
>=20
> Cheers,
>=20
> Zac

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

RE: [PyMOL] comments ?

[Schubert, C. [PRDUS] <CSC...@pr...>]

Just for the sake of the uninitiated ....

What are .p1m files and how do they differ from regular .pml files. I took a
quick look at Sebastians file and it looked pretty much like a regular .pml
file to me. 


Cheers,

	Carsten

-----Original Message-----
From: Ezequiel H Panepucci [mailto:za...@pa...]
Sent: Tuesday, August 02, 2005 10:05 AM
To: Sebastien Moretti
Cc: pymol-users
Subject: Re: [PyMOL] comments ?



> But, '#' doesn't work in p1m file.
>     Error: unrecognized keyword: #second
> The # line involves an error but the script goes on.

I think indeed you found a bug with the parsing of p1m files.
I have the same behaviour on my Linux computer.

Nice choice of colors by the way.

Cheers,

Zac




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Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

> Yes -- this is a bug -- thanks for pointing it out.
>=20
> Cheers,
> Warren
>=20
>=20

It seems that the 'print "..."' commands is unrecognized in p1m files too=
.

>>
>>>But, '#' doesn't work in p1m file.
>>>    Error: unrecognized keyword: #second The # line=20
>>
>>involves an error=20
>>
>>>but the script goes on.
>>
>>I think indeed you found a bug with the parsing of p1m files.
>>I have the same behaviour on my Linux computer.
>>
>>Nice choice of colors by the way.
>>
>>Cheers,
>>
>>Zac

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] sessions and movies

[Joel T. <joe...@ot...>]

Hi Nadine,

To answer the first part, there is a much easier way...use the scene 
function in 0.98 version. This allows you to jump between individual 
"screenshots". You can then save this as a .psw file and view it as full 
screen or embed it in powerpoint. (See my previous post "Pymol scenes to 
movies"). Essentaially you set up view 1 and hit append, then view 2 , 
append etc. you can then scroll thru your views.

The second question, can't help.

Cheers

J

Nadine Atwood wrote:

>
> Hi,
>
> I have come across a problem that I cannot find a way around and would 
> greatly appreciate some help. I have made a movie showing several 
> protein models and numerous distances to illustrate residue 
> interactions in different structures. This movie is rather long, and I 
> wanted to make a very short version containing certain "screenshots" 
> of the original. I have created *.pse files corresponding to the 
> frames I would want in the short movie, but cannot find a way of 
> loading these in a script. (I can view them "manually" by opening them 
> one at a time through the command line, but that rather defeats the 
> point.) I wanted to load these using mset and mdo commands, but of 
> course, as soon as I load the first one, PyMOL's memory returns to the 
> state that was saved and the new movie is deleted. I suppose I need to 
> save these files in another format, but have not been able to find 
> anything that seems appropriate.
>
> I have also encountered another small problem that I do not need a 
> solution to but thought I would mention as it might be a bug (though 
> it could be due to my very amateurish programming): when running the 
> long movie (which creates and deletes a large number of distances), if 
> the movie is stopped and then start again, some distances (I suppose 
> corresponding to commands given in frames where the movie was stopped) 
> are not deleted, whereas if the movie is run without interruption, all 
> distances are handled correctly. (I am using version 0.97)
>
> I am not very computer literate, so a simple explanation would be 
> fantastic.    ;)
> Thanks for your advice.
>
> Nadine
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's 
> FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
>
>
> -------------------------------------------------------
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-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

[PyMOL] showing van der waals radius for atoms in pymol

[Rongjin G. <gu...@um...>]

Dear pymol-users=A3=AC

I want to show close contacts (or stereo clashes) in protein-ligand c=
omplex
by showing the overlapped van der waals radius sphere (not CPK mode).
Can pymol do this? if, how?

Thanks

Rongjin Guan

[PyMOL] sessions and movies

[Nadine A. <nad...@ho...>]

Hi,

I have come across a problem that I cannot find a way around and would 
greatly appreciate some help. I have made a movie showing several protein 
models and numerous distances to illustrate residue interactions in 
different structures. This movie is rather long, and I wanted to make a very 
short version containing certain "screenshots" of the original. I have 
created *.pse files corresponding to the frames I would want in the short 
movie, but cannot find a way of loading these in a script. (I can view them 
"manually" by opening them one at a time through the command line, but that 
rather defeats the point.) I wanted to load these using mset and mdo 
commands, but of course, as soon as I load the first one, PyMOL's memory 
returns to the state that was saved and the new movie is deleted. I suppose 
I need to save these files in another format, but have not been able to find 
anything that seems appropriate.

I have also encountered another small problem that I do not need a solution 
to but thought I would mention as it might be a bug (though it could be due 
to my very amateurish programming): when running the long movie (which 
creates and deletes a large number of distances), if the movie is stopped 
and then start again, some distances (I suppose corresponding to commands 
given in frames where the movie was stopped) are not deleted, whereas if the 
movie is run without interruption, all distances are handled correctly. (I 
am using version 0.97)

I am not very computer literate, so a simple explanation would be fantastic. 
    ;)
Thanks for your advice.

Nadine

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Re: [PyMOL] Pymol sessions

[Tsjerk W. <ts...@gm...>]

Hi John,

I've never met this problem, and have saved very large session files.
Which version are you using?

Tsjerk

On 8/3/05, John Whitlow <whi...@gm...> wrote:
> > I've been loading the results of my docking runs, which are
> > multi-hundred SD files, into pymol and saving the session for
> > use in colaborating.  I cannot save the session past a
> > certain size.  I think the largest successfully saved session
> > was 40 something megs.
> >
> > I've tried saving on multiple systems (both windows and
> > Linux)and pymol consistently crashes while saving large
> > sessions.  Is this standard behavior?  Are there any known
> > workarounds?
> >
> > Thanks!
> >
> > John
> >
>=20
>=20
> -------------------------------------------------------
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>

[PyMOL] Pymol sessions

[John W. <whi...@gm...>]

> I've been loading the results of my docking runs, which are
> multi-hundred SD files, into pymol and saving the session for
> use in colaborating.  I cannot save the session past a
> certain size.  I think the largest successfully saved session
> was 40 something megs.
>
> I've tried saving on multiple systems (both windows and
> Linux)and pymol consistently crashes while saving large
> sessions.  Is this standard behavior?  Are there any known
> workarounds?
>
> Thanks!
>
> John
>

Re: [PyMOL] Name length in names panel

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

Hellow Sebastien,

* Sebastien Moretti <seb...@ig...> [2005-08-01 08:48] wrote:
> >Hello Sebastien,
> >>Hello,
> >>Is there a way to expand the names panel to be able to read object and 
> >>selection names larger than 16 characters ?
> >
> > 
> >At the bottom left corner of the panel, just to the left of the "VCR
> >controls" is a little vertical bar.  You can drag it to change the width
> >of the panel.
> >
> >Cheers,
> >Rob
> 
> I haven't seen this vertical bar before. I don't think it is described 
> in the PyMOL user's guide ?
> Thanks
> 
> Now I can more easily see large names instead of using the 'rename 
> object' action.

I've attached a small png image of that part of the screen with the
"vertical bar" circled in red.  Hopefully that makes it more clear.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] New transform_odb script

[Mark A S. <sa...@um...>]

The "transform_odb" script transforms the coordinates of a selection  
and creates a new object with the transformed coordinates. The  
transformation matrix is read from a file containing an "O"-style  
tranformation matrix (.odb) written by "O" or by any of the Uppsala  
Software Factory programs (from Gerard Klegweit) such as LSQMAN.

See http://www.pymolwiki.org/index.php/Transform_odb

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> But, '#' doesn't work in p1m file.
>     Error: unrecognized keyword: #second
> The # line involves an error but the script goes on.

I think indeed you found a bug with the parsing of p1m files.
I have the same behaviour on my Linux computer.

Nice choice of colors by the way.

Cheers,

Zac

[PyMOL] Re: PyMOL-users digest, Vol 1 #963 - 12 msgs

[tree <jav...@ut...>]

Sreekala,

You want to 'split_states'.  Load the biological unit into Pymol then
run 'split_states'.

Check out the PyMolWiki: http://www.pymolwiki.org/index.php/Split_States
where it's described more fully.

-- Jason


On Mon, 2005-08-01 at 20:22 -0700,
pym...@li... wrote:
> Hello,
> 
>   I am trying to view the dimeric structure of the aspartate receptor
> =
> (1VLS) in pymol. The biological moleclule is a dimer made up of two
> four =
> helix bundles related by a two fold axis. I downloaded the co
> ordinates =
> for the biological molecule from the pdb website
> (filename:1VLS.pdb1).=20
> 
>   However, I am able to view only one four helix bundle when this file
> =
> is opened in pymol. The atom numbers for both model1 and model 2 are =
> numbered from 1 to 1145 . Is there an option  to view the dimer in
> pymol =
> or should I alter the helix header lines and atom numbers in the pdb =
> file in order to view the dimer.
> 
> 
>   thanks.
> 
>   Sreekala.
-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

>> '#' seems to be incorrect:
>=20
> It is not incorrect.
>=20
> If you post your script and how you use it we might be able to help.
>=20
> Also, if you have something in you $HOME/.pymolrc or $HOME/.pymolrc.py
> you should try temporarily moving these files elsewhere and trying agai=
n.
> Something may have gone wrong in one of those files, it happened to me=20
> before.
>=20
> Zac

I didn't properly test the '#' character.
It works in the external GUI and in standard scripts like in pml files.

But, '#' doesn't work in p1m file.
	Error: unrecognized keyword: #second
The # line involves an error but the script goes on.

I join an example where I removed the embedded lines with the structure=20
because the e-mail size was too large for the mailist server.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] NOTIFICATION

[freelotto_net <fre...@ya...>]

THE FREELOTTO COMPANY
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SUITE 23-30, LION TOWERS
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ted from a batch of 50,000,000 international emails. Your email address e=
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innings:

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FAX: +44 701333845
TEL: +44 7031845683
Email:con...@wa...

N.B: This is steps to claim your prize:


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Mail sent from WebMail service at http://www.truckdriving.com/

Re: [PyMOL] Pymol Scenes to Movies

[Joel T. <joe...@ot...>]

Hi Chris,

I've been using this function a lot  in my teaching. You don't need to 
convert it to a movie, just save session as a .psw (pymol show file) 
with the scenes embedded in there. Then from within powerpoint just set 
up a hyperlink (Insert hyperlink) and point it to the .psw file. In 
presentation mode when you click on the hyperlink pymol automatically 
boots and you can scroll thru your scens like a full screen powerpoint 
presentation. You have to make sure that you have pymol installed on 
your presentation computer (and you have your psw file)  and just click 
OK when powerpoint warns of the perils of non-microsoft products. the 
final scene will return to your powerpoint presentation without any effort.

(Haven't tried it on a mac but should work fine)

Cheers

Joel

Christopher Bond wrote:

> Hi All,
>
>   I'm using Pymol 0.98 on a mac G5. I've created a number of scenes 
> using the append command and would like to convert these scenes to a 
> format suitable for a powerpoint presentation. I've tried in vain to 
> make a movie which plays through these scenes using mset and mdo with 
> no success. Any suggestions on how to make this work.
>
> Thanks,
>
> Chris
> ______________________________________________
> Christopher J Bond
> Postdoctoral Scholar
> Department of Micorbiology and Immunology
> Stanford University
>
> 650.498.7111
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

[PyMOL] view dimeric structure

[Sreekala B. <ba...@co...>]

Hello,

  I am trying to view the dimeric structure of the aspartate receptor =
(1VLS) in pymol. The biological moleclule is a dimer made up of two four =
helix bundles related by a two fold axis. I downloaded the co ordinates =
for the biological molecule from the pdb website (filename:1VLS.pdb1).=20

  However, I am able to view only one four helix bundle when this file =
is opened in pymol. The atom numbers for both model1 and model 2 are =
numbered from 1 to 1145 . Is there an option  to view the dimer in pymol =
or should I alter the helix header lines and atom numbers in the pdb =
file in order to view the dimer.


  thanks.

  Sreekala.

[PyMOL] Bonds or lines with user set colors..

[Tarak U. <sol...@ya...>]

Hey

I'm trying to make bonds.. or lines/connections
between the C-alphas of various residues. I found that
bond can do this, however the bond color is adopted
from the color of the atoms that the bond connects. Is
there a way to isolate a bond object and set the color
of it independent of the atoms it is attached to?

If not, is there another method to produce this effect
besides "bond"... possibly by using endpoint
coordinates to define lines?

Thanks!

TJU




		
____________________________________________________
Start your day with Yahoo! - make it your home page 
http://www.yahoo.com/r/hs 
 

[PyMOL] Pymol Scenes to Movies

[Christopher B. <cb...@st...>]

Hi All,

   I'm using Pymol 0.98 on a mac G5. I've created a number of scenes 
using the append command and would like to convert these scenes to a 
format suitable for a powerpoint presentation. I've tried in vain to 
make a movie which plays through these scenes using mset and mdo with 
no success. Any suggestions on how to make this work.

Thanks,

Chris
______________________________________________
Christopher J Bond
Postdoctoral Scholar
Department of Micorbiology and Immunology
Stanford University

650.498.7111

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> '#' seems to be incorrect:

It is not incorrect.

If you post your script and how you use it we might be able to help.

Also, if you have something in you $HOME/.pymolrc or $HOME/.pymolrc.py
you should try temporarily moving these files elsewhere and trying again.
Something may have gone wrong in one of those files, it happened to me before.

Zac

Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

>> I try to add comment lines in my pml scripts but I don't know how to d=
o.
>> I tried #, /*, //, <!-- or <-- characters but everything fails.
>=20
> use '#' but  on a line of its own not at the end of
> line containing a pymol command, like this:
>=20
> # color 1DHS in red
> color red, 1DHS

'#' seems to be incorrect:
	#second essai
	Error: unrecognized keyword: #second
	delete AaA

The script goes on but it sends an error message

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> I try to add comment lines in my pml scripts but I don't know how to do.
> I tried #, /*, //, <!-- or <-- characters but everything fails.

use '#' but  on a line of its own not at the end of
line containing a pymol command, like this:

# color 1DHS in red
color red, 1DHS

Re: [PyMOL] comments ?

[<li...@ul...>]

On Monday 01 August 2005 11:08, Sebastien Moretti wrote:
> Hello,
> I try to add comment lines in my pml scripts but I don't know how to do.
> I tried #, /*, //, <!-- or <-- characters but everything fails.
...
> How can I use comments in PyMOL scripts ?

The hash character (#) works to include comments on separate lines, but not at 
the end of a line that contains commands. So you can do

# Create separate dimer
create dimer,(chain A,B)

but not

create dimer,(chain A,B)  # Create separate dimer

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

[PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

Hello,
I try to add comment lines in my pml scripts but I don't know how to do.
I tried #, /*, //, <!-- or <-- characters but everything fails.

I got this kind of error messages:
	color red, 1DHS #color
	Selector-Error: Invalid Selection Name.
	( 1DHS #color )<--
or
	color red, 1DHS
	<-- second essai -->
	Error: unrecognized keyword: <--

How can I use comments in PyMOL scripts ?
Thanks

I use PyMOL 0.98 on Linux OS.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] unit cell and cell packing

[Tsjerk W. <ts...@gm...>]

Hi Zhenbo,

If you mean the triclinic unit cell, you can show it with 'show cell',
given that it's provided in the pdb file. If you want a different
representation, you need a script. Also for the cell packing, you'd
need a script. If it's just a translation lattice, I think I have what
you need, just let me know. If it involves rotation I can't help you
further than this at present. Maybe you can find something on Robert
Campbells site:

http://adelie.biochem.queensu.ca/~rlc/work/pymol/

Hope it helps,

Tsjerk

On 8/1/05, zhenbo cao <zh...@ch...> wrote:
> Hi everyone,
>=20
> I was wondering if there's a simple way to display the unit cell in
> Pymol? it will be even better if anybody know how to show the cell
> packing.
> Thanks for you help!
>=20
> Cheers,
>=20
> zhenbo
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclic=
k
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] unit cell and cell packing

[zhenbo c. <zh...@ch...>]

Hi everyone,

I was wondering if there's a simple way to display the unit cell in 
Pymol? it will be even better if anybody know how to show the cell 
packing.
Thanks for you help!

Cheers,

zhenbo