pymol-users Mailing List for PyMOL Molecular Graphics System

Carlos Frazao wrote:

> I recently received an advertisment from PixelTech on an LCD for 
> crystallography,
>                           
> http://www.pixeltech.fr/index.php?path=stereoscopie&page=perceiva
> However, I  have not tested it ... Has anyone experience on such a
solution?

It seems to work with built in polarizers (every other column or row)
and polaroid glasses.  Either that or they've done a fantastic job
of miniaturizing the emitter and the electronics in the glasses :-).

See the pictures here:

http://www.nuvision3d.com/download/Perceiva%20sheet-corp-mid.pdf


David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

David,

Even if displays were to accept a high referesh-rate signal, there are two
other problems:

(1) the publisheed response times are usually gray-to-gray, not
full-on-to-full-off.  At 120 Hz stereo 3D, the display needs to go full-off
to full-on and back to full-off in 8.3 ms total (roughly equivalent to 4 ms
white-to-black response time).

and

(2) to be equivalent to a CRT and thus work with existing emitters and
shutter glasses, there can be no delay involved in converting the analog
SVGA signal to a digital image.  Based on what I've seen experimenting with
stereo 3D oon LCDs, this isn't normally true -- updates are shifted out of a
phase relative to an equivalent CRT.

I'm optimistic that high-end LCDs will eventually get there in terms of
response, eliminating issue (1).  However, the phasing problem (2) may
require special hardware to solve.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of David Mathog
> Sent: Wednesday, October 31, 2007 8:20 AM
> To: Sabuj Pattanayek
> Cc: pym...@li...
> Subject: Re: [PyMOL] 3D Glasses. Where to buy them ?
> 
> 
> 
> On Tue, 30 Oct 2007, Sabuj Pattanayek wrote:
> 
> > EPF (Esben Peter Friis) wrote:
> >> Hi David
> >>
> >> Try http://www.edimensional.com/. They have a UK sales office.
> >
> > Do these only work for programs under Linux that specifically 
> > implement page flipping stereo? The software that they 
> describe which 
> > must be installed seems to be only for Windows (which also 
> gives you 
> > page flipping stereo on LCDs).
> 
> Does somebody sell an LCD display now which will work (well) with
> stereo goggles?   I've seen LCD displays advertised with fast enough
> response times - but none so far that will accept a signal 
> much above  70 Hz, which is a bit on the slow side for page 
> swapped stereo.
> 
> Regards,
> 
> David Mathog
> 
> --------------------------------------------------------------
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Hi there,

We have bought glasses, LCD stereo displays and a stereo projection 
system from Inition here in the UK (www.inition.co.uk - based near 
Liverpool Street in London).  They carry a wide range, and know a lot 
about the field.  Definitely worth talking to if you are in the market 
for this sort of kit!

Regards,

Andrew

-- 
Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
phone: +44 (0)1223 252830   fax: +44 (0)1223 252835
web: www.mrc-dunn.cam.ac.uk email: And...@mr...

On Tue, 30 Oct 2007, Sabuj Pattanayek wrote:

> EPF (Esben Peter Friis) wrote:
>> Hi David
>>
>> Try http://www.edimensional.com/. They have a UK sales office.
>
> Do these only work for programs under Linux that specifically implement
> page flipping stereo? The software that they describe which must be
> installed seems to be only for Windows (which also gives you page
> flipping stereo on LCDs).

Does somebody sell an LCD display now which will work (well) with
stereo goggles?   I've seen LCD displays advertised with fast enough
response times - but none so far that will accept a signal much
above  70 Hz, which is a bit on the slow side for page swapped
stereo.

Regards,

David Mathog

Hi,

EPF (Esben Peter Friis) wrote:
> Hi Sabuj
> 
>> Do these only work for programs under Linux that specifically 
>> implement page flipping stereo? 
> 
> They deliver some drivers, which is for Windows only. On Linux, You must
> use a stereo-enabled graphics card (ie. most Nvidia Quadro series, no
> cheap GForce cards). 

That's what I thought, but then I saw this:

http://imsb.au.dk/pipermail/o-info/2003-April/006644.html


> The edimensional glasses also comes with a
> "break-out box" to mount between the graphics card and the monitor. This
> cannot be used with Linux, but the IR-emitter fits directly in the
> stereo port on the graphics card.

Still it's cheaper than stereo card + nuvision or stereographics. Do you 
know if these work on SGI's? How long is the cable on the IR transmitter?

Thanks,
Sabuj

Hi Sabuj

> Do these only work for programs under Linux that specifically=20
> implement page flipping stereo?=20

Yes. The application must support OpenGL stereo. I have tested with the
following programs:

- VMD
- PyMOL
- Accelrys InsightII
- Accelrys DiscoveryStudio

> The software that they=20
> describe which must be installed seems to be only for Windows=20
> (which also gives you page flipping stereo on LCDs).

They deliver some drivers, which is for Windows only. On Linux, You must
use a stereo-enabled graphics card (ie. most Nvidia Quadro series, no
cheap GForce cards). The edimensional glasses also comes with a
"break-out box" to mount between the graphics card and the monitor. This
cannot be used with Linux, but the IR-emitter fits directly in the
stereo port on the graphics card.


All the best

Esben

Konrad,

Sorry -- the curent brick code only supports orthogonal maps. =20

The only way to accomplish this at present is to write a =
crystallographic
map in one of the supported formats (XPLOR ASCII, CCP4 binary, or =
DSN6/BRIX)
and then read that map into PyMOL.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
=20
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Konrad Hinsen
> Sent: Monday, October 29, 2007 1:16 PM
> To: pymol-users
> Subject: [PyMOL] Non-orthogonal maps from Python code
>=20
> I would like to create electron density maps for a=20
> non-orthogonal crystal unit cell from a Python script for=20
> PyMol. However, it seems that chempy.brick is only made for=20
> orthogonal maps (it's hard to be sure since there is no=20
> explicit documentation). Is there some other way to generate=20
> non-orthgonal maps?
>=20
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Mol=E9culaire, CNRS Orl=E9ans
> Synchrotron Soleil - Division Exp=E9riences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hi...@cn...
> ---------------------------------------------------------------------
>=20
>=20
>=20
>=20
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and=20
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Paride,

One option is to simply create and modify coordinates real-time using
Python.  See example particle01.py

<http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/pa
rticle01.py?view=markup>

for a live animation of a particle system.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Paride Legovini
> Sent: Monday, October 29, 2007 5:23 AM
> To: pym...@li...
> Subject: [PyMOL] file format for homebrew MD software
> 
> I'm writing a simple molecular dynamics simulation software 
> and I'd like to visualize its results with pymol. More in 
> detail I have to simulate the behavior of chain of bounded 
> monomers (a polymer) in certain conditions. The monomers are 
> _generic_, i.e. I don't want to specify any particular 
> element for them (one good thing could be specifying their 
> diameter). I'd like to show the bonds between the monomers.
> 
> Which file format should I use for my output? At the moment 
> I'm trying with XYZ, but its quite unsuitable for the things 
> I've just remarked.
> 
> Sorry for the eventual trivial question, but I'm a newbie in MD.
> 
> Thank you,
> p.
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and 
> a browser.
> Download your FREE copy of Splunk now >> 
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EPF (Esben Peter Friis) wrote:
> Hi David
> 
> Try http://www.edimensional.com/. They have a UK sales office.

Do these only work for programs under Linux that specifically implement 
page flipping stereo? The software that they describe which must be 
installed seems to be only for Windows (which also gives you page 
flipping stereo on LCDs).

Thanks,
Sabuj

Hi David

Try http://www.edimensional.com/. They have a UK sales office.

We use those glasses with our Linux systems, and they work fine :-)


/Esben


____________________________________________________________=20
Best Regards
Esben Peter Friis
Phone: +45 44461334
E-mail: ep...@no...

Novozymes A/S (reg. no.: 10007127)
Krogshoejvej 36
DK-2880 Bagsvaerd, Denmark

This e-mail (including any attachments) is for the intended addressee(s)
only and may contain confidential and/or proprietary information
protected by law. You are hereby notified that any unauthorized reading,
disclosure, copying or distribution of this e-mail or use of information
herein is strictly prohibited. If you are not an intended recipient you
should delete this e-mail immediately. Thank you.

=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of David McGiven
> Sent: 29. oktober 2007 11:36
> To: pym...@li...
> Subject: [PyMOL] 3D Glasses. Where to buy them ?
>=20
>=20
> Dear PyMol Users,
>=20
> I know this isn't strictly pymol related but I suppose there=20
> are other users interested on that.
>=20
> I've been trying to contact 3D Glasses dealers for the last=20
> months but have no luck.
>=20
> There's REALD and Nuvision 3D manufacturers, but they don't=20
> seem to reply emails. Strange.
>=20
> Has anybody bought glasses from them in the last months ?=20
> Specifically from Europe.
>=20
> Best Regards,
>=20
> David McGiven
>=20
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and=20
> a browser.
> Download your FREE copy of Splunk now >>=20
> http://get.splunk.com/ _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

In my work I have to show how a polymer interacts with a membrane, that
I (at the moment) modelize as a potential barrier. I want to show it in
my simulation, so I'm wondering if there is a way to draw something like
a wall with pymol?

Thank you,
p.

I would like to create electron density maps for a non-orthogonal =20
crystal unit cell from a Python script for PyMol. However, it seems =20
that chempy.brick is only made for orthogonal maps (it's hard to be =20
sure since there is no explicit documentation). Is there some other =20
way to generate non-orthgonal maps?

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Mol=E9culaire, CNRS Orl=E9ans
Synchrotron Soleil - Division Exp=E9riences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hi...@cn...
---------------------------------------------------------------------

set_view (...your matrix here...)
view F1,store

set_view (...your matrix here...)
view F2,store

view F1, animate=3

view F2, animate=7

etc.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Richard Baxter
> Sent: Saturday, October 27, 2007 7:09 PM
> To: pym...@li...
> Subject: [PyMOL] move to go between set_view statements
> 
> Dear pymol-users,
> 
> I have two figures and the specific orientation, depth, etc. 
> is in the script as a set_view command. Can I write a movie 
> script to go from set_view(1) to set_view(2) in a certain 
> number of frames?
> 
> thanks for your help,
> 
> Richard Baxter
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and 
> a browser.
> Download your FREE copy of Splunk now >> 
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

http://www.pymolwiki.org/index.php/Windows_Install
 
http://support.microsoft.com/default.aspx?scid=kb;en-us;324767


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of surendra negi
> Sent: Monday, October 29, 2007 9:58 AM
> To: pym...@li...
> Subject: [PyMOL] pymol installalation
> 
> Dear Users,
>  I am unable to install new pymol build in XP.. After running 
> setup file it is doing nothing.. any idea? though I am able 
> to install other softwares like vmd etc. 
> thank you.
> 
> 
> 
> 
> __________________________________________________
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> Tired of spam?  Yahoo! Mail has the best spam protection 
> around http://mail.yahoo.com 
> 
> --------------------------------------------------------------
> -----------
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> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and 
> a browser.
> Download your FREE copy of Splunk now >> 
> http://get.splunk.com/ _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

After one hour wait it is showing following message :

The request to end the selected 16 bit task has timed out. The Win 16
Subsystem may be unstable. Press OK to terminate the Win 16 Subsystem or
Calcel to leave it running.

Any help?
thanks


Message: 9
Date: Mon, 29 Oct 2007 09:58:06 -0700 (PDT)
From: surendra negi <ne...@ya...>
Subject: [PyMOL] pymol installalation
To: pym...@li...
Message-ID: <153...@we...>
Content-Type: text/plain; charset=us-ascii

Dear Users,
 I am unable to install new pymol build in XP.. After running setup
 file it is doing nothing.. any idea? though I am able to install other
 softwares
like vmd etc. 
thank you.








__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

Dear Users,
 I am unable to install new pymol build in XP.. After running setup file it is doing nothing.. any idea? though I am able to install other softwares
like vmd etc. 
thank you.




__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

I'm writing a simple molecular dynamics simulation software and I'd like
to visualize its results with pymol. More in detail I have to simulate
the behavior of chain of bounded monomers (a polymer) in certain
conditions. The monomers are _generic_, i.e. I don't want to specify any
particular element for them (one good thing could be specifying their
diameter). I'd like to show the bonds between the monomers.

Which file format should I use for my output? At the moment I'm trying
with XYZ, but its quite unsuitable for the things I've just remarked.

Sorry for the eventual trivial question, but I'm a newbie in MD.

Thank you,
p.

Dear PyMol Users,

I know this isn't strictly pymol related but I suppose there are other
users interested on that.

I've been trying to contact 3D Glasses dealers for the last months but
have no luck.

There's REALD and Nuvision 3D manufacturers, but they don't seem to
reply emails. Strange.

Has anybody bought glasses from them in the last months ? Specifically
from Europe.

Best Regards,

David McGiven

Dear pymol-users,

I have two figures and the specific orientation, depth, etc. is in the script as a 
set_view command. Can I write a movie script to go from set_view(1) to set_view(2) in 
a certain number of frames?

thanks for your help,

Richard Baxter

Hi Michael

If the system is very big and causes the ray tracing to crash, try to
lower the hash_max setting. I think the default is 100. If the setting
is lower, it will be slower, but use less memory. (and vice versa :-)

All the best

Esben



> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of DeLano Scientific
> Sent: 25. oktober 2007 18:11
> To: 'Michael Lerner'; 'pymol mailinglist'
> Subject: Re: [PyMOL] Trouble making pictures in a script
>=20
> Michael,
>=20
> The "-c" option forces PyMOL to run in command-line-only mode=20
> which means it doesn't have access to the OpenGL hardware=20
> (used by cmd.draw and interactive graphics).  In=20
> command-line-only mode, ray tracing (cmd.ray) is the only option.
>=20
> Cheers,
> Warren
> =20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of=20
> > Michael Lerner
> > Sent: Thursday, October 25, 2007 8:31 AM
> > To: pymol mailinglist
> > Subject: [PyMOL] Trouble making pictures in a script
> >=20
> > Hi,
> >=20
> > I have a Python script that sets a system up and then calls
> > cmd.png() to render an image. I use it to process several=20
> files at a=20
> > time, and there's no need to look at it while it's working, so I use
> >=20
> > pymol -qcr myscript.py
> >=20
> > to launch it. It works fine when I ray trace things, but if=20
> I just set=20
> > the system up and call cmd.png(), I get this error:
> >=20
> >  ScenePNG-WARNING: invalid context or no image.
> >=20
> > Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
> > Any ideas? Some of the systems are big enough that=20
> cmd.ray() fails, so=20
> > I'd like to be able to find a workaround.
> >=20
> > Thanks,
> >=20
> > -michael
> >=20
> > --
> > Biophysics Graduate Student
> > Carlson Lab, University of Michigan
> > http://www.umich.edu/~mlerner
> >=20
> > --------------------------------------------------------------
> > -----------
> > This SF.net email is sponsored by: Splunk Inc.
> > Still grepping through log files to find problems?  Stop.
> > Now Search log events and configuration files using AJAX and a=20
> > browser.
> > Download your FREE copy of Splunk now >> http://get.splunk.com/=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and=20
> a browser.
> Download your FREE copy of Splunk now >>=20
> http://get.splunk.com/ _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Jeff,

PyMOL isn't a homology modeling tool, but in combination with something like
GROMACS, you might able to accomplish something like this.

Although one can easily use PyMOL to graft and assemble molecules, that last
step of cleaning up the "joints" and any missing residues requires an
external minimization.  Here is an example of coordinate grafting:

# load HIV protease (symmetric dimer)

load $TUT/1hpv.pdb

# map chain A coordinates onto chain B

coord_dict = {}

iterate_state 1, chain A, coord_dict[(resi,name)]=(x,y,z)

alter_state 1, chain B, (x,y,z)=coord_dict.get((resi,name),(x,y,z))


Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Yang Mingjun
> Sent: Wednesday, October 24, 2007 6:33 AM
> To: pymol-users
> Subject: [PyMOL] Superposition and connect of two segment
> 
>  Dear all,
>    A new user to pymol. 
>    I have a question about the superposition of two 
> molecules. To say it clearly, for example, there are two 
> structures of a molecule in two pdb files, one including 
> 20-200 residues, the other including 10-180 residues, where 
> the structures of shared residues 10-180 are almost the same.
>    What I want to do is to incorporate the coordinate 
> information in one pdb file(containing residues 10-180, in 
> which the residues 10-19 are missed in the other file) into 
> the other one, which includes residues 20-200. The final 
> result is a pdb file containing residues 10-200, with a 
> correct connected bond and orientation between residue 19 and 
> 20. The coordinates of residues 20-180 are almost the same 
> but not exact.
> 
>  I am wondering whether PyMol can solve this question exact and how.
>  Any suggestion is greatly appreciated.
> 
>  Thanks.
> 
> ------
> Jeff
> 
> 
> 
> 

Michael,

The "-c" option forces PyMOL to run in command-line-only mode which means it
doesn't have access to the OpenGL hardware (used by cmd.draw and interactive
graphics).  In command-line-only mode, ray tracing (cmd.ray) is the only
option.

Cheers,
Warren
 
> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Michael Lerner
> Sent: Thursday, October 25, 2007 8:31 AM
> To: pymol mailinglist
> Subject: [PyMOL] Trouble making pictures in a script
> 
> Hi,
> 
> I have a Python script that sets a system up and then calls 
> cmd.png() to render an image. I use it to process several 
> files at a time, and there's no need to look at it while it's 
> working, so I use
> 
> pymol -qcr myscript.py
> 
> to launch it. It works fine when I ray trace things, but if I 
> just set the system up and call cmd.png(), I get this error:
> 
>  ScenePNG-WARNING: invalid context or no image.
> 
> Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
> Any ideas? Some of the systems are big enough that cmd.ray() 
> fails, so I'd like to be able to find a workaround.
> 
> Thanks,
> 
> -michael
> 
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and 
> a browser.
> Download your FREE copy of Splunk now >> 
> http://get.splunk.com/ _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

I have a Python script that sets a system up and then calls cmd.png()
to render an image. I use it to process several files at a time, and
there's no need to look at it while it's working, so I use

pymol -qcr myscript.py

to launch it. It works fine when I ray trace things, but if I just set
the system up and call cmd.png(), I get this error:

 ScenePNG-WARNING: invalid context or no image.

Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
Any ideas? Some of the systems are big enough that cmd.ray() fails, so
I'd like to be able to find a workaround.

Thanks,

-michael

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner

 Dear all,
   A new user to pymol. 
   I have a question about the superposition of two molecules. To say it clearly, for example, there are two structures of a molecule in two pdb files, one including 20-200 residues, the other including 10-180 residues, where the structures of shared residues 10-180 are almost the same.
   What I want to do is to incorporate the coordinate information in one pdb file(containing residues 10-180, in which the residues 10-19 are missed in the other file) into the other one, which includes residues 20-200. The final result is a pdb file containing residues 10-200, with a correct connected bond and orientation between residue 19 and 20. The coordinates of residues 20-180 are almost the same but not exact.

 I am wondering whether PyMol can solve this question exact and how.
 Any suggestion is greatly appreciated.

 Thanks.

------
Jeff

David,

Here's an example of using the translate command to achieve what you're
seeking.

fetch 1t46,async=0
fetch 1oky,async=0
as cartoon
align 1t46////CA, 1oky////CA
orient 1t46 and organic
turn z,180
translate [50,0,0], 1oky
zoom
show sph, organic
color white, organic and elem c

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of David Garboczi
> Sent: Sunday, October 21, 2007 3:33 PM
> To: pym...@li...
> Subject: [PyMOL] How to move aligned objects apart
> 
> I have three molecules aligned on each other.  I would like 
> to move them apart so that I can make a .png file with all 
> three of them aligned, but simply translated apart.
> 
> I have tried the translate [x, x, x] command but no success.
> 
> Advice?
> 
> thanks,
> 
> Dave
> -- 
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