pymol-users Mailing List for PyMOL Molecular Graphics System

There is an update for the bbPlane script.

Changes:
 * support proline residues
 * support two_sided_lighting setting
 * speed improvement

http://pymolwiki.org/index.php/BbPlane

Cheers,
  Thomas

Jason Vertrees wrote:
> Greetings,
>
> First, after a reading a recent post that piqued my interest, I
> implemented a script that will draw a plane through backbone atoms.
> This could be useful to anyone wanting to see or teach the planarity
> of the main chain atom.  The script and example images are here:
> http://pymolwiki.org/index.php/BbPlane.  Just provide the selection
> and you're done.  You can also specify color and transparency.
>
> Next, if someone is interested in helping maintain/update the
> PyMOLWiki, please let me know.  We still get 800-1200 unique visitors
> per day and that means spam.
>
> Last, thanks for being patient recently with my slow responses on the
> PyMOL-users list.  To more effectively support and develop PyMOL, I
> packed up moved to NYC to be in the Schrodinger main office.  This
> gives me better access to bright minds and resources that should lead
> to quicker improvements for PyMOL.
>
> Cheers,
>
> -- Jason

--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi all,
 
We have a number of workstations equipped w. Quadro FX 3800, 3D-Vision
Stereo 
Glasses and Samsung 2233RZ 120 Hz Monitors. We are using OpenGL quad
buffered 
Stereo under openSuSE LINUX 11.2 with pymol. 
 
An attempt to equip the workstations with an additional set of the same 
Graphics Card, Monitors, Stereo Emitter, Keyboard and Mouse to realize a

multiseat configuration however was not successful in respect to stereo
display: 
 
We configured the computers essentially as shown in 
http://wpkg.org/Configuring_multiseat_X_workstation
and this at a first glance seemed to work. 
 
Unfortunately the second seat configuration did not recognize the second
USB 
Stereo Emitter and subsequently on this seat stereo was disabled. 
The error message in the Xorg.1.log was
"Failed to claim USB interface for stereo emitter device. Disabling
stereo"
On the second stereo emitter the led was slowly blinking in red.
 
On the other hand both Stereo-Emitters were listed in
/proc/bus/usb/devices. 
 
Does anyone have a hint how to set the second stereo emitter into
function?

Regards,
 
Joachim
 
--
Dr. rer. nat. Joachim Greipel
Med. Hochschule Hannover
Biophys. Chem. OE 4350
Carl-Neuberg-Str. 1
30625 Hannover
Germany
 
Fon: +49-511-532-3718
Fax: +49-511-532-8924
 
 
 

Cannot compile neither by pyton-like style (python setup.py build
install) nor by general gnu case
./configure; make; make install

In 1st case i obtained:
modules/cealign/src/ccealignmodule.H:70: error: ‘PyObject’ was not
declared in this scope

in 2nd case:
"Cmd.c:88:21: error: ce_types.h: No such file or directory"
I've tried on both cygwin and linux debian lenny machines with no
success. Revision to install - 	3910.


I've read before troubles of Hari
(http://www.mail-archive.com/pym...@li.../msg07678.html)
but its not seems to be my case :(

-- 
King regards,
Sergey Ivanov

Hi Mark,

The surface representation of a protein, in PyMol, shows the
"Connolly" surface or the surface that would be traced out by the
_surfaces_ of waters in contact with the protein at all possible
positions.  Also, since PDBs don't have hydrogens, and PyMOL will
calculate the surface for whatever is present, you should add and
render surfaces for a protein with hydrogens.  I think this will give
you the most biophysically relevant representation for you published
image.

Cheers,

-- Jason

On Mon, Jun 28, 2010 at 6:46 PM, Mark A Saper <sa...@um...> wrote:
> If a model is modified, the "rebuild" command does not always update the surface.  For example,
>
>        show lines, theProtein and not elem H
>        show surface
>
>        show lines, elem H
>        rebuild
>
> The surface does not change.  But if I now,
>
>        hide surface
>        show surface
>
> the surface swells slightly to account for the hydrogens.
>
> Is this a bug?  or a feature?  Also, is it appropriate to show surfaces in publication in the presence of the H's?  Or does the 1.4 Å probe sphere that PyMOL uses intended to account for them?
>
> Mark
> _________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry
> University of Michigan
> sa...@um...     phone (734) 764-3353     fax (734) 764-3323
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

If a model is modified, the "rebuild" command does not always update the surface.  For example,

	show lines, theProtein and not elem H
	show surface

	show lines, elem H
	rebuild

The surface does not change.  But if I now,

	hide surface
	show surface

the surface swells slightly to account for the hydrogens.

Is this a bug?  or a feature?  Also, is it appropriate to show surfaces in publication in the presence of the H's?  Or does the 1.4 Å probe sphere that PyMOL uses intended to account for them?

Mark
_________________________________
Mark A. Saper, Ph.D.				
Associate Professor of Biological Chemistry
University of Michigan
sa...@um...     phone (734) 764-3353     fax (734) 764-3323

Hello,
Take the following scenario. I have two cube files, the first one holds some
values of a function (electron localization function),
while in the second cube for each value in the first cube file i can have
either one of the numbers from 0 to 6.
After loading the first cube file in Pymol, I create an isosurface of a
given value for the contour level, lets say 0.8 a.u.
Next I want to color this isosurface based on the values in the second cube
file, e.g. all points that have a value of 3 in the second cube
should be colored red etc.
Any ideas on how to accomplish this? If needed, I could provide the two cube
files for a simple test case
Thank you
Marius

Jakob,

Try,

rotate [xAxis, yAxis, zAxis], someAngle, yourSelection


For example:

# grab a protein
fetch 1cll, async=0
# zoom & color
zoom i. 20-25
color blue, i. 20-25
# rotate some selected atoms
rotate [0.25, 0.4, 0], -12.5, i. 20-25

Cheers,

-- Jason

On Mon, Jun 28, 2010 at 11:14 AM, Jakob Nielsen
<jto...@gm...> wrote:
> thanks, how can I flip a selection of atoms around an arbitrary axis?
>
> 2010/6/28 Edward A. Berry <Be...@up...>
>>
>> Jakob Nielsen wrote:
>> > Dear Pymol users,
>> > I would like to modify a protein pdb file with a "crankshaft" flip,
>> > which is the anti-correlated double change: psi(i-1) += delta and phi(i)
>> > -= delta. Such a change should leave the protein coordinates unchanged
>> > effecting only atoms in residues i-1 and i. However implementation in
>> > pymol (see below) changes the coordinates of _all_ residues from i-1 to
>> > the C-terminal.
>>
>> I think this is expected because in general psi(i-1) and phi(i)
>> will be rotating about different axes. You might try flipping
>> the residue itself about an axis passing through its N and O atoms,
>> followed by some regularization to fix the geometry.
>>
>> Ed
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Prija,

Electrostatics can be done through the APBS plugin
(http://pymolwiki.org/index.php/APBS).  Michael Lerner has done a
fantastic job on that.

There are many scripts online that will help you calculate the solvent
accessible surface area (for various features), but for any loaded
object you can always type:
  get_area objectName and not solvent

Last, try "help get_area", its PyMOLWiki page
(http://pymolwiki.org/index.php/Get_Area) and another PyMOLWik page
for biochemical properties
(http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Surface-Related).

Cheers,

-- Jason

On Mon, Jun 28, 2010 at 12:55 PM, Prija Ponnan <pri...@gm...> wrote:
> Hello
> I want to calculate electrostatic potential and solvant accessible area of
> protein.
> How can I do the above mentioned calculations using Pymol.
> Please guide me using tutorials.
>
> Thank you
>
> --
> Prija Ponnan
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Greetings,

First, after a reading a recent post that piqued my interest, I
implemented a script that will draw a plane through backbone atoms.
This could be useful to anyone wanting to see or teach the planarity
of the main chain atom.  The script and example images are here:
http://pymolwiki.org/index.php/BbPlane.  Just provide the selection
and you're done.  You can also specify color and transparency.

Next, if someone is interested in helping maintain/update the
PyMOLWiki, please let me know.  We still get 800-1200 unique visitors
per day and that means spam.

Last, thanks for being patient recently with my slow responses on the
PyMOL-users list.  To more effectively support and develop PyMOL, I
packed up moved to NYC to be in the Schrodinger main office.  This
gives me better access to bright minds and resources that should lead
to quicker improvements for PyMOL.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hello
I want to calculate electrostatic potential and solvant accessible area of
protein.
How can I do the above mentioned calculations using Pymol.
Please guide me using tutorials.

Thank you

-- 
Prija Ponnan

Hi Lies,

here a few among many options:

http://www.salilab.org/modeller/

http://swissmodel.expasy.org/

http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi




On Mon, Jun 28, 2010 at 06:15, Lies Van Nieuwenhove
<LVN...@it...> wrote:
> Dear Sir, Ms,
>
> I don't know enough about bio-informatics but I need a molecular model and
> pdb file for 2 proteins. I only have the protein sequence and a protein that
> can be used for homology modelling.
>
> Could you tell me if and how I can do this in pymol?
>
> Thank you,
>
> Sincerely yours,
>
>                  Lies Van Nieuwenhove
>
> #####################################################################################
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> #####################################################################################
>
> This e-mail and any attachments thereto may contain information which is confidential and/or protected by intellectual property rights and are intended for the sole use of the recipient(s)named above. Any use of the information contained herein (including, but not limited to, total or partial reproduction, communication or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer.
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>

thanks, how can I flip a selection of atoms around an arbitrary axis?

2010/6/28 Edward A. Berry <Be...@up...>

> Jakob Nielsen wrote:
> > Dear Pymol users,
> > I would like to modify a protein pdb file with a "crankshaft" flip,
> > which is the anti-correlated double change: psi(i-1) += delta and phi(i)
> > -= delta. Such a change should leave the protein coordinates unchanged
> > effecting only atoms in residues i-1 and i. However implementation in
> > pymol (see below) changes the coordinates of _all_ residues from i-1 to
> > the C-terminal.
>
> I think this is expected because in general psi(i-1) and phi(i)
> will be rotating about different axes. You might try flipping
> the residue itself about an axis passing through its N and O atoms,
> followed by some regularization to fix the geometry.
>
> Ed
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

thanks for your help, it is difficult for me to imagine the effect of this
operation, but I have read a few places that this should be the effect, but
I might be wrong. Anyway, what I want is using two consecutive C-alphas as
"flexible hinges" rotating the peptide plane between this two C-alphas
around the imaginary bond between them leaving the coordinates of the rest
of the molecule unchanged. How would I accomplish this?

best, Jakob

2010/6/28 Robert Campbell <rob...@qu...>

> Dear Jakob,
>
> On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen <
> jto...@gm...>
> wrote:
>
> > I would like to modify a protein pdb file with a "crankshaft" flip, which
> > is the anti-correlated double change: psi(i-1) += delta and phi(i) -=
> delta.
> > Such a change should leave the protein coordinates unchanged effecting
> only
> > atoms in residues i-1 and i. However implementation in pymol (see below)
> > changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
> > you help me? Can I somehow do the two changes simultanious?...
> >
> > set_dihedral 21/n, 21/ca, 21/c, 22/n,  148.435 #was 168.4
> > set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704  #was -103.7
>
> I don't see how this change can leave the other coordinates unchanged.
>  Even
> if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the
> angles CA-C-N and C-N-CA are exactly the same, which they are not
> necessarily), rotation of the psi(i-1) bond will move the N(i) and
> CA(i) atoms, so therefore while a rotation in the opposite direction of the
> phi(i) bond will tend to keep the rest of the change travelling in the
> direction it was before those two counter-rotations, the backbone itself
> will
> be shifted.  One textbook I consulted lists the angles at the C(i-1) and
> N(i)
> atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are
> not
> even theoretically going to be parallel.  In practice, with "real"
> structures, they certainly are not usually going to be parallel.
>
> Cheers,
> Rob
>
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Jakob Nielsen wrote:
> Dear Pymol users,
> I would like to modify a protein pdb file with a "crankshaft" flip,
> which is the anti-correlated double change: psi(i-1) += delta and phi(i)
> -= delta. Such a change should leave the protein coordinates unchanged
> effecting only atoms in residues i-1 and i. However implementation in
> pymol (see below) changes the coordinates of _all_ residues from i-1 to
> the C-terminal.

I think this is expected because in general psi(i-1) and phi(i)
will be rotating about different axes. You might try flipping
the residue itself about an axis passing through its N and O atoms,
followed by some regularization to fix the geometry.

Ed

Dear Jakob,

On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen <jto...@gm...>
wrote:

> I would like to modify a protein pdb file with a "crankshaft" flip, which
> is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
> Such a change should leave the protein coordinates unchanged effecting only
> atoms in residues i-1 and i. However implementation in pymol (see below)
> changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
> you help me? Can I somehow do the two changes simultanious?...
> 
> set_dihedral 21/n, 21/ca, 21/c, 22/n,  148.435 #was 168.4
> set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704  #was -103.7

I don't see how this change can leave the other coordinates unchanged.  Even
if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the
angles CA-C-N and C-N-CA are exactly the same, which they are not
necessarily), rotation of the psi(i-1) bond will move the N(i) and
CA(i) atoms, so therefore while a rotation in the opposite direction of the
phi(i) bond will tend to keep the rest of the change travelling in the
direction it was before those two counter-rotations, the backbone itself will
be shifted.  One textbook I consulted lists the angles at the C(i-1) and N(i)
atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are not
even theoretically going to be parallel.  In practice, with "real"
structures, they certainly are not usually going to be parallel.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Dear Sir, Ms,

I don't know enough about bio-informatics but I need a molecular model and
pdb file for 2 proteins. I only have the protein sequence and a protein that
can be used for homology modelling.

Could you tell me if and how I can do this in pymol?

Thank you,

Sincerely yours,

                  Lies Van Nieuwenhove

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______________________________________________________________________

Dear Pymol users,

I would like to modify a protein pdb file with a "crankshaft" flip, which
is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
Such a change should leave the protein coordinates unchanged effecting only
atoms in residues i-1 and i. However implementation in pymol (see below)
changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
you help me? Can I somehow do the two changes simultanious?...

set_dihedral 21/n, 21/ca, 21/c, 22/n,  148.435 #was 168.4
set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704  #was -103.7

best regards,

Jakob

[[ Important Changes:

   More information about registration at the hotel.

   Our location chair has organized special social
   activities, both geeky (FermiLab Tour) and
   cultured (Theatre). See below for more.
]]

17th Annual Tcl/Tk Conference (Tcl'2010)
http://www.tcl.tk/community/tcl2010/

October 11 - 15, 2010
Hilton Suites/Conference Center

Chicago/Oakbrook Terrace, Illinois, USA

Important Dates:

Abstracts and proposals due   August   1, 2010
Notification to authors       August  15, 2010
WIP and BOF reservations open August   1, 2010
Author materials due          October  1, 2010
Tutorials Start               October 11, 2010
Conference starts             October 13, 2010

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2010 will be held in Chicago/Oakbrook Terrace, Illinois USA
from October 11 - 15, 2010. The program committee is asking for papers
and presentation proposals from anyone using or developing with Tcl/Tk
(and extensions). Past conferences have seen submissions covering a
wide variety of topics including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

This year is the third year that the Tcl community is participating in
the Google Summer of Code.  The conference program committee would
like to encourage submissions that report on the Tcl projects selected
for Google SoC 2010.

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to <tclconference AT googlegroups DOT com> no later than August 15,
2010. Authors of accepted abstracts will have until October 1, 2010 to
submit their final paper for the inclusion in the conference
proceedings. The proceedings will be made available on digital media,
so extra materials such as presentation slides, code examples, code
for extensions etc. are encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com

The authors will have 25 minutes to present their paper at the
conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 1, 2010. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in June 2010. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (http://www.tcl.tk/community/tcl2010/) and will be published on
various Tcl/Tk-related information channels.

Reservations for hotel suites and $25 airport shuttle rides can be
made at
http://www.hilton.com/en/hi/groups/personalized/CHIOTHS-TCL-20101010/index.jhtml?WT.mc_id=POG

To keep in touch with news regarding the conference and Tcl events in
general, subscribe to the tcl-announce list. See:
http://aspn.activestate.com/ASPN/Mail/ to subscribe to the
tcl-announce mailing list.


Special Social Activites

October 15, 2010 - Friday afternoon -- Tour of Fermilab

Fermi National Accelerator Laboratory,   http://www.fnal.gov/

A tour lasts about two hours and begins in Wilson Hall. Visitors view
the Laboratory from the 15th floor windows and visit various displays
located there. The tour moves to the Linear Accelerator building where
visitors see the Cockcroft-Walton, the components in the linear
accelerator gallery and the Main Control Room.  There is a docent for
every 20 people. Registration required since tours must be arranged in
advance.

October 15, 2010 - Friday evening 

Dinner-theater at the award winning Drury Lane theater located next to
our hotel.  .

Special package price for dinner and theater at $44.00 per
person. Regularly $64 per person.

"Seven Brides for Seven Brothers"  http://www.drurylaneoakbrook.com/

Bill Jenkins is one of the newest and most exciting new directors on
the Chicago scene. As Chairman of the Department of Theatre and Dance
at Ball State University, he heads one of the nation's largest theatre
programs. After admiring his work with other Chicago area theatres, we
are very pleased for this opportunity to showcase his talent at Drury
Lane. Once Bill shared some of the fresh ideas and insights he had for
“Seven Brides for Seven Brothers”, we knew we would have a great
show for the holidays.


Conference Committee

Clif Flynt              Noumena Corp                    General Chair, Website Admin
Andreas Kupries         ActiveState Software Inc.       Program Chair
Cyndy Lilagan           Iomas Research, LLC             Facilities Coordination
Brian Griffin           Mentor Graphics
Ron Fox                 NSCL/FRIB Michigan State University
Arjen Markus            Deltares
Mike Doyle              Iomas Research, LLC
Gerald Lester           KnG Consulting, LLC
Donal Fellows           University of Manchester
Jeffrey Hobbs           ActiveState Software Inc.
Steve Landers           Digital Smarties
Kevin Kenny             GE Global Research Center
Larry Virden            Tcl FAQ Maintainer
Steve Redler IV		SR Technology

Contact Information     tcl...@go...


Tcl'2010 would like to thank those who are sponsoring the conference:

ActiveState Software Inc.
Buonacorsi Foundation
Mentor Graphics
Noumena Corp.
SR Technology
Tcl Community Association

Hi Robert,

There's still the basic documentation on the commands, which in the
case of save goes (check the NOTES):

PyMOL>help save

DESCRIPTION

    "save" writes selected atoms to a file.  The file format is
    autodetected if the extesion is ".pdb", ".pse", ".mol", ".mmod", or
    ".pkl"

    Note that if the file extension ends in ".pse" (PyMOL Session), the
    complete PyMOL state is always saved to the file (the selection and
    state parameters are thus ignored).

USAGE

    save file [,(selection) [,state [,format]] ]

PYMOL API

    cmd.save(file, selection, state, format)

NOTES

    When saving a session file, then "state" has no effect.
    When state = 0 (default), only the current state is written.
    When state = -1, then a multi-state output file is written (PDB only).

SEE ALSO

    load, get_model


By the way, you may want to update the name you use for the user list
in your address book (as in the cc.).

Cheers,

Tsjerk

On Wed, Jun 23, 2010 at 7:04 PM, R. Bryn Fenwick
<rob...@ir...> wrote:
>
> Hi,
>
> I have a pdb file that has some models in it. when I open this file
> they are read in as frames, however now I would like to write them out
> as frames in a model file. how can i do that?
>
> Many thanks,
>
> R. Bryn Fenwick
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

Hi,

I have a pdb file that has some models in it. when I open this file  
they are read in as frames, however now I would like to write them out  
as frames in a model file. how can i do that?

Many thanks,

R. Bryn Fenwick

Try probe.

http://kinemage.biochem.duke.edu/software/probe.php


On Wed, Jun 23, 2010 at 11:37 AM, Prija Ponnan <pri...@gm...>wrote:

> Yes, coumarin is not sperical and so its diificult to calculate the radius
> by determining its volume.
> I am given task to calculate the vdw radius of a diacetoxy coumarin
> molecule and I happen to find that  PYMOL has an option to label vdw radius.
> But the PYMOL could label vdw radius of individual atom. Can anyone suggest
> me how i could determine vdw radius using any software.
>
> Thank you
>
> On Wed, Jun 23, 2010 at 2:58 PM, Prija Ponnan <pri...@gm...>wrote:
>
>> Hello
>>
>> I want to determine van der waals radius of a coumarin molecule.
>> Pymol has an option to calculate van  der waals radius, but it calculate
>> vdw radius of individual atoms.
>> Is it possible to determine vdw radius of the molecule as a whole.
>>
>> Thank you
>>
>> --
>> Prija Ponnan
>>
>
>
>
> --
> Prija Ponnan
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jiamu Du, Ph.D.
Postdoctoral Research Fellow
Laboratory of Structural Biology
Memorial Sloan-Kettering Cancer Center
RRL 269, 430 E 67th Street
New York, NY, 10021
E-mail: du...@ms...
Tel: (917) - 292 - 4616

Yes, coumarin is not sperical and so its diificult to calculate the radius
by determining its volume.
I am given task to calculate the vdw radius of a diacetoxy coumarin molecule
and I happen to find that  PYMOL has an option to label vdw radius. But the
PYMOL could label vdw radius of individual atom. Can anyone suggest me how i
could determine vdw radius using any software.

Thank you

On Wed, Jun 23, 2010 at 2:58 PM, Prija Ponnan <pri...@gm...>wrote:

> Hello
>
> I want to determine van der waals radius of a coumarin molecule.
> Pymol has an option to calculate van  der waals radius, but it calculate
> vdw radius of individual atoms.
> Is it possible to determine vdw radius of the molecule as a whole.
>
> Thank you
>
> --
> Prija Ponnan
>



-- 
Prija Ponnan

Hello

I want to determine van der waals radius of a coumarin molecule.
Pymol has an option to calculate van  der waals radius, but it calculate vdw
radius of individual atoms.
Is it possible to determine vdw radius of the molecule as a whole.

Thank you

-- 
Prija Ponnan

Hi all,

Joel's correct: to get the ray traced image to match the viewport, you
must set the viewport to the same aspect ratio as the output image:

# setup the viewport
viewport 800, 600

# zoom on the visible
zoom visible

# ray the scene
ray 800,600

# scale it up
ray 1600, 1200

Cheers,

-- Jason


On Tue, Jun 22, 2010 at 9:32 PM, Joel Tyndall <joe...@ot...> wrote:
> Try setting your Pymol viewer to square dimensions first:
>
> Viewport 600,600
>
> Then try the ray command
>
> This should work
>
> Joel
>
> _________________________________
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
> Ph / Waea               +64 3 4797293
> Fax / Waeawhakaahua     +64 3 4797034
>
>
> -----Original Message-----
> From: Gudrun Lotze [mailto:gud...@gm...]
> Sent: Wednesday, 23 June 2010 12:30 p.m.
> To: pym...@li...
> Subject: [PyMOL] Question about ray
>
> Dear Pymol-Users,
>
> I tried to ray my protein to get a good looking picture. I tried set
> ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my
> protein and parts where not visible.
> How can I get rid of that black border line and how can I ray my
> protein so it is on the whole page visible and not in a box cut off.
> Thank you and kind regards
> Gudrun Lotze
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Try setting your Pymol viewer to square dimensions first:

Viewport 600,600

Then try the ray command

This should work

Joel

_________________________________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

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


-----Original Message-----
From: Gudrun Lotze [mailto:gud...@gm...] 
Sent: Wednesday, 23 June 2010 12:30 p.m.
To: pym...@li...
Subject: [PyMOL] Question about ray

Dear Pymol-Users,

I tried to ray my protein to get a good looking picture. I tried set  
ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my  
protein and parts where not visible.
How can I get rid of that black border line and how can I ray my  
protein so it is on the whole page visible and not in a box cut off.
Thank you and kind regards
Gudrun Lotze


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate 
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the 
lucky parental unit.  See the prize list and enter to win: 
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...