pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs

[surendra n. <ne...@ya...>]

check this link!
http://www.csb.yale.edu/userguides/graphics/pymol/electro.html

Hope it wud help.
best sn

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> Today's Topics:
> 
>    1. Displaying an electrostatic potential on msms
> (Anna Feldman-Salit)
>    2. Re: Displaying an electrostatic potential on
> msms (Peter Adrian Meyer)
> 
> --__--__--
> 
> Message: 1
> Date: Mon, 12 Sep 2005 11:25:39 +0200
> From: Anna Feldman-Salit
> <ann...@em...>
> To:  pym...@li...
> Subject: [PyMOL] Displaying an electrostatic
> potential on msms
> 
> Dear All,
> 
> I have a 0.98 PyMol version with APBS and
> Iso_Sliders plugins. However,
> my aim is not just visualize isosurfaces of
> electrostatic potential at
> certain values, but to display/map it on molecular
> surface.
> 
> Would you be so kind to share your knowledge with me
> on this subject?
> 
> I'd appreciate any help or advice of yours!
> 
> Thanks,
> 
> Anna.
> 
> 
> --__--__--
> 
> Message: 2
> Date: Mon, 12 Sep 2005 12:03:54 -0400 (EDT)
> Subject: Re: [PyMOL] Displaying an electrostatic
> potential on msms
> From: "Peter Adrian Meyer" <pa...@co...>
> To: "Anna Feldman-Salit"
> <ann...@em...>
> Cc: pym...@li...
> 
> Hi Anna,
> I generally run apbs seperately (due to difficulties
> with Alphas), but use
> the plugin  to display with pymol.  apbs will
> produce two output files,
> acc.dx and pot.dx.  acc.dx is the electrostatic
> potential mapped to the
> solvent accessible surface; pot.dx is the
> electrostatic potential over the
> grid.  What I generally do is to load acc.dx into
> pymol, and they use the
> plugin->apbs->display to show the surface (not sure
> of the exact sequence;
> pymol's doing a ray-tracing job for me at the moment
> so I can't check).
> 
> Hope this helps...I've never tried the iso_sliders
> plugin.  I believe the
> author of the apbs plugin is on this list, and will
> probably give you
> clearer answers.
> 
> Pete
> 
> > Dear All,
> >
> > I have a 0.98 PyMol version with APBS and
> Iso_Sliders plugins. However,
> my aim is not just visualize isosurfaces of
> electrostatic potential at
> certain values, but to display/map it on molecular
> surface.
> >
> > Would you be so kind to share your knowledge with
> me on this subject?
> >
> > I'd appreciate any help or advice of yours!
> >
> > Thanks,
> >
> > Anna.
> >
> >
> >
>
-------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software
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> September 19-22, 2005 * San Francisco, CA *
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> Practices
> > Agile & Plan-Driven Development * Managing
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> > PyM...@li...
> >
>
https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
> 
> 
> 
> 
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
>
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> 
> 
> End of PyMOL-users Digest
> 


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Re: [PyMOL] Displaying an electrostatic potential on msms

[Peter A. M. <pa...@co...>]

Hi Anna,
I generally run apbs seperately (due to difficulties with Alphas), but use
the plugin  to display with pymol.  apbs will produce two output files,
acc.dx and pot.dx.  acc.dx is the electrostatic potential mapped to the
solvent accessible surface; pot.dx is the electrostatic potential over the
grid.  What I generally do is to load acc.dx into pymol, and they use the
plugin->apbs->display to show the surface (not sure of the exact sequence;
pymol's doing a ray-tracing job for me at the moment so I can't check).

Hope this helps...I've never tried the iso_sliders plugin.  I believe the
author of the apbs plugin is on this list, and will probably give you
clearer answers.

Pete

> Dear All,
>
> I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However,
my aim is not just visualize isosurfaces of electrostatic potential at
certain values, but to display/map it on molecular surface.
>
> Would you be so kind to share your knowledge with me on this subject?
>
> I'd appreciate any help or advice of yours!
>
> Thanks,
>
> Anna.
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
September 19-22, 2005 * San Francisco, CA * Development Lifecycle
Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing &
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Displaying an electrostatic potential on msms

[Anna Feldman-S. <ann...@em...>]

Dear All,

I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However,
my aim is not just visualize isosurfaces of electrostatic potential at
certain values, but to display/map it on molecular surface.

Would you be so kind to share your knowledge with me on this subject?

I'd appreciate any help or advice of yours!

Thanks,

Anna.

RE: [PyMOL] Atom name and actual atom not consistent

[Warren D. <wa...@de...>]

Donald,

Strange!  Try making sure that you are running in "millions" of colors
mode in the Display settings of System Preferences.  If that doesn't
solve your problem, then try the latest beta version
http://delsci.com/beta to see if the problem still exists with the
current code.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Don Ronning
> Sent: Friday, September 09, 2005 1:14 PM
> To: Pymol List-Serve
> Subject: [PyMOL] Atom name and actual atom not consistent
>=20
> Hi all
>=20
> I just installed MacPyMOL 0.98 on a G5. PyMOL draws the=20
> protein correctly and colors the atoms correctly. However,=20
> when I click on an atom, say a backbone N, Pymol thinks I=20
> just clicked on the carbonyl carbon. It is difficult to draw=20
> H-bonds this way, because the bond is made with the carbonyl=20
> carbon instead of the nitrogen. Any ideas about how to fix=20
> this. Can I go back to an older version to avoid this? Thanks=20
> in advance.
>=20
> --
> Dr. Donald Ronning
> Assistant Professor
> University of Toledo
> Department of Chemistry
> 2801 W. Bancroft St.
> Wolfe Hall 4207B
> Toledo, OH 43606
> Phone: 419 530-1591
> Fax: 419 530-4033
> e-mail: Don...@ut...
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices Agile & Plan-Driven Development *=20
> Managing Projects & Teams * Testing & QA Security * Process=20
> Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

[PyMOL] Atom name and actual atom not consistent

[Don R. <Don...@ut...>]

Hi all

I just installed MacPyMOL 0.98 on a G5. PyMOL draws the protein  
correctly and colors the atoms correctly. However, when I click on an  
atom, say a backbone N, Pymol thinks I just clicked on the carbonyl  
carbon. It is difficult to draw H-bonds this way, because the bond is  
made with the carbonyl carbon instead of the nitrogen. Any ideas  
about how to fix this. Can I go back to an older version to avoid  
this? Thanks in advance.

--
Dr. Donald Ronning
Assistant Professor
University of Toledo
Department of Chemistry
2801 W. Bancroft St.
Wolfe Hall 4207B
Toledo, OH 43606
Phone: 419 530-1591
Fax: 419 530-4033
e-mail: Don...@ut...

RE: [PyMOL] minor irreproducible bugs

[Warren D. <wa...@de...>]

Al,

Bummer...

Next time PyMOL won't start or is acting freaky, can you try launching
PyMOL via command line as follows:

Start Menu->Run then enter: cmd

Assuming PyMOL is in the default location, paste in the following line:

"c:\program files\delano scientific\pymol\pymolwin.exe" +2

And then please send me the resulting output.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Al_...@vr...
> Sent: Friday, September 09, 2005 10:56 AM
> To: pym...@li...
> Subject: [PyMOL] minor irreproducible bugs
>=20
>=20
> I have a couple of problems with pymol 0.98, but they only=20
> happen once in a while and for no apparent reason.  The=20
> problem I'm having right now is that pymol just won't start=20
> up.  I double-click the pymol icon (or try to open a PDB or=20
> pse file), it goes into the 'launching pymol' routine, the=20
> pymol tab appears in the bar at the bottom of the screen, but=20
> then a second later it disappears and pymol never starts up. =20
> This problem tends to go away on its own, but sometimes it=20
> takes a while.=20
> The second problem is that occaisionally the pymol graphics=20
> will become very slow and choppy.  It seems that somehow the=20
> graphics card isn't getting used anymore.  This problem can=20
> always be fixed by restarting the computer, but it's a bit of=20
> a hassle.  I guess this might be an OS problem rather than a=20
> pymol problem.=20
>=20
> My system is a pentium 4 running Windows XP with an NVIDIA=20
> Vanta graphics card and I'm running the precompiled binaries=20
> of pymol.  I know this isn't much information to work with,=20
> and I can certainly live with these issues, but if anyone can=20
> think what might be causing these problems I'd like to give a=20
> shot at fixing them.=20
>=20
> Thanks,
> Al Pierce
>=20

[PyMOL] minor irreproducible bugs

[<Al_...@vr...>]

I have a couple of problems with pymol 0.98, but they only happen once in 
a while and for no apparent reason.  The problem I'm having right now is 
that pymol just won't start up.  I double-click the pymol icon (or try to 
open a PDB or pse file), it goes into the 'launching pymol' routine, the 
pymol tab appears in the bar at the bottom of the screen, but then a 
second later it disappears and pymol never starts up.  This problem tends 
to go away on its own, but sometimes it takes a while.
The second problem is that occaisionally the pymol graphics will become 
very slow and choppy.  It seems that somehow the graphics card isn't 
getting used anymore.  This problem can always be fixed by restarting the 
computer, but it's a bit of a hassle.  I guess this might be an OS problem 
rather than a pymol problem.

My system is a pentium 4 running Windows XP with an NVIDIA Vanta graphics 
card and I'm running the precompiled binaries of pymol.  I know this isn't 
much information to work with, and I can certainly live with these issues, 
but if anyone can think what might be causing these problems I'd like to 
give a shot at fixing them.

Thanks,
Al Pierce

RE: [PyMOL] conformational states in the mutagenesis wizard

[Warren D. <wa...@de...>]

> I beleive the mutagensis wizard in the newer ( > 0.98) will=20
> incorporate the Dunbrack library in some way or another.

Indeed:  the mutagenesis wizard in the latest betas incorporates the
full bb-independent rotamer library and a sampled subset of the
bb-dependent library covering populated regions of ramachandran space.
http://delsci.com/beta


Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Dan Kulp
> Sent: Thursday, September 08, 2005 9:31 AM
> To: Xavier Deupi
> Cc: pym...@li...
> Subject: Re: [PyMOL] conformational states in the mutagenesis wizard
>=20
> Hey,
>     The rotamer toggle script originally loaded the Dunbrack=20
> Backbone-Dependent rotamer library upon PyMOL startup. =20
> However, I've changed it so that it will get loaded the first=20
> time you try to access the rotamer menu instead.  The code is=20
> fixed on www.PyMOLwiki.org .  Now PyMOL will start at regular=20
> speed. Thanks for the catching the 'bug' Xavier.
>=20
> I beleive the mutagensis wizard in the newer ( > 0.98) will=20
> incorporate the Dunbrack library in some way or another.
>=20
> ~Dan Kulp
>=20
> Xavier Deupi wrote:
>=20
> > Hi,
> >
> > I've just realized that through the mutagenesis wizard you can=20
> > view/select different conformations for a sidechain. I've=20
> been playing=20
> > around, and it seems that the conformations are selected=20
> according to=20
> > a backbone-independent rotamer library. Am I correct? Which library=20
> > has been used?
> >
> > I would also like to know if there is anybody out there using the=20
> > rotamer toggle plugin. I've just installed it, and although=20
> it seems=20
> > extremely useful, it makes PyMOL very slow to start. I'm=20
> running PyMOL
> > 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM=20
> (running MacOS=20
> > X 10.4.2)
> >
> > Thanks in advance,
> >
> > Xavier
> >
>=20
>=20
> --=20
>    Dan Kulp
>    Biophysics Graduate Student @ UPenn
>    dw...@ma...
>    http://dwkulp.homelinux.net/tiki/tiki-index.php
> --
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices Agile & Plan-Driven Development *=20
> Managing Projects & Teams * Testing & QA Security * Process=20
> Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

RE: [PyMOL] out of memory with PyMOL in batch mode

[Warren D. <wa...@de...>]

Nicholas,

Hmm.  At this point, I'm stumped.  PyMOL may indeed be leaking =
memory...we'll have to take a look at this.  Could you please email me =
your complete script/program so that we can attempt to reproduce the =
problem.

In the meantime, I suggest breaking up the rendering job into smaller =
chunks or using a Python loop to load and render each frame separately, =
being sure to disable auto_zoom so that the camera doesn't move around =
between frames.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Nicolas Sapay [mailto:n....@ib...]=20
> Sent: Thursday, September 08, 2005 5:32 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: RE: [PyMOL] out of memory with PyMOL in batch mode
>=20
> Warren,
> I have tried my script after setting defer_builds_mode and/or=20
> -D option to 2. PyMOL still crashes after approximately the=20
> same time than previously. The error message is slightly=20
> different this time :
>=20
> MoviePNG: wrote /tmp/nsapay_pymol/top0185.png here 185
> VLAMalloc-ERR: realloc failed
> **************************************************************
> **************
> *** EEK!  PyMOL just ran out of memory and crashed.  To get=20
> around this,
> ***
> *** you may need to reduce the quality, size, or complexity=20
> of the scene
> ***
> *** that you are viewing or rendering.    Sorry for the=20
> inconvenience...
> ***
> **************************************************************
> *************
>=20
> In fact, several pictures have been created, corresponding to=20
> the first
> 185 frames. And pictures have been indeed generated "on the=20
> fly", not in same time.Where is the problem? I ask to PyMOL=20
> to generate an important at each step surface. Can the crash=20
> be due to this? (I know, I ask a lot to PyMOL :-))
>=20
> Cheers,
> Nicolas
>=20
> Le mer 07/09/2005 =E0 19:46, Warren DeLano a =E9crit :
> > Nicolas,
> >=20
> > PyMOL is probably running out of RAM during geometry construction,=20
> > which is done by default for all 1000 frames (to enable fastest=20
> > refresh rates).  In your case, you want to disable that=20
> behavior and=20
> > only generate geometry for the frame being rendered.  This is=20
> > something I added to 0.98:
> >=20
> > set defer_builds_mode, 2
> >=20
> > or launch with options: -D 2
> >=20
> > defer_builds_mode 1 only generates generates geometry when it is=20
> > needed, but then keeps it around.  defer_builds_mode 2 does=20
> that and=20
> > additionally actively purges unused geometry.
> >=20
> > Cheers,
> > Warren
> >=20
> > --
> > Warren L. DeLano, Ph.D.                    =20
> > Principal Scientist
> >=20
> > . DeLano Scientific LLC =20
> > . 400 Oyster Point Blvd., Suite 213          =20
> > . South San Francisco, CA 94080 USA  =20
> > . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> > . Fax:(650)-872-0273  Cell:(650)-346-1154
> > . mailto:wa...@de...     =20
> > =20
> >=20
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of=20
> > > Nicolas Sapay
> > > Sent: Wednesday, September 07, 2005 10:15 AM
> > > To: pym...@li...
> > > Subject: [PyMOL] out of memory with PyMOL in batch mode
> > >=20
> > > Dear all,
> > > I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
> > > Fortunately, I can use a Linux cluster with a PBS server. I have=20
> > > create a small script that :
> > > 	1- loads PDB files (coming from a MD trajectory)
> > > 	2- set up the scene (light, color etc.)
> > > 	3- renders the movie
> > >=20
> > > at the end of my script I have thus:
> > > mset 1 -1000
> > > set ray_trace_frames, 1
> > > set cache_frames, 0
> > > mclear
> > > mpng /tmp/nsapay_pymol/foo
> > >=20
> > > However, it seems that PyMOL doesn't clear its cache since the=20
> > > process fills the memory until crash. No picture is rendered and=20
> > > PyMOL clearly tells me that it ran out of memory. It seems to me=20
> > > that with the cache turned off, frames should be rendered=20
> > > successively and not stored in the memory.
> > > I have make some tests, it seems that PyMOL indeed loads=20
> all PDB but=20
> > > crashes just after the mpng command line. So, is the=20
> problem could=20
> > > be due to an error in my script? Or may be because my system is=20
> > > quite large (> 15000 atoms * > 1000 frames!).
> > > Any suggestion will be welcome!
> > >=20
> > > Nicolas
> > >=20
> > > PS : congratulation to PyMOL authors! It's a=20
> well-conceived and well=20
> > > documented software.
> > > =20
> > > --
> > > _ Nicolas Sapay ____________________________________________
> > >   Ph.D sudent in structural bioinformatics
> > >   Institut de Biologie et Chimie des Proteines
> > >   CNRS - Claude Bernard University, Lyon I
> > >=20
> > >   > contact :
> > >     7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
> > >     69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
> > >     France                     Web: http://pbil.ibcp.fr/
> > >=20
> > >=20
> > >=20
> > > -------------------------------------------------------
> > > SF.Net email is Sponsored by the Better Software=20
> Conference & EXPO=20
> > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
> > > Practices Agile & Plan-Driven Development * Managing Projects &=20
> > > Teams * Testing & QA Security * Process Improvement &=20
> Measurement *=20
> > > http://www.sqe.com/bsce5sf=20
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >=20
> > >=20
> > >=20
> --
> _ Nicolas Sapay ____________________________________________
>   Ph.D sudent in structural bioinformatics
>   Institut de Biologie et Chimie des Proteines
>   CNRS - Claude Bernard University, Lyon I
>=20
>   > contact :
>     7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
>     69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
>     France                     Web: http://pbil.ibcp.fr/
>=20
>=20
>=20
>=20

Re: [PyMOL] runing pymol on linux cluster

[Jason T. M. <jtm...@sh...>]

Yes=2C and it is pretty easy to implement=2E

Display disable=3A
pymol=2Ecom -c pymolscript=2Epml

Cheers=2C
JTM

=22We can be sure that if a detailed understanding of the molecular basis=
 of chemo-therapeutic activity were to be obtained=2C the advance of medi=
cine would be greatly accelerated=2E=22

Linus Pauling=2C Nobel Laureate 1954

=22=2E=2E=2Eeverything that living things do can be understood in terms o=
f the jigglings and wigglings of atoms=2E=22

Richard Feynman=2C Nobel Laureate 1965

*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
jason=40biochem=2Eualberta=2Eca
*************************

----- Original Message -----
From=3A Geoui Thibault =3Cgeoui=40embl-grenoble=2Efr=3E
Date=3A Thursday=2C September 8=2C 2005 7=3A32 am
Subject=3A =5BPyMOL=5D runing pymol on linux cluster

=3E Hi list=2C
=3E do you know if it is possible to run Pymol on a linux cluster with =

=3E display disable in order to calculate frames of a movie faster and =

=3E taking advatage of the power of the cluster =3F
=3E =

=3E =

=3E Thanks
=3E =

=3E Thibault G=E9oui=2E
=3E =

=3E =

=3E -------------------------------------------------------
=3E SF=2ENet email is Sponsored by the Better Software Conference =26 EXP=
O
=3E September 19-22=2C 2005 * San Francisco=2C CA * Development Lifecycle=
 =

=3E PracticesAgile =26 Plan-Driven Development * Managing Projects =26 =

=3E Teams * Testing =26 QA
=3E Security * Process Improvement =26 Measurement * =

=3E http=3A//www=2Esqe=2Ecom/bsce5sf=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F
=3E PyMOL-users mailing list
=3E PyMOL-users=40lists=2Esourceforge=2Enet
=3E https=3A//lists=2Esourceforge=2Enet/lists/listinfo/pymol-users
=3E 

Re: [PyMOL] conformational states in the mutagenesis wizard

[Dan K. <dw...@ma...>]

Hey,
    The rotamer toggle script originally loaded the Dunbrack 
Backbone-Dependent rotamer library upon PyMOL startup.  However, I've 
changed it so that it will get loaded the first time you try to access 
the rotamer menu instead.  The code is fixed on www.PyMOLwiki.org .  Now 
PyMOL will start at regular speed. Thanks for the catching the 'bug' Xavier.

I beleive the mutagensis wizard in the newer ( > 0.98) will incorporate 
the Dunbrack library in some way or another.

~Dan Kulp

Xavier Deupi wrote:

> Hi,
>
> I've just realized that through the mutagenesis wizard you can 
> view/select different conformations for a sidechain. I've been playing 
> around, and it seems that the conformations are selected according to 
> a backbone-independent rotamer library. Am I correct? Which library 
> has been used?
>
> I would also like to know if there is anybody out there using the 
> rotamer toggle plugin. I've just installed it, and although it seems 
> extremely useful, it makes PyMOL very slow to start. I'm running PyMOL 
> 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM (running MacOS 
> X 10.4.2)
>
> Thanks in advance,
>
> Xavier
>


-- 
   Dan Kulp
   Biophysics Graduate Student @ UPenn
   dw...@ma...
   http://dwkulp.homelinux.net/tiki/tiki-index.php
--

[PyMOL] runing pymol on linux cluster

[Geoui T. <ge...@em...>]

Hi list,
do you know if it is possible to run Pymol on a linux cluster with=20
display disable in order to calculate frames of a movie faster and=20
taking advatage of the power of the cluster ?


Thanks

Thibault G=E9oui.

RE: [PyMOL] out of memory with PyMOL in batch mode

[Nicolas S. <n....@ib...>]

Warren,
I have tried my script after setting defer_builds_mode and/or -D option
to 2. PyMOL still crashes after approximately the same time than
previously. The error message is slightly different this time :

MoviePNG: wrote /tmp/nsapay_pymol/top0185.png
here 185
VLAMalloc-ERR: realloc failed
***************************************************************************=
*
*** EEK!  PyMOL just ran out of memory and crashed.  To get around this,
***
*** you may need to reduce the quality, size, or complexity of the scene
***
*** that you are viewing or rendering.    Sorry for the inconvenience...
***
***************************************************************************

In fact, several pictures have been created, corresponding to the first
185 frames. And pictures have been indeed generated "on the fly", not in
same time.Where is the problem? I ask to PyMOL to generate an important
at each step surface. Can the crash be due to this? (I know, I ask a lot
to PyMOL :-))

Cheers,
Nicolas

Le mer 07/09/2005 =E0 19:46, Warren DeLano a =E9crit :
> Nicolas,
>=20
> PyMOL is probably running out of RAM during geometry construction, which
> is done by default for all 1000 frames (to enable fastest refresh
> rates).  In your case, you want to disable that behavior and only
> generate geometry for the frame being rendered.  This is something I
> added to 0.98:
>=20
> set defer_builds_mode, 2
>=20
> or launch with options: -D 2
>=20
> defer_builds_mode 1 only generates generates geometry when it is needed,
> but then keeps it around.  defer_builds_mode 2 does that and
> additionally actively purges unused geometry.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
> =20
>=20
> > -----Original Message-----
> > From: pym...@li...=20
> > [mailto:pym...@li...] On Behalf Of=20
> > Nicolas Sapay
> > Sent: Wednesday, September 07, 2005 10:15 AM
> > To: pym...@li...
> > Subject: [PyMOL] out of memory with PyMOL in batch mode
> >=20
> > Dear all,
> > I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
> > Fortunately, I can use a Linux cluster with a PBS server. I=20
> > have create a small script that :
> > 	1- loads PDB files (coming from a MD trajectory)
> > 	2- set up the scene (light, color etc.)
> > 	3- renders the movie
> >=20
> > at the end of my script I have thus:
> > mset 1 -1000
> > set ray_trace_frames, 1
> > set cache_frames, 0
> > mclear
> > mpng /tmp/nsapay_pymol/foo
> >=20
> > However, it seems that PyMOL doesn't clear its cache since=20
> > the process fills the memory until crash. No picture is=20
> > rendered and PyMOL clearly tells me that it ran out of=20
> > memory. It seems to me that with the cache turned off, frames=20
> > should be rendered successively and not stored in the memory.=20
> > I have make some tests, it seems that PyMOL indeed loads all=20
> > PDB but crashes just after the mpng command line. So, is the=20
> > problem could be due to an error in my script? Or may be=20
> > because my system is quite large (> 15000 atoms * > 1000 frames!).
> > Any suggestion will be welcome!
> >=20
> > Nicolas
> >=20
> > PS : congratulation to PyMOL authors! It's a well-conceived=20
> > and well documented software.
> > =20
> > --
> > _ Nicolas Sapay ____________________________________________
> >   Ph.D sudent in structural bioinformatics
> >   Institut de Biologie et Chimie des Proteines
> >   CNRS - Claude Bernard University, Lyon I
> >=20
> >   > contact :
> >     7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
> >     69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
> >     France                     Web: http://pbil.ibcp.fr/
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference &=20
> > EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> > Lifecycle Practices Agile & Plan-Driven Development *=20
> > Managing Projects & Teams * Testing & QA Security * Process=20
> > Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> >=20
> >=20
--=20
_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, Lyon I

  > contact :
    7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
    69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
    France                     Web: http://pbil.ibcp.fr/

RE: [PyMOL] out of memory with PyMOL in batch mode

[Warren D. <wa...@de...>]

Nicolas,

PyMOL is probably running out of RAM during geometry construction, which
is done by default for all 1000 frames (to enable fastest refresh
rates).  In your case, you want to disable that behavior and only
generate geometry for the frame being rendered.  This is something I
added to 0.98:

set defer_builds_mode, 2

or launch with options: -D 2

defer_builds_mode 1 only generates generates geometry when it is needed,
but then keeps it around.  defer_builds_mode 2 does that and
additionally actively purges unused geometry.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Nicolas Sapay
> Sent: Wednesday, September 07, 2005 10:15 AM
> To: pym...@li...
> Subject: [PyMOL] out of memory with PyMOL in batch mode
>=20
> Dear all,
> I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
> Fortunately, I can use a Linux cluster with a PBS server. I=20
> have create a small script that :
> 	1- loads PDB files (coming from a MD trajectory)
> 	2- set up the scene (light, color etc.)
> 	3- renders the movie
>=20
> at the end of my script I have thus:
> mset 1 -1000
> set ray_trace_frames, 1
> set cache_frames, 0
> mclear
> mpng /tmp/nsapay_pymol/foo
>=20
> However, it seems that PyMOL doesn't clear its cache since=20
> the process fills the memory until crash. No picture is=20
> rendered and PyMOL clearly tells me that it ran out of=20
> memory. It seems to me that with the cache turned off, frames=20
> should be rendered successively and not stored in the memory.=20
> I have make some tests, it seems that PyMOL indeed loads all=20
> PDB but crashes just after the mpng command line. So, is the=20
> problem could be due to an error in my script? Or may be=20
> because my system is quite large (> 15000 atoms * > 1000 frames!).
> Any suggestion will be welcome!
>=20
> Nicolas
>=20
> PS : congratulation to PyMOL authors! It's a well-conceived=20
> and well documented software.
> =20
> --
> _ Nicolas Sapay ____________________________________________
>   Ph.D sudent in structural bioinformatics
>   Institut de Biologie et Chimie des Proteines
>   CNRS - Claude Bernard University, Lyon I
>=20
>   > contact :
>     7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
>     69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
>     France                     Web: http://pbil.ibcp.fr/
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices Agile & Plan-Driven Development *=20
> Managing Projects & Teams * Testing & QA Security * Process=20
> Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

[PyMOL] out of memory with PyMOL in batch mode

[Nicolas S. <n....@ib...>]

Dear all, 
I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
Fortunately, I can use a Linux cluster with a PBS server. I have create
a small script that :
	1- loads PDB files (coming from a MD trajectory)
	2- set up the scene (light, color etc.)
	3- renders the movie

at the end of my script I have thus:
mset 1 -1000
set ray_trace_frames, 1
set cache_frames, 0
mclear
mpng /tmp/nsapay_pymol/foo

However, it seems that PyMOL doesn't clear its cache since the process
fills the memory until crash. No picture is rendered and PyMOL clearly
tells me that it ran out of memory. It seems to me that with the cache
turned off, frames should be rendered successively and not stored in the
memory. I have make some tests, it seems that PyMOL indeed loads all PDB
but crashes just after the mpng command line. So, is the problem could
be due to an error in my script? Or may be because my system is quite
large (> 15000 atoms * > 1000 frames!).
Any suggestion will be welcome!

Nicolas

PS : congratulation to PyMOL authors! It's a well-conceived and well
documented software.
 
-- 
_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, Lyon I

  > contact :
    7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
    69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
    France                     Web: http://pbil.ibcp.fr/

Re: [PyMOL] ray tracing problem

[Lari L. <lar...@he...>]

Thank you Warren and Jacob,

I pressed stop and then ray tracing went fine. I don't know who pressed tha=
t=20
play-button, but it wasn't me...

~Lari~=20

On Friday 02 September 2005 18:41, Lari Lehtio wrote:
> Hello,
>
> I'm in a process of making a whole bunch of figures for a paper and I have
> an irritating problem. Some of the figures just do _not_ get ray traced. =
It
> processes the image, but the image stays normal (=3Dugly).
>
> I'm running 0.98 on an amd64 box with gentoo and I've tried the binary
> distribution as well as compiled pymol from the source. If I start from
> scratch and make similar objects, it works fine again.
>
> Has anyone else seen this kind of behaviour?
>
> ~Lari~
>
> _______________________________________
> Lari Lehti=F6
> University of Helsinki
> Institute of Biotechnology
> Macromolecular X-ray crystallography
> P.O.Box 65
> 00014 HY
> Finland
> http://www.biocenter.helsinki.fi/~lehtio/
> _______________________________________
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic=
es
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

RE: [PyMOL] Refinement in auto_sculpt

[Warren D. <wa...@de...>]

Jim,

(we discussed this at ACS, but just for the mailing list record).

PyMOL does not yet support real-space refinement internally.  However, I
suspect one could use cctbx to accomplish this with PyMOL.  Perhaps
someone familiar with both open-source projects would like to take a
stab at it?

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Jim Nettles [mailto:jn...@em...]=20
> Sent: Tuesday, August 30, 2005 6:00 AM
> To: Warren DeLano
> Cc: pym...@li...; Mathieu Coincon
> Subject: Re: [PyMOL] Refinement in auto_sculpt
>=20
> Hello all,=20
>=20
>=20
>         Perhaps I'm awaking from hibernation or something,=20
> but the communication below came as a surprise to me.=20
>=20
>=20
>         Do I read this correctly that Pymol does real space=20
> refining into electron density using the sculpting function?=20
> If so, that is great! I apologize if this has been discussed=20
> before and I missed it. Could someone please clue me in as to=20
> how to best use this function?=20
>=20
>=20
>         Thanks,=20
>=20
>=20
>         Jim Nettles=20
>=20
>=20
> On Aug 30, 2005, at 8:33 AM, Warren DeLano wrote:=20
>=20
>=20
> Mathieu,=20
>=20
>  =20
>=20
> Deselect Sculpting from the builder menu or "unset sculpting"=20
>=20
>  =20
>=20
> Note that if you're doing this a lot, then create some custom=20
> on/off function keys as follows:=20
>=20
>  =20
>=20
> # F1 to turn on sculpting=20
>=20
> cmd.set_key('F1',lambda=20
> :(cmd.set("sculpting"),cmd.set("auto_sculpt")))=20
>=20
>  =20
>=20
> # F2 to turn off sculpting=20
>=20
> cmd.set_key('F2',lambda=20
> :(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))=20
>=20
>  =20
>=20
> Cheers,=20
>=20
> Warren=20
>=20
>=20
> From: pym...@li... on behalf of=20
> Mathieu Coincon=20
>=20
> Sent: Mon 8/29/2005 8:26 AM=20
>=20
> To: pym...@li...=20
>=20
> Subject: [PyMOL] Refinement in auto_sculpt=20
>=20
>=20
>=20
>=20
>=20
> Hi,=20
>=20
> i'm usinig pymol for modelling my protein in electron density.=20
>=20
> I like it very much but there is one thing I would like to=20
> understand.=20
>=20
> Is there a way to stop the refinement of the geometry:=20
>=20
>     I'm using auto_sculpt and I protect/deprotect the protein=20
> but sometimes the=20
>=20
> refinemt run during a long time I would like to stop it ? i=20
> played with the=20
>=20
> number  of cycles and other parameters but it didn't work.=20
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------=20
>=20
> SF.Net email is Sponsored by the Better Software Conference & EXPO=20
>=20
> September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices=20
>=20
> Agile & Plan-Driven Development * Managing Projects & Teams *=20
> Testing & QA=20
>=20
> Security * Process Improvement & Measurement *=20
> http://www.sqe.com/bsce5sf=20
>=20
> _______________________________________________=20
>=20
> PyMOL-users mailing list=20
>=20
> PyM...@li...=20
>=20
> https://lists.sourceforge.net/lists/listinfo/pymol-users=20
>=20
>=20
>=20
>=20

[PyMOL] Moving labels in Pymol

[Akanksha N. <gt...@ma...>]

Dear PyMol Users:

Does anyone knows how to move labels to the desired position using PyMol?
Any suggestions are appreciated.

Thanks,
Akanksha

--
Akanksha Nagpal, Ph.D.
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta, GA 30332

[PyMOL] ray tracing problem

[Lari L. <lar...@he...>]

Hello,

I'm in a process of making a whole bunch of figures for a paper and I have =
an=20
irritating problem. Some of the figures just do _not_ get ray traced. It=20
processes the image, but the image stays normal (=3Dugly).

I'm running 0.98 on an amd64 box with gentoo and I've tried the binary=20
distribution as well as compiled pymol from the source. If I start from=20
scratch and make similar objects, it works fine again.=20

Has anyone else seen this kind of behaviour?=20

~Lari~

_______________________________________
Lari Lehti=F6
University of Helsinki
Institute of Biotechnology
Macromolecular X-ray crystallography
P.O.Box 65
00014 HY
=46inland
http://www.biocenter.helsinki.fi/~lehtio/
_______________________________________

[PyMOL] pymol install succeeds - freeglut issues resolved - other issues

[<an...@bi...>]

Many thanks to Rob Campbell for, well, not giving the solution to my=20
problem, but pointing me into the right direction and making me keep=20
digging...

Robert Campbell wrote:
> Hello Andreas,
>=20
> Yes you need the Mesa development files and yes there is a conflict
> between FireGL and Mesa.
>=20
> I use Debian so the package names will not be exactly the same, but
> for me the GL/gl.h and GL/glu.h files are provided by the packages
> xlibmesa-gl-dev and xlibmesa-glu-dev respectively. I also use an
> ATI card with the ATI proprietary drivers and I need to force the
> installation of that to overwrite the /usr/X11R6/lib/libGL.so.1.2 file
> contained in the xlibmesa-gl (not xlibmesa-gl-dev) package. I don't use
> Xorg, yet, but I'm sure that doesn not change any of the above.

For Fedora and xorg, the situtation is a little different.  Mesa=20
development files are nowhere to be found in any Fedora repository.=20
Instead, there is a xorg-x11-devel (note the conspicuous absence of=20
anything mesa-like).  I tried to install it.  xorg-x11-devel requires=20
freetype-devel, which in turn requires fontconfig-devel.  What would the=20
world be without rpm and DSL?  Finally, everything installed.  The=20
FireGL driver has no issues with all this.  glxgears gives the same=20
numbers as before, and O10 runs smoothly.

Then I took another shot at pymol - and suffered another failure, though=20
much later in the process.  png.h doesn't exist, which is, surprisingly=20
for me, not provided by libpng.  Completely lost again, then flash of=20
very bright light (or was it the dawn of the new day?):  libpng-devel!=20
And this indeed solved the last problem, and pymol is now installed!


Thanks Rob, thanks Warren!!


Andreas



--=20
    -->       Andreas F=F6rster       <--
  8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
       www.biochem.utah.edu/~andreas
    b5foan at skype and yahoo messenger
docandreas & andreasenfrance.blogspot.com

Re: [PyMOL] pymol install fails - freeglut issues

[Tru H. <tr...@pa...>]

On Wed, Aug 31, 2005 at 09:37:05PM +0200, Andreas F=F6rster wrote:
> Hey all,
>=20
> sorry for taking to the list what seems to me a trivial problem.  But I=
=20
> can't get over it and I'm afraid to modified my system too much since I=
=20
> don't know what I'm doing.
>=20
> Basically, what I've done is download the pymol sources=20
> (pymol-0_98-src.tgz) from delsci.com.  I made sure I've installed all=20
> the requirements (python2.3.4, Numeric, Pmw, tcl8.4, tk8.4.7, libpng,=20
> zlib, freeglut2.2).  This is on a standard Fedora Core 3 system, nothin=
g=20
> fancy.

do you have the freeglut-devel package installed?

Cheers,

Tru
--=20
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tr...@pa... | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France =
=20

[PyMOL] MasterMovie.py

[Shingo N. <sn...@ri...>]

Hi all pymolers !

I'm trying to install MasterMovie.py made by Seth Harris and others but I
couldn't have this installed. What I get when I restart PyMol is the
following error message:

Exception in plugin 'MasterMovie' -- Traceback follows...
Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\PMGApp.py",
line 143, in initialize_plugins
    __builtin__.__import__(mod_name)
  File "C:\Program Files\DeLano
Scientific\PyMOL\modules\pmg_tk\startup\MasterMovie.py", line 443
     goes through a CNS-style peaks file from a map, visiting each selected
peak
     ^
 SyntaxError: invalid syntax
Error: unable to initialize plugin 'MasterMovie'.  

Any suggestions are welcome.

Thank you,

Shingo

[PyMOL] pymol install fails - freeglut issues

[<an...@bi...>]

Hey all,

sorry for taking to the list what seems to me a trivial problem.  But I=20
can't get over it and I'm afraid to modified my system too much since I=20
don't know what I'm doing.

Basically, what I've done is download the pymol sources=20
(pymol-0_98-src.tgz) from delsci.com.  I made sure I've installed all=20
the requirements (python2.3.4, Numeric, Pmw, tcl8.4, tk8.4.7, libpng,=20
zlib, freeglut2.2).  This is on a standard Fedora Core 3 system, nothing=20
fancy.

I run `python2.3 setup.py install` and get a bunch of error messages=20
relating to the absence of GL/gl.h and GL/glu.h.  Supposedly, freeglut=20
combines them into GL/glut.h.  So I change all occurences of GL/gl.h and=20
GL/glu.h in the pymol source to GL/glut.h.  More errors!  It turns out=20
that freeglut is also asking for GL/gl.h and GL/glu.h.  I have the faint=20
notion that Mesa provides GL/gl.h and GL/glu.h, but aren't Mesa and=20
freeglut supposed to do the same thing?  Both provide libGLU.so.  Should=20
I install Mesa?  And wasn't there some FireGL/xorg/Mesa incopatibility=20
issue?


Any suggestions?


Andreas


--=20
    -->       Andreas F=F6rster       <--
  8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
       www.biochem.utah.edu/~andreas
    b5foan at skype and yahoo messenger
docandreas & andreasenfrance.blogspot.com

Re: [PyMOL] Refinement in auto_sculpt

[mathieu c. <mat...@um...>]

Hi,

i just set auto_sculpt and after I protect all my protein but the=
=20
residue (group of residues) i want to sculpt. I wrote several .pml to=
=20
switch to the next residue or deprotect only the side_chain,fix an at=
om=20
  (protect pk1) etc... that I call from the script_box (see the links=
 on=20
the web-site).
It works really well for me it's twice faster than with O (but i'm no=
t=20
really good with O).

Thanks to warren for this software.

Jim Nettles a =E9crit :
> Hello all,
>=20
> Perhaps I'm awaking from hibernation or something, but the communic=
ation=20
> below came as a surprise to me.
>=20
> Do I read this correctly that Pymol does real space refining into=
=20
> electron density using the sculpting function? If so, that is great=
! I=20
> apologize if this has been discussed before and I missed it. Could=
=20
> someone please clue me in as to how to best use this function?
>=20
> Thanks,
>=20
> Jim Nettles
>=20
> On Aug 30, 2005, at 8:33 AM, Warren DeLano wrote:
>=20
>     Mathieu,
>     =20
>     Deselect Sculpting from the builder menu or "unset sculpting"
>     =20
>     Note that if you're doing this a lot, then create some custom o=
n/off
>     function keys as follows:
>     =20
>     # F1 to turn on sculpting
>     cmd.set_key('F1',lambda :(cmd.set("sculpting"),cmd.set("auto_sc=
ulpt")))
>     =20
>     # F2 to turn off sculpting
>     cmd.set_key('F2',lambda
>     :(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))
>     =20
>     Cheers,
>     Warren
>=20
>     *From:* pym...@li... on behalf of Ma=
thieu
>     Coincon
>     *Sent:* Mon 8/29/2005 8:26 AM
>     *To:* pym...@li...
>     *Subject:* [PyMOL] Refinement in auto_sculpt
>=20
>=20
>=20
>=20
>     Hi,
>     i'm usinig pymol for modelling my protein in electron density.
>     I like it very much but there is one thing I would like to unde=
rstand.
>     Is there a way to stop the refinement of the geometry:
>         I'm using auto_sculpt and I protect/deprotect the protein b=
ut
>     sometimes the
>     refinemt run during a long time I would like to stop it ? i pla=
yed
>     with the
>     number  of cycles and other parameters but it didn't work.
>=20
>=20
>=20
>=20
>=20
>     -------------------------------------------------------
>     SF.Net email is Sponsored by the Better Software Conference & E=
XPO
>     September 19-22, 2005 * San Francisco, CA * Development Lifecyc=
le
>     Practices
>     Agile & Plan-Driven Development * Managing Projects & Teams *
>     Testing & QA
>     Security * Process Improvement & Measurement *
>     http://www.sqe.com/bsce5sf
>     _______________________________________________
>     PyMOL-users mailing list
>     PyM...@li...
>     https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20

RE: [PyMOL] Refinement in auto_sculpt

[Warren D. <wa...@de...>]

Mathieu,
=20
Deselect Sculpting from the builder menu or "unset sculpting"
=20
Note that if you're doing this a lot, then create some custom on/off =
function keys as follows:
=20
# F1 to turn on sculpting
cmd.set_key('F1',lambda :(cmd.set("sculpting"),cmd.set("auto_sculpt")))
=20
# F2 to turn off sculpting
cmd.set_key('F2',lambda =
:(cmd.unset("sculpting"),cmd.unset("auto_sculpt")))
=20
Cheers,
Warren

________________________________

From: pym...@li... on behalf of Mathieu =
Coincon
Sent: Mon 8/29/2005 8:26 AM
To: pym...@li...
Subject: [PyMOL] Refinement in auto_sculpt





Hi,
i'm usinig pymol for modelling my protein in electron density.
I like it very much but there is one thing I would like to understand.
Is there a way to stop the refinement of the geometry:
    I'm using auto_sculpt and I protect/deprotect the protein but =
sometimes the
refinemt run during a long time I would like to stop it ? i played with =
the
number  of cycles and other parameters but it didn't work.





-------------------------------------------------------
SF.Net email is Sponsored by the Better Software Conference & EXPO
September 19-22, 2005 * San Francisco, CA * Development Lifecycle =
Practices
Agile & Plan-Driven Development * Managing Projects & Teams * Testing & =
QA
Security * Process Improvement & Measurement * =
http://www.sqe.com/bsce5sf
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users