pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] torsion + movie

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

Try something like this:

# Save as a .pml file

load $PYMOL_PATH/test/dat/pept.pdb

for st in range(2,31): \
   cmd.create("pept","pept",st-1,st) \
   cmd.frame(st) \
   cmd.edit("4/cb","4/ca") \
   cmd.torsion(5)=20

edit

movie.sweep

rewind

mplay

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...
> [mailto:pym...@li...] On Behalf Of Xavier=20
> Deupi
> Sent: Monday, August 15, 2005 11:38 AM
> To: pym...@li...
> Subject: [PyMOL] torsion + movie
>=20
> Hi,
>=20
> I'm trying to create a simple movie showing the rotation around a=20
> dihedral angle. I'm sure it's an extremely easy task, but I can't=20
> figure out the way of loading each state (i.e. conformation of the=20
> dihedral
> angle) into the movie object. I mean, the 'load' command (as in "load
> foo1.pdb,mov") expects a pdb file as an argument, but I want to load=20
> the current state as shown in PyMOL (after modifying the torsion=20
> angle, for instance).
> Any help?
>=20
> Thanks in advance,
>=20
> Xavier
>=20
> --
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology Beckman Center for=20
> Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine Stanford, CA=20
> 94305 (USA)
>=20
> E-mail: Xav...@st...
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO=20
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
> Practices Agile & Plan-Driven Development * Managing Projects & Teams=20
> * Testing & QA Security * Process Improvement & 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

[PyMOL] torsion + movie

[Xavier D. <Xav...@st...>]

Hi,

I'm trying to create a simple movie showing the rotation around a 
dihedral angle. I'm sure it's an extremely easy task, but I can't figure 
out the way of loading each state (i.e. conformation of the dihedral 
angle) into the movie object. I mean, the 'load' command (as in "load 
foo1.pdb,mov") expects a pdb file as an argument, but I want to load the 
current state as shown in PyMOL (after modifying the torsion angle, for 
instance).
Any help?

Thanks in advance,

Xavier

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

Re: [PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?

[Neema S. <nsa...@it...>]

I agree with the Logitech sentiment.  I have a MX 700 for my iMac,  
and installing the software was a bad idea when I had Panther.  I  
haven't tried installing it on Tiger, but all the buttons (8 of them)  
are assignable in the System preferences menu.  In addition, it's  
cordless, and the battery lasts a good while before it needs charging.


On Aug 15, 2005, at 9:00 AM, geek theory wrote:


> I have one of each of the Logitech MX 500, 510, 518 series and they
> all have worked (and are still working) fine for me, albeit on windows
> and linux.  I don't have any experience with the cordless version, but
> after a little google searching it looks like the logitech software is
> buggy on macs.  You might try uninstalling it and letting the OS think
> its a generic 3-button mouse.
>
> hope it helps,
> -Tzintzuni Garcia
>
>
> On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote:
>
>
>> I use a cheap microsoft optical (or basic optical) usb mouse on  
>> linux,
>> so it should work on your macosx.
>>
>> If you want something more configurable under macosx and don't  
>> want to
>> destroy the "Appleness" of your computer with an MS mouse then this
>> might work for you http://www.apple.com/mightymouse/ . I hear  
>> there will
>> be a wireless version soon.
>>
>> Sarina Bromberg wrote:
>>
>>
>>> I have a logitech MX700 Cordless Optical Mouse that claims to be  
>>> a 3-
>>> button mouse, but I can never get it to produce the results provided
>>> for 3-button viewing or editing by PyMOL.  Perhaps I do not have it
>>> configured correctly (I cannot find a clue in the instructions or in
>>> simple experiments), or perhaps this is not the kind of 3-button   
>>> mouse
>>> I need. Does anyone have a good solution?
>>> Tx,
>>> Sarina Bromberg
>>>
>>>
>>> -------------------------------------------------------
>>> 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
>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> 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
>>
>>
>>
>
>
> -------------------------------------------------------
> 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
>
>
>
>

Re: [PyMOL] Builder Question

[James R. G. <jam...@ma...>]

Hello Warren,

Thanks for the response.

That is exactly what I have done--taken structures produced with  
builder and brought them into GROMACS and have obtained minimized  
structures, but as Jim Nettles mentioned, such techniques can depend  
on what the initial structure is, so I was just wondering whether  
there were any constraints placed upon amino acids as they are placed  
that might mimic chemical synthesis methods. I know it's quite a  
reach, but thought I'd ask anyway. ;)

james


On Aug 15, 2005, at 12:12 PM, Warren DeLano wrote:

> James,
>
> PyMOL's peptide & small molecular builder is no more rigorous that a
> handheld plastic model.  Unfortunately, DeLano Scientific doesn't have
> the developer "bandwidth" right now to get into the simulations
> business.  Instead, we hope to facilitate and encourage integration  
> with
> existing external packages via PyMOL wizards and simple Python glue.
>
> Thus, our near-term goal with the builder is to simply provide
> scientists like yourself with a user interface for building molecules
> and setting up *initial* poses that will then be subjected to rigorous
> computations external to PyMOL.
>
> There are plenty of integrations options out there, from free and/or
> open-source tools like GROMACS, APBS, Tinker, ArgusLab, GAMESS US, and
> MMTK, to academic codes like Amber, Charmm, Dock, and Autodock, to
> commercial codes like Szybki (MMFF), Fred, Glide, BatchMin, MOE,  
> Sybyl,
> or Discover.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Jim Nettles
>> Sent: Monday, August 15, 2005 8:56 AM
>> To: James R. Graham
>> Cc: pym...@li...
>> Subject: Re: [PyMOL] Builder Question
>>
>> Hello James,
>>
>> There is really a lot of room for discussion regarding your
>> questions.
>> Considering peptide conformations is complicated business and
>> there is generally not "a" structure. There is great
>> conformational flexibility even for small, constrained,
>> cyclic peptides. As for the MD - yes, a classical MD
>> trajectory is entirely determined by the starting structure.
>> One can introduce random number seeds, high temperature, etc
>> ... to explore greater space, but where you start is
>> definitely worthy of thoughtful consideration.
>>
>> I can send references and more discussion off list, if you
>> are interested.
>>
>> Cheers,
>>
>> Jim N.
>> ________________________________________________________
>> James Nettles, Ph. D. Computational Pharmacology
>> Liotta/Snyder Group, Modeling Division, Department of
>> Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322
>> jn...@em...  TEL: (404)966-4617  FAX: (404)728-0991
>> ________________________________________________________
>>
>> On Aug 15, 2005, at 11:36 AM, James R. Graham wrote:
>>
>>
>>> Hello All,
>>>
>>> How "physiological" are the structures that are produced
>>>
>> from builder?
>>
>>> Meaning, how are the angles, etc. determined? Might such a
>>>
>> resulting
>>
>>> structure mimic a chemically-synthesized peptide?
>>>
>>> I have taken peptides I created using builder and done some MD
>>> simulations and the structures certainly change, but I
>>>
>> wonder whether
>>
>>> the changes are limited by the initial starting
>>>
>> structure...which is,
>>
>>> of course, a question for another mailing list, I suppose. ;)
>>>
>>> james
>>>
>>>
>>> -------------------------------------------------------
>>> 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
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> 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
>>
>>
>>
>>
>

RE: [PyMOL] Builder Question

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

James,

PyMOL's peptide & small molecular builder is no more rigorous that a
handheld plastic model.  Unfortunately, DeLano Scientific doesn't have
the developer "bandwidth" right now to get into the simulations
business.  Instead, we hope to facilitate and encourage integration with
existing external packages via PyMOL wizards and simple Python glue.

Thus, our near-term goal with the builder is to simply provide
scientists like yourself with a user interface for building molecules
and setting up *initial* poses that will then be subjected to rigorous
computations external to PyMOL.

There are plenty of integrations options out there, from free and/or
open-source tools like GROMACS, APBS, Tinker, ArgusLab, GAMESS US, and
MMTK, to academic codes like Amber, Charmm, Dock, and Autodock, to
commercial codes like Szybki (MMFF), Fred, Glide, BatchMin, MOE, Sybyl,
or Discover. =20

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
> Jim Nettles
> Sent: Monday, August 15, 2005 8:56 AM
> To: James R. Graham
> Cc: pym...@li...
> Subject: Re: [PyMOL] Builder Question
>=20
> Hello James,
>=20
> There is really a lot of room for discussion regarding your=20
> questions. =20
> Considering peptide conformations is complicated business and=20
> there is generally not "a" structure. There is great=20
> conformational flexibility even for small, constrained,=20
> cyclic peptides. As for the MD - yes, a classical MD=20
> trajectory is entirely determined by the starting structure.=20
> One can introduce random number seeds, high temperature, etc=20
> ... to explore greater space, but where you start is=20
> definitely worthy of thoughtful consideration.
>=20
> I can send references and more discussion off list, if you=20
> are interested.
>=20
> Cheers,
>=20
> Jim N.
> ________________________________________________________
> James Nettles, Ph. D. Computational Pharmacology=20
> Liotta/Snyder Group, Modeling Division, Department of=20
> Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322=20
> jn...@em...  TEL: (404)966-4617  FAX: (404)728-0991=20
> ________________________________________________________
>=20
> On Aug 15, 2005, at 11:36 AM, James R. Graham wrote:
>=20
> > Hello All,
> >
> > How "physiological" are the structures that are produced=20
> from builder?=20
> > Meaning, how are the angles, etc. determined? Might such a=20
> resulting=20
> > structure mimic a chemically-synthesized peptide?
> >
> > I have taken peptides I created using builder and done some MD=20
> > simulations and the structures certainly change, but I=20
> wonder whether=20
> > the changes are limited by the initial starting=20
> structure...which is,=20
> > of course, a question for another mailing list, I suppose. ;)
> >
> > james
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO=20
> > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
> > Practices Agile & Plan-Driven Development * Managing=20
> Projects & Teams=20
> > * Testing & QA Security * Process Improvement & 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
>=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

Re: [PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?

[geek t. <gee...@gm...>]

I have one of each of the Logitech MX 500, 510, 518 series and they
all have worked (and are still working) fine for me, albeit on windows
and linux.  I don't have any experience with the cordless version, but
after a little google searching it looks like the logitech software is
buggy on macs.  You might try uninstalling it and letting the OS think
its a generic 3-button mouse.

hope it helps,
-Tzintzuni Garcia


On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote:
> I use a cheap microsoft optical (or basic optical) usb mouse on linux,
> so it should work on your macosx.
>=20
> If you want something more configurable under macosx and don't want to
> destroy the "Appleness" of your computer with an MS mouse then this
> might work for you http://www.apple.com/mightymouse/ . I hear there will
> be a wireless version soon.
>=20
> Sarina Bromberg wrote:
> > I have a logitech MX700 Cordless Optical Mouse that claims to be a 3-
> > button mouse, but I can never get it to produce the results provided
> > for 3-button viewing or editing by PyMOL.  Perhaps I do not have it
> > configured correctly (I cannot find a clue in the instructions or in
> > simple experiments), or perhaps this is not the kind of 3-button  mouse
> > I need. Does anyone have a good solution?
> > Tx,
> > Sarina Bromberg
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract=
ices
> > Agile & Plan-Driven Development * Managing Projects & Teams * Testing &=
 QA
> > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5=
sf
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
> -------------------------------------------------------
> 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 & Q=
A
> 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] Builder Question

[Jim N. <jn...@em...>]

Hello James,

There is really a lot of room for discussion regarding your questions.  
Considering peptide conformations is complicated business and there is 
generally not "a" structure. There is great conformational flexibility 
even for small, constrained, cyclic peptides. As for the MD - yes, a 
classical MD trajectory is entirely determined by the starting 
structure. One can introduce random number seeds, high temperature, etc 
... to explore greater space, but where you start is definitely worthy 
of thoughtful consideration.

I can send references and more discussion off list, if you are 
interested.

Cheers,

Jim N.
________________________________________________________
James Nettles, Ph. D. Computational Pharmacology
Liotta/Snyder Group, Modeling Division, Department of Chemistry
Emory University 1515 Pierce Dr. Atlanta, Ga. 30322
jn...@em...  TEL: (404)966-4617  FAX: (404)728-0991
________________________________________________________

On Aug 15, 2005, at 11:36 AM, James R. Graham wrote:

> Hello All,
>
> How "physiological" are the structures that are produced from builder? 
> Meaning, how are the angles, etc. determined? Might such a resulting 
> structure mimic a chemically-synthesized peptide?
>
> I have taken peptides I created using builder and done some MD 
> simulations and the structures certainly change, but I wonder whether 
> the changes are limited by the initial starting structure...which is, 
> of course, a question for another mailing list, I suppose. ;)
>
> james
>
>
> -------------------------------------------------------
> 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

[PyMOL] Builder Question

[James R. G. <jam...@ma...>]

Hello All,

How "physiological" are the structures that are produced from  
builder? Meaning, how are the angles, etc. determined? Might such a  
resulting structure mimic a chemically-synthesized peptide?

I have taken peptides I created using builder and done some MD  
simulations and the structures certainly change, but I wonder whether  
the changes are limited by the initial starting structure...which is,  
of course, a question for another mailing list, I suppose. ;)

james

Re: [PyMOL] Setting transparency for CGOs

[Michael G. L. <ml...@um...>]

>> Quoting tan...@st...:
>> 
>> # Hi everybody,
>> #
>> # i've just created many CGOs, which show up solid surfaces like spheres 
>> and
>> # ellipsoids. Is it possible to set the transparency of some CGO's to
>> i.e. 0.5
>> # and leave the others solid?
>> # I've checked out the reference and the manual, and found something like:
>> #
>> # set transparency=0.5, object
>> #
>> # But this actually does not work for CGO's.
>> # Any ideas....
>> #
>> # Yusuf

The last time I looked at this, it seemed like the easiest (only?) way to 
do this was to tweak the transparency at creation time.  So, I typically 
have functions that look like this:

def makeSphere(name,x,y,z,r,transparency=0,...):
    ...
    obj = []
    ...
    obj.extend([cgo.ALPHA,1-transparency])
    obj.extend([cgo.SPHERE,x,y,z,r])
    ...
    cmd.load_cgo(obj,name,1)

I don't know how to change it later, though.

Hope that helps,

-michael

>> #
>> #
>> # --
>> # Yusuf Tanrikulu
>> # Bioinformatics Diploma Student
>> # Department of Biosciences
>> # Johann-Wolfgang-Goethe Univerity Frankfurt
>> # Siesmayerstrasse 70
>> # 60326 Frankfurt am Main
>> # - Germany -
>> # tan...@bi...
>> #
>> #

Re: [PyMOL] Setting transparency for CGOs

[<tan...@st...>]

Lari,

the way you've described is a nice workaround for images and presentations,
which I had in mind, too. But it is not applicable while I am working with
PyMOL online and want to make my CGO's transparent to see what is in them
(including ability to rotate and zomm in/out the scene (which is not very
doable in static pictures ;-)).
I'm familiar with scripting in PyMOL. Probably I can change any transparenc=
y
variable while creating my triangles, which result in my CGO's? Isn't there=
 a
implemented command in PyMOL, which does what I need?

Cheers,

Yusuf

--
Yusuf Tanrikulu
Bioinformatics Diploma Student
Department of Biosciences
Johann-Wolfgang-Goethe Univerity Frankfurt
Siesmayerstrasse 70
60326 Frankfurt am Main
- Germany -
tan...@bi...

Quoting Lari Lehti=F6 <lar...@he...>:

> Hi,
>
> I've done this by rendering two images (actually 4 to get stereo). 
> One without
> the CGOs and one with them. Then I overlaid them with photoshop and 
> changed the
> trasnparency of the CGO containing layer. I just used triangles and it lo=
oked
> rather nice.
>
> ~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/
> _______________________________________
>
>
> Quoting tan...@st...:
>
> # Hi everybody,
> #
> # i've just created many CGOs, which show up solid surfaces like spheres =
and
> # ellipsoids. Is it possible to set the transparency of some CGO's to 
> i.e. 0.5
> # and leave the others solid?
> # I've checked out the reference and the manual, and found something like=
:
> #
> # set transparency=3D0.5, object
> #
> # But this actually does not work for CGO's.
> # Any ideas....
> #
> # Yusuf
> #
> #
> # --
> # Yusuf Tanrikulu
> # Bioinformatics Diploma Student
> # Department of Biosciences
> # Johann-Wolfgang-Goethe Univerity Frankfurt
> # Siesmayerstrasse 70
> # 60326 Frankfurt am Main
> # - Germany -
> # tan...@bi...
> #
> #
> # -------------------------------------------------------
> # SF.Net email is Sponsored by the Better Software Conference & EXPO
> # September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract=
ices
> # Agile & Plan-Driven Development * Managing Projects & Teams * Testing &=
 QA
> # Security * Process Improvement & Measurement * http://www.sqe.com/bsce5=
sf
> # _______________________________________________
> # PyMOL-users mailing list
> # PyM...@li...
> # https://lists.sourceforge.net/lists/listinfo/pymol-users
> #
>
>
> -------------------------------------------------------
> 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 & Q=
A
> 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] Saving a carved section of a map.

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

> > I was wondering if it is possible to save a carved out section of a=20
> > map and the read it back into pymol as a separate map.

> Pymol won't do it

Not so, as of today (grin). =20

In 0.99beta11 and beyond, the newly implemented command to carry this
out is "map_trim".  (Windows build at http://delsci.com/beta or compile
from source).

map_trim map-name, selection-name, buffer

Combined with the convenient new object-name wildcards (!!!), you could
for example trim all your maps to 3 Angstroms around ligands with one
commmand as follows

map_trim *, organic, 3

With map size now reduced, the map_double command can come in handy to
increase mesh density on your figure.

map_double *

Also in this new beta:  Dunbrack rotamers, nucleic acid cartoons, new
pop-up menus, etc.

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 Tim Fenn
> Sent: Saturday, August 13, 2005 11:38 AM
> To: Schubert, Carsten [PRDUS]
> Cc: pym...@li...
> Subject: Re: [PyMOL] Saving a carved section of a map.
>=20
> On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten=20
> [PRDUS] wrote:
> >=20
> > I was wondering if it is possible to save a carved out section of a=20
> > map and the read it back into pymol as a separate map.
>=20
> Pymol won't do it, but if its something thats urgent,=20
> povscript+ saves maps in GTS format (including vertex colors):
>=20
> http://gts.sf.net
> http://www.stanford.edu/~fenn/povscript/gts_fileformat.html
>=20
> HTH,
> Tim
>=20
> --
> ---------------------------------------------------------
>=20
>         Tim Fenn
>         fe...@st...
>         Stanford University, School of Medicine
>         James H. Clark Center
>         318 Campus Drive, Room E300
>         Stanford, CA  94305-5432
>         Phone:  (650) 736-1714
>         FAX:  (650) 736-1961
>=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

Re: [PyMOL] Saving a carved section of a map.

[Tim F. <fe...@st...>]

On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten [PRDUS] wrote:
> 
> I was wondering if it is possible to save a carved out section of a map and
> the read it back into pymol as a separate map.

Pymol won't do it, but if its something thats urgent, povscript+ saves
maps in GTS format (including vertex colors):

http://gts.sf.net
http://www.stanford.edu/~fenn/povscript/gts_fileformat.html

HTH,
Tim

-- 
---------------------------------------------------------

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

---------------------------------------------------------

RE: [PyMOL] conformational states in the mutagenesis wizard

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

Xavier,

PyMOL 0.99beta09 and earlier use a crude backbone-independent rotamer
library.

However, current development versions (PyMOL 0.99beta10 on up) now
provide both the Dunbrack backbone-dependent and backbone-independent
rotamers.

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
> Xavier Deupi
> Sent: Friday, August 12, 2005 2:34 PM
> To: pym...@li...
> Subject: [PyMOL] conformational states in the mutagenesis wizard
>=20
> Hi,
>=20
> I've just realized that through the mutagenesis wizard you=20
> can view/select different conformations for a sidechain. I've=20
> been playing around, and it seems that the conformations are=20
> selected according to a backbone-independent rotamer library.=20
> Am I correct? Which library has been used?
>=20
> I would also like to know if there is anybody out there using=20
> the rotamer toggle plugin. I've just installed it, and=20
> although it seems extremely useful, it makes PyMOL very slow=20
> to start. I'm running PyMOL
> 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM=20
> (running MacOS X
> 10.4.2)
>=20
> Thanks in advance,
>=20
> Xavier
>=20
> --
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology Beckman=20
> Center for Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine=20
> Stanford, CA 94305 (USA)
>=20
> E-mail: Xav...@st...
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>=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] Shadows

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

Hi Corinne, Sabuj,

You're right with regards to the CGO. An example script (written by
Gareth Stockwell) can be found at
http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the
raytracing, don't be fooled, I'd say this was Pymol's internal
raytracer :)

Hope it helps,

Tsjerk

On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote:
> It looks like a CGO (compiled graphics object) behind the molecule, then
> rendered using pov-ray, probably a script floating around to do this
> somewhere on the internets.
>=20
> Corinne Zeitler wrote:
> > Hi,
> >
> > I was wondering if anyone knows how to produce the type of image in
> > Pymol that is on the Pymol Galleray page
> > (http://pymol.sourceforge.net/pmimag.html).  I would like to know
> > specifically how to make the shadow of the molecule appear in the
> > background.  Thank you!
> >
> > Corinne Zeitler
> > Graduate Student
> > Baylor College of Medicine
>=20
>=20
>=20
> -------------------------------------------------------
> 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 & Q=
A
> 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] What is the best 3 button mouse for PyMOL on a Mac OSX?

[Sabuj P. <sab...@va...>]

I use a cheap microsoft optical (or basic optical) usb mouse on linux, 
so it should work on your macosx.

If you want something more configurable under macosx and don't want to 
destroy the "Appleness" of your computer with an MS mouse then this 
might work for you http://www.apple.com/mightymouse/ . I hear there will 
be a wireless version soon.

Sarina Bromberg wrote:
> I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- 
> button mouse, but I can never get it to produce the results provided  
> for 3-button viewing or editing by PyMOL.  Perhaps I do not have it  
> configured correctly (I cannot find a clue in the instructions or in  
> simple experiments), or perhaps this is not the kind of 3-button  mouse 
> I need. Does anyone have a good solution?
> Tx,
> Sarina Bromberg
> 
> 
> -------------------------------------------------------
> 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

Re: [PyMOL] Shadows

[Sabuj P. <sab...@va...>]

It looks like a CGO (compiled graphics object) behind the molecule, then 
rendered using pov-ray, probably a script floating around to do this 
somewhere on the internets.

Corinne Zeitler wrote:
> Hi,
> 
> I was wondering if anyone knows how to produce the type of image in 
> Pymol that is on the Pymol Galleray page 
> (http://pymol.sourceforge.net/pmimag.html).  I would like to know 
> specifically how to make the shadow of the molecule appear in the 
> background.  Thank you!
> 
> Corinne Zeitler
> Graduate Student
> Baylor College of Medicine

[PyMOL] conformational states in the mutagenesis wizard

[Xavier D. <Xav...@st...>]

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

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

Re: [PyMOL] comments ?

[Michael C. <msc...@sy...>]

Hi 

I have installed version 0.98 on my new dual processor machine running
windows XP. Pymol runs fine, but when trying to load a large PDB file
(~4Mb), the program crashes and I get a runtime error:

"This application has requested the Runtime to terminate it in an
unusual way"


Does anyone have some advice?


Thanks,

Michael






Michael S. Cosgrove, Ph.D.
Assistant Professor
Syracuse University
Department of Biology
406D Lyman Hall
108 College Place
Syracuse, NY 13244

Phone: (315) 443-2964
Fax: (315) 443-2156
Email: msc...@sy...

RE: [PyMOL] Newline character in scene annotation message

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

Carsten,

Hmm...

Unfortunately, the PyMOL command language currently provide any way of
expressing a newline character, so you will need to use the API form of
the scene command.  Note that it is perfectly legal to use that form in
a ".pml" file as follows, without an intervening variable:

cmd.scene("new","store","line1\nline2")

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
> Schubert, Carsten [PRDUS]
> Sent: Friday, August 12, 2005 12:57 PM
> To: pym...@li...
> Subject: [PyMOL] Newline character in scene annotation message
>=20
> Hi=20
>=20
> I am trying to combine a scene with annotations spanning=20
> several lines.=20
> So far something like=20
> > scene new, store, message=3D"Line1\nLine2"=20
>=20
> would produce some nice coloration effects but not a newline=20
> character.=20
>=20
> I was able to use the api function to do the trick=20
> >mesg=3D"line1\nline2"=20
> >cmd.scene("new","store",message=3Dmesg)
>=20
> but I was wondering is there a way to use the non API=20
> function in the same way?=20
>=20
> Thanks=20
>=20
>         Carsten=20
>=20
>=20

[PyMOL] Newline character in scene annotation message

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

Hi

I am trying to combine a scene with annotations spanning several lines.
So far something like 
> scene new, store, message="Line1\nLine2"

would produce some nice coloration effects but not a newline character.

I was able to use the api function to do the trick
>mesg="line1\nline2"
>cmd.scene("new","store",message=mesg)

but I was wondering is there a way to use the non API function in the same
way?

Thanks

	Carsten

[PyMOL] Shadows

[Corinne Z. <cze...@gm...>]

Hi,

I was wondering if anyone knows how to produce the type of image in Pymol=
=20
that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.htm=
l).=20
I would like to know specifically how to make the shadow of the molecule=20
appear in the background. Thank you!

Corinne Zeitler
Graduate Student
Baylor College of Medicine

RE: [PyMOL] Saving a carved section of a map.

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

Hi Carsten,

This isn't yet possible from within PyMOL, but it will be soon since it
is a recurring request.  In the meantime unforutnately, you will need to
truncate the maps outside of PyMOL in order to generate smaller session
files.

Sorry about that!

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
> Schubert, Carsten [PRDUS]
> Sent: Friday, August 12, 2005 11:56 AM
> To: pym...@li...
> Subject: [PyMOL] Saving a carved section of a map.
>=20
> Hi=20
>=20
> I was wondering if it is possible to save a carved out=20
> section of a map and the read it back into pymol as a=20
> separate map. The background is that I'd like to distribute=20
> .psw files with a couple of maps, but they get rather large=20
> (>50 MB) since the map data is not compressed in pymol. I am=20
> only interested in a small portion of the map centered around=20
> a ligand and some residues, so the rest of the map would be=20
> unnecessary since it will not be shown anyway.=20
>=20
> I have tried if mapman could do the trick but apparently not.=20
> I could probably restrict the calculation of the map to be=20
> only centered around a region of interest, but was wondering=20
> if this would be possible in pymol.
>=20
>=20
> Thanks=20
>=20
>         Carsten=20
>=20
>=20

[PyMOL] Saving a carved section of a map.

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

Hi 

I was wondering if it is possible to save a carved out section of a map and
the read it back into pymol as a separate map. The background is that I'd
like to distribute .psw files with a couple of maps, but they get rather
large (>50 MB) since the map data is not compressed in pymol. I am only
interested in a small portion of the map centered around a ligand and some
residues, so the rest of the map would be unnecessary since it will not be
shown anyway. 
I have tried if mapman could do the trick but apparently not. I could
probably restrict the calculation of the map to be only centered around a
region of interest, but was wondering if this would be possible in pymol.


Thanks

	Carsten

[PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?

[Sarina B. <sa...@di...>]

I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- 
button mouse, but I can never get it to produce the results provided  
for 3-button viewing or editing by PyMOL.  Perhaps I do not have it  
configured correctly (I cannot find a clue in the instructions or in  
simple experiments), or perhaps this is not the kind of 3-button  
mouse I need. Does anyone have a good solution?
Tx,
Sarina Bromberg

[PyMOL] PML files

[Avram S. <as...@co...>]

Hi,

does anyone know what file type to save text as (in OS X) for a .pml 
file?  I can't get PyMol to recognize RTF, etc...

thanks

Avram Slovic