pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Missing parts in cartoon mode

[<ran...@ic...>]

The two missing loops of the 1DAN structure when in cartoon mode are
located to res. 183-189 and 220-220. I=B4m using a standard PC with
Windows 2000.

Any suggestions? A fellow collegue in my lab is having identical
troubles but he=B4s also using a PC with win2000. Its quite frustrating
because the rest of the structure looks great in PyMol!

=20

Cheers Kasper

=20



<-----Original Message----->

 	  	 From: Joel Tyndall
Sent: 10/17/2005 12:07:00 AM
To: ran...@ic...
Subject: Re: [PyMOL] Missing parts in cartoon mode=20

Hey Kasper,=20

which loops can't you see (amino acid nos./chain/)? what OS are you on=20
(OSX, PC, Linux?) I have had a look and it looks ok on windows=20

Cheers=20

J=20

ran...@ic... wrote:=20

> Hi everybody=20
> I am getting quite desperate! For some strange reason PyMol do not=20
> display certain areas (several loops) of my .pdb file (1DAN) when in=20
> cartoon display mode. When I display the structure in "lines" or=20
> "sticks" everything is ok. Other pdb-viewers dont have this problem=20
> with the same .pdb file. I have tried several things:=20
> 1. Upgraded to the newest version og PyMol.=20
> 2. Redefined secondary structure using the "alter" command.=20
> 3. Imported the .pdb file into SwissViewer, saved as the imported=20
> structure as a .pdb file, and then imported into PyMOl.=20
>=20
> None of these things have solved the problem. Help please! (I would=20
> hate to have to start using another pdb-viewer!!) Cheers Kasper=20
>=20
> _______________________________________________________________=20
> ICQ - You get the message, anywhere!=20
> Get it @ http://www.icq.com=20
>=20
>=20
>=20

--=20
Joel Tyndall, PhD=20

Lecturer=20
National School of Pharmacy=20
University of Otago=20
PO Box 913 Dunedin=20
New Zealand=20

Pukenga=20
Te Kura Taiwhanga Putaiao=20
Te Whare Wananga o Otago=20
Pouaka Poutapeta 913 Otepoti=20
Aotearoa=20

Ph / Waea +64 3 4797293=20
Fax / Waeawhakaahua +64 3 4797034=20


.=20
=09


<P><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">_______________________________________________________________<BR><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">ICQ - You get the message, anywhere!<br>Get it @ <a href="http://www.icq.com" target=new>http://www.icq.com</a></font><br><br>&nbsp;</font></font>

[PyMOL] Re:

[Kostas T. <ko...@nm...>]

On Tuesday 18 October 2005 16:36, pym...@li... 
wrote:
Hi Warren
It's been a long time since my last post. Anyway I tried the polar contacts 
identifier as written below
> dist name, sel1, sel2, mode=3D2
and I get the following error
Traceback (most recent call last):
  File "/home/kostas/pymol/modules/pymol/parser.py", line 191, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "/home/kostas/pymol/modules/pymol/querying.py", line 400, in distance
    str(selection2),int(mode),float(cutoff),
ValueError: invalid literal for int(): 3D2
using the last version  pymol-0_99beta20
Any clue
Another important notion regarded the 0.99 versions and on is that incorrectly 
draw bonds between methyl protons. As you understand I work with NMR 
structures but I don't have this misinterpretation with previous versions. 
The same appeared with 13 and 20 releases. Please keep it in mind.

cheers kostas

RE: [PyMOL] set_dihedral

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

> I guess that the moral of the story is that it's better to be=20
> as specific as possible when making selections...

Yes, this is an important thing to understand, and something I seen come
up frequently with new users.  The thing to remember is:

As soon as you "create" a new object based on existing object, there
will then be two sets of atoms in PyMOL that possess identical segment,
chain, residue, and atom identifiers.  Both sets will match in selection
unless you specify the object name too.

# here there is just one object, so residue id alone is fine:

load prot.pdb
show sticks, 10-15/
create my_loop, 10-15/

# now there are two objects, so you must specify the
# object name if you want to act on it independently

color red, prot///10-15/
color blue, my_loop///10-15/

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

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

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

>>But does this problem look like a bug ?
>=20
>=20
> No, it works as intended.  The issue here is that the GUI just does not=
 (yet) provide the capability of coloring representations, just atoms.  S=
o if you color representations directly using a command, then you'll need=
 to use a command uncolor them.
>=20
> At present, only a small fraction of PyMOL's capabities are directly ex=
posed in the user interface.  The rest must be accessed through commands,=
 scripts, and/or Python programs.  I'm not saying that is good...it is ju=
st how things are right now.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist

Ok thanks,

So, a script command cannot be canceled from the GUI, but it must be=20
from the same kind of (another) script command.

>>>>>Sebastien,
>>>>>
>>>>>
>>>>>
>>>>>>I cannot
>>>>>>change the color for rendering modes I defined.
>>>>>
>>>>>I do not understand what you mean by this.
>>>>>
>>>>>Cheers,
>>>>>Warren
>>>>
>>>>I mean that the color, for cartoon view, is unchangeable when 'set=20
>>>>cartoon_color' is defined in the $HOME/.pymolrc file.
>>>>Thus, when I define 'set cartoon_color' in the=20
>>
>>$HOME/.pymolrc file, I=20
>>
>>>>cannot change the color, for the cartoons, from the GUI.
>>>>
>>>>The color is kept whatever I do.
>>>
>>>I take it that you mean that choosing the "C" box on the right-hand=20
>>>menu for the object in question and then selecting a colour or=20
>>>colouring scheme results in no change to your cartoon=20
>>
>>representation.=20
>>
>>>In that case, I think that what you need to do is type:
>>>
>>>  set cartoon_color, default
>>>
>>>Then the cartoon is not forced to be the colour that you=20
>>
>>set (slate)=20
>>
>>>but takes on the colour of the atoms in the object.
>>>
>>>Cheers,
>>>Rob
>>
>>Yes, that's it.
>>I know that I only have to comment or change this line.
>>
>>But does this problem look like a bug ?

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

RE: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]]

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

> But does this problem look like a bug ?

No, it works as intended.  The issue here is that the GUI just does not =
(yet) provide the capability of coloring representations, just atoms.  =
So if you color representations directly using a command, then you'll =
need to use a command uncolor them.

At present, only a small fraction of PyMOL's capabities are directly =
exposed in the user interface.  The rest must be accessed through =
commands, scripts, and/or Python programs.  I'm not saying that is =
good...it is just how things are right now.

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
> Sebastien Moretti
> Sent: Monday, October 17, 2005 11:45 PM
> To: pymol-users
> Subject: [Re: [PyMOL] [colors frozen for rendering modes=20
> defined in .pymolrc]]
>=20
> >>>Sebastien,
> >>>
> >>>
> >>>>I cannot
> >>>>change the color for rendering modes I defined.
> >>>
> >>>I do not understand what you mean by this.
> >>>
> >>>Cheers,
> >>>Warren
> >>
> >>I mean that the color, for cartoon view, is unchangeable when 'set=20
> >>cartoon_color' is defined in the $HOME/.pymolrc file.
> >>Thus, when I define 'set cartoon_color' in the=20
> $HOME/.pymolrc file, I=20
> >>cannot change the color, for the cartoons, from the GUI.
> >>
> >>The color is kept whatever I do.
> >=20
> > I take it that you mean that choosing the "C" box on the right-hand=20
> > menu for the object in question and then selecting a colour or=20
> > colouring scheme results in no change to your cartoon=20
> representation.=20
> > In that case, I think that what you need to do is type:
> >=20
> >   set cartoon_color, default
> >=20
> > Then the cartoon is not forced to be the colour that you=20
> set (slate)=20
> > but takes on the colour of the atoms in the object.
> >=20
> > Cheers,
> > Rob
>=20
> Yes, that's it.
> I know that I only have to comment or change this line.
>=20
> But does this problem look like a bug ?
>=20
> --
> S=E9bastien Moretti
> http://www.igs.cnrs-mrs.fr/
> CNRS - IGS
> 31 chemin Joseph Aiguier
> 13402 Marseille cedex
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] feed value to pymol -qrc script.py

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

Andrea

pymol -qrc script.py arg1 arg2

will work if you add a double-hyphen before the first argument in order
to signal Pymol to stop interpreting arguments:

pymol -qrc script.py -- arg1 arg2

Then your script can get these arguments as follows:

from sys import argv
my_argv =3D argv[argv.index("--"):]
print my_argv[1], my_argv[2]

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
> andrea spitaleri
> Sent: Tuesday, October 18, 2005 12:47 AM
> To: Pymol users
> Subject: [PyMOL] feed value to pymol -qrc script.py
>=20
> Hi there,
> I made a script in pymol and I'd like to use it as pymol -qrc=20
> script.py argv[1] argv[2] ...
> but it seems not working properly. It says that it cannot=20
> open such file, even if the argument is a number...
> In fact, if I replace the sys.argv[] with the values into=20
> script.py, it woks.
> Any help?
>=20
> Regards
>=20
> andrea
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

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

Yes,

dist name, sele1, sele2, mode=3D2

eg.

load $TUT/1hvp.pdb

dist name, solvent, protein, mode=3D2

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
> Marc Bruning
> Sent: Tuesday, October 18, 2005 5:03 AM
> To: pym...@li...
> Cc: Warren DeLano; Michael Weber
> Subject: Re: [PyMOL] automated H-bond computation &=20
> visualization in pyMOL?
>=20
> hello,
>=20
> is this feature accessible from the command line as well?
>=20
> cheers,
> marc
>=20
> On Monday 17 October 2005 22:16, Warren DeLano wrote:
> > Michael
> >
> > d/l a recent build http://delsci.com/beta
> >
> > and use the "find"->"polar contacts" option under the=20
> objects Action "A"
> > menu in the viewer window.
> >
> > 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 =20
> > Cell:(650)-346-1154 . mailto:wa...@de...
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of=20
> > > Michael Weber
> > > Sent: Monday, October 17, 2005 5:03 AM
> > > To: pym...@li...
> > > Subject: [PyMOL] automated H-bond computation & visualization in=20
> > > pyMOL?
> > >
> > > Hello everybody,
> > > I am new to PyMOL and I have a short question: In pyMOL - is it=20
> > > possible to automatically compute and visualize H-bonds in .PDB=20
> > > files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe=20
> there is a=20
> > > pyMOL script for this purpose? I need such a function for my work=20
> > > with catalytically active RNA molecules (e.g. PDB # 2A2E, 2A64,=20
> > > 1NBS, 1U9S). Would be nice if someone could help me with this=20
> > > problem...
> > >
> > > All the best & thanks in advance,
> > > Michael.
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by:
> > Power Architecture Resource Center: Free content, downloads,=20
> > discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] automated H-bond computation & visualization in pyMOL?

[Michael W. <we...@st...>]

Hi Warren,
thanks a lot for the quick & useful information concerning H-bond 
visualization.

All the best,
Michael.

----- Original Message ----- 
> On Monday 17 October 2005 22:16, Warren DeLano wrote:
>> Michael
>>
>> d/l a recent build http://delsci.com/beta
>>
>> and use the "find"->"polar contacts" option under the objects Action "A"
>> menu in the viewer window.
>>
>> 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
>> > Michael Weber
>> > Sent: Monday, October 17, 2005 5:03 AM
>> > To: pym...@li...
>> > Subject: [PyMOL] automated H-bond computation & visualization
>> > in pyMOL?
>> >
>> > Hello everybody,
>> > I am new to PyMOL and I have a short question: In pyMOL - is
>> > it possible to automatically compute and visualize H-bonds in
>> > .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe
>> > there is a pyMOL script for this purpose? I need such a
>> > function for my work with catalytically active RNA molecules
>> > (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone
>> > could help me with this problem...
>> >
>> > All the best & thanks in advance,
>> > Michael. 

[PyMOL] gradient transparency

[Neil R. <n.a...@le...>]

Dear All,

I think I know the answer to this, but is there any way in which a
transparency gradient can be set up?

I have an electron density map (ccp4) with fitted atomic coordinates. I'd
like to have the electron density transition smoothly from transparent to
opaque across the structure.

Any ideas?

Cheers,
Neil.

 

 

*************************************

Neil Ranson PhD

University Research Fellow,

Astbury Centre for Structural Molecular Biology,

Institute of Molecular & Cellular Biology,

University of Leeds,

Leeds, LS2 9JT. UK.

 

Tel: +44 (0) 113 343 7065

Fax: +44 (0) 113 343 3167

n.a...@le...

 

*************************************

 

Re: [PyMOL] automated H-bond computation & visualization in pyMOL?

[Marc B. <br...@mp...>]

hello,

is this feature accessible from the command line as well?

cheers,
marc

On Monday 17 October 2005 22:16, Warren DeLano wrote:
> Michael
>
> d/l a recent build http://delsci.com/beta
>
> and use the "find"->"polar contacts" option under the objects Action "A"
> menu in the viewer window.
>
> 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
> > Michael Weber
> > Sent: Monday, October 17, 2005 5:03 AM
> > To: pym...@li...
> > Subject: [PyMOL] automated H-bond computation & visualization
> > in pyMOL?
> >
> > Hello everybody,
> > I am new to PyMOL and I have a short question: In pyMOL - is
> > it possible to automatically compute and visualize H-bonds in
> > .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe
> > there is a pyMOL script for this purpose? I need such a
> > function for my work with catalytically active RNA molecules
> > (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone
> > could help me with this problem...
> >
> > All the best & thanks in advance,
> > Michael.
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] feed value to pymol -qrc script.py

[andrea s. <and...@gm...>]

Hi there,
I made a script in pymol and I'd like to use it as pymol -qrc script.py 
argv[1] argv[2] ...
but it seems not working properly. It says that it cannot open such 
file, even if the argument is a number...
In fact, if I replace the sys.argv[] with the values into script.py, it 
woks.
Any help?

Regards

andrea

Re: [PyMOL] How to raw_input() from windows Pymol?

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

Evangelos,

Maybe you could write a wizard instead of a script, look at

C:\......\pymol\modules\pymol\wizard\renaming.py

Zac

evangelos papadopoulos wrote:
> Hello all,
> 
>   I am using the windows binaries for PyMol. Whereas in Python it is 
> easy to do a:
> a=raw_input()
> When I use PyMol under windows it either gets crashed or halted while I 
> am unable to input from keybord. I searched in this email list and I 
> found some similar questions but no answer.
> I need this for a script that I am writing to get input from the user. 
> Is there any way to do that under windows or any other way to 
> interactivelly input some data from the keybord into a Pymol script 
> under windows? Has any ever done it and could it be that just I have 
> some wrong settings in windows or in the way I run the script?  Maybe 
> that can be done under linux/unix Pymol and be imposible under windows?
> Thank you & Best wishes
> /Cheers, Evangelos.
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 

[Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]]

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

>>>Sebastien,
>>>
>>>
>>>>I cannot=20
>>>>change the color for rendering modes I defined.
>>>
>>>I do not understand what you mean by this.
>>>
>>>Cheers,
>>>Warren
>>
>>I mean that the color, for cartoon view, is unchangeable when 'set=20
>>cartoon_color' is defined in the $HOME/.pymolrc file.
>>Thus, when I define 'set cartoon_color' in the $HOME/.pymolrc file, I=20
>>cannot change the color, for the cartoons, from the GUI.
>>
>>The color is kept whatever I do.
>=20
> I take it that you mean that choosing the "C" box on the right-hand men=
u
> for the object in question and then selecting a colour or colouring
> scheme results in no change to your cartoon representation. In that
> case, I think that what you need to do is type:
>=20
>   set cartoon_color, default
>=20
> Then the cartoon is not forced to be the colour that you set (slate) bu=
t
> takes on the colour of the atoms in the object.
>=20
> Cheers,
> Rob

Yes, that's it.
I know that I only have to comment or change this line.

But does this problem look like a bug ?

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

[PyMOL] set_dihedral

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

Hi,

I'm trying to apply the command 'set_dihedral' to residue from a 
molecule object which contains only three non-consecutive residues from 
the original protein. The program complains with the following error 
message:

GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 2 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 3 doesn't contain a single atom/vertex.
GetDihedral-Error: Selection 4 doesn't contain a single atom/vertex.

The command works fine on another object which contains 14 consecutive 
residues.

Is there any restriction on where you can apply this command?

Thanks in advance,

xavi

-- 
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] Geowall Testing

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

Esben,

Fantastic! I wasn't aware that nVidia quadro cards could do this.  That
provides a compelling reason to purchase nVidia Quadro cards for passive
stereo under Linux. =20

For the record: to configure passive stereo using the quadbuffer API
with a Quadro card under Linux, XF86Config needs to be configured as
follows:

Option "TwinView"
Option "TwinViewOrientation" "Clone"
Option "Connectedmonitor" "CRT, CRT"
Option "MetaModes" "1024x768,1024x768"
Option "Stereo" "4"

This approach should work great with existing versions of PyMOL.  You'll
only need the new PyMOL build if you are using a non-quadro graphics
card to drive your geowall.

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
> EPF (Esben Peter Friis)
> Sent: Monday, October 17, 2005 2:23 PM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: RE: [PyMOL] Geowall Testing
>=20
>=20
> Ahaaaa...
>=20
> That make things a bit clearer :-)  We do have a geowall, but=20
> the Linux driver supplied by Nvidia directly supports sending=20
> the left and right images of the quad-buffered stereo to the=20
> two separate video heads on the card, which are then=20
> connected to the two projectors. This eliminates the need for=20
> the very expensive active-to-passive stereo converter. This=20
> do require a Quadro-card, though. It is not supported by the=20
> cheaper GeForce cards.
>=20
> I think the Linux driver also support the type of stereo you=20
> mention here: Making a kind of side-by-side stereo, which is=20
> then converted to "real" stereo by doubling the desktop=20
> width, and splitting desktop between the two heads. I haven't=20
> tried, but I guess that is also supported by the GeForce=20
> cards. If it is not too difficult, I'll give it a try!
>=20
> I would argue that even though you can save a few hundred=20
> bucks (difference between a Quadro and a GeForce card), the=20
> Quadro card solution is easier. A Quadro FX 1300 card is=20
> around for about $300-400, which is still small compared to=20
> the Geowall system. But for Mac (and maybe Windows?) users,=20
> this driver option may not be available.
>=20
>=20
> Cheers
>=20
> Esben
>=20
>=20
> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: Mon 2005-10-17 22:43
> To: EPF (Esben Peter Friis)
> Subject: RE: [PyMOL] Geowall Testing
>=20
> Esben,
>=20
> If that is the case, then you don't actually have a "Geowall"=20
> -- you have a professional stereo device setup that converts=20
> the active-stereo signal sent from the nVidia cards into a=20
> passive-stereo signal for the two projectors.  That's=20
> equivalent to QBS stereo on a CRT with glasses, but typically=20
> costs quite a bit more (as much as $50k USD)
>=20
> Geowalls are a low-end alternative the geologists came up=20
> with a few years back.  Instead of requiring a stereo-capable=20
> video card, they use a normal (not necessarily=20
> stereo-capable) dual-headed video card to drive two=20
> projecters straight from the PC.
>=20
> That can bring the cost down to under $5k total, but it means=20
> that the software needs to draw the complete image twice,=20
> including the GUI, hence these changes.
>=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 EPF=20
> > (Esben Peter Friis)
> > Sent: Monday, October 17, 2005 1:30 PM
> > To: Warren DeLano
> > Cc: pym...@li...
> > Subject: RE: [PyMOL] Geowall Testing
> >
> >
> > I'll try it when I get back to work tomorrow - but I'm a=20
> bit confused=20
> > :-)  The features you mention, haven't they been part of PyMOL for=20
> > some time already? We have active stereo glasses for our=20
> workstations,=20
> > and use the same PyMOL version
> > (0.99beta14) for those and the Geowall.
> >
> >
> > Cheers,
> >
> > Esben
> >
> >
> > -----Original Message-----
> > From: Warren DeLano [mailto:wa...@de...]
> > Sent: Mon 2005-10-17 22:06
> > To: EPF (Esben Peter Friis)
> > Subject: RE: [PyMOL] Geowall Testing
> >
> > Esben,
> >
> > Great!
> >
> > Added: support for the internal gui, pop-up menus, sequence viewer,=20
> > and command line when using a passive stereo setup (versus active=20
> > stereo setups that cost about 10X more).
> >
> > Can you try the build at http://delsci.com/beta?
> >
> > Cheers,
> > Warren
> >
> >
> >
> > --
> > Warren L. DeLano, Ph.D.                 =20
> > Principal Scientist
> >
> > . DeLano Scientific LLC
> > . 400 Oyster Point Blvd., Suite 213       =20
> > . South San Francisco, CA 94080 USA
> > . Biz:(650)-872-0942  Tech:(650)-872-0834 . Fax:(650)-872-0273 =20
> > Cell:(650)-346-1154
> > . mailto:wa...@de...  =20
> >
> >
> >
> >
> >
> > ________________________________
> >
> >         From: EPF (Esben Peter Friis) [mailto:EP...@no...]
> >         Sent: Monday, October 17, 2005 12:58 PM
> >         To: Warren DeLano
> >         Subject: RE: [PyMOL] Geowall Testing
> >      =20
> >      =20
> >
> >
> >         Yep - we have one, which we use mostly for PyMOL=20
> presentations
> > :-)
> >         Stereo already works great, so I'm curious what you have in=20
> > mind. The computer connected to it is running Linux (Fedora Core 2)=20
> > and uses an Nvidia Quadro 750GLX card.
> >      =20
> >      =20
> >         Cheers,
> >      =20
> >         Esben
> >      =20
> >         -----Original Message-----
> >         From: pym...@li... on behalf of=20
> > Warren DeLano
> >         Sent: Mon 2005-10-17 16:27
> >         To: pym...@li...
> >         Subject: [PyMOL] Geowall Testing
> >      =20
> >         PyMOL Users:
> >      =20
> >         Regarding "geowalls" [also known as dual-projector passive=20
> > stereo setups
> >         that use polarized lenses & glasses to deliver=20
> low-cost stereo=20
> > 3D to
> >         large audiences]...
> >      =20
> >         Does anyone have one set up right now who might be able to=20
> > test a new
> >         PyMOL build with improved geowall stereo support?
> >      =20
> >         Cheers,
> >         Warren
> >      =20
> >         --
> >         Warren L. DeLano, Ph.D.                 =20
> >         Principal Scientist
> >      =20
> >         . DeLano Scientific LLC
> >         . 400 Oyster Point Blvd., Suite 213       =20
> >         . South San Francisco, CA 94080 USA
> >         . Biz:(650)-872-0942  Tech:(650)-872-0834 =20
> >         . Fax:(650)-872-0273  Cell:(650)-346-1154
> >         . mailto:wa...@de...  =20
> >      =20
> >      =20
> >      =20
> >         -------------------------------------------------------
> >         This SF.Net email is sponsored by:
> >         Power Architecture Resource Center: Free content,=20
> downloads,=20
> > discussions,
> >         and more. http://solutions.newsforge.com/ibmarch.tmpl
> >         _______________________________________________
> >         PyMOL-users mailing list
> >         PyM...@li...
> >         https://lists.sourceforge.net/lists/listinfo/pymol-users
> >      =20
> >      =20
> >
> >
> >
> >
> >
>=20
>=20
>=20
>=20

RE: [PyMOL] Geowall Testing

[EPF \(E. P. Friis\) <EP...@no...>]

Ahaaaa...=20

That make things a bit clearer :-)  We do have a geowall, but the Linux =
driver supplied by Nvidia directly supports sending the left and right =
images of the quad-buffered stereo to the two separate video heads on =
the card, which are then connected to the two projectors. This =
eliminates the need for the very expensive active-to-passive stereo =
converter. This do require a Quadro-card, though. It is not supported by =
the cheaper GeForce cards.=20

I think the Linux driver also support the type of stereo you mention =
here: Making a kind of side-by-side stereo, which is then converted to =
"real" stereo by doubling the desktop width, and splitting desktop =
between the two heads. I haven't tried, but I guess that is also =
supported by the GeForce cards. If it is not too difficult, I'll give it =
a try!

I would argue that even though you can save a few hundred bucks =
(difference between a Quadro and a GeForce card), the Quadro card =
solution is easier. A Quadro FX 1300 card is around for about $300-400, =
which is still small compared to the Geowall system. But for Mac (and =
maybe Windows?) users, this driver option may not be available.=20


Cheers

Esben


-----Original Message-----
From: Warren DeLano [mailto:wa...@de...]
Sent: Mon 2005-10-17 22:43
To: EPF (Esben Peter Friis)
Subject: RE: [PyMOL] Geowall Testing
=20
Esben,

If that is the case, then you don't actually have a "Geowall" -- you
have a professional stereo device setup that converts the active-stereo
signal sent from the nVidia cards into a passive-stereo signal for the
two projectors.  That's equivalent to QBS stereo on a CRT with glasses,
but typically costs quite a bit more (as much as $50k USD)

Geowalls are a low-end alternative the geologists came up with a few
years back.  Instead of requiring a stereo-capable video card, they use
a normal (not necessarily stereo-capable) dual-headed video card to
drive two projecters straight from the PC.=20

That can bring the cost down to under $5k total, but it means that the
software needs to draw the complete image twice, including the GUI,
hence these changes.

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
> EPF (Esben Peter Friis)
> Sent: Monday, October 17, 2005 1:30 PM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: RE: [PyMOL] Geowall Testing
>=20
>=20
> I'll try it when I get back to work tomorrow - but I'm a bit=20
> confused :-)  The features you mention, haven't they been=20
> part of PyMOL for some time already? We have active stereo=20
> glasses for our workstations, and use the same PyMOL version=20
> (0.99beta14) for those and the Geowall.
>=20
>=20
> Cheers,
>=20
> Esben
>=20
>=20
> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: Mon 2005-10-17 22:06
> To: EPF (Esben Peter Friis)
> Subject: RE: [PyMOL] Geowall Testing
>=20
> Esben,
>=20
> Great!
>=20
> Added: support for the internal gui, pop-up menus, sequence=20
> viewer, and command line when using a passive stereo setup=20
> (versus active stereo setups that cost about 10X more).
>=20
> Can you try the build at http://delsci.com/beta?
>=20
> Cheers,
> Warren
>=20
>=20
>=20
> --
> Warren L. DeLano, Ph.D.                  =20
> Principal Scientist
>=20
> . DeLano Scientific LLC
> . 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
>=20
>=20
>=20
> ________________________________
>=20
>         From: EPF (Esben Peter Friis) [mailto:EP...@no...]
>         Sent: Monday, October 17, 2005 12:58 PM
>         To: Warren DeLano
>         Subject: RE: [PyMOL] Geowall Testing
>       =20
>       =20
>=20
>=20
>         Yep - we have one, which we use mostly for PyMOL presentations
> :-)
>         Stereo already works great, so I'm curious what you=20
> have in mind. The computer connected to it is running Linux=20
> (Fedora Core 2) and uses an Nvidia Quadro 750GLX card.
>       =20
>       =20
>         Cheers,
>       =20
>         Esben
>       =20
>         -----Original Message-----
>         From: pym...@li... on=20
> behalf of Warren DeLano
>         Sent: Mon 2005-10-17 16:27
>         To: pym...@li...
>         Subject: [PyMOL] Geowall Testing
>       =20
>         PyMOL Users:
>       =20
>         Regarding "geowalls" [also known as dual-projector=20
> passive stereo setups
>         that use polarized lenses & glasses to deliver=20
> low-cost stereo 3D to
>         large audiences]...
>       =20
>         Does anyone have one set up right now who might be=20
> able to test a new
>         PyMOL build with improved geowall stereo support?
>       =20
>         Cheers,
>         Warren
>       =20
>         --
>         Warren L. DeLano, Ph.D.                  =20
>         Principal Scientist
>       =20
>         . DeLano Scientific LLC
>         . 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
>       =20
>         -------------------------------------------------------
>         This SF.Net email is sponsored by:
>         Power Architecture Resource Center: Free content,=20
> downloads, discussions,
>         and more. http://solutions.newsforge.com/ibmarch.tmpl
>         _______________________________________________
>         PyMOL-users mailing list
>         PyM...@li...
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
>       =20
>       =20
>=20
>=20
>=20
>=20
>=20

RE: [PyMOL] Pharmacophore visualizations

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

Andrew,

It's either-or for now.  Either you can render pharmacophores using CGOs
or you can represent them as molecules and thus align them.

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
> Andrew D. Fant
> Sent: Friday, October 14, 2005 3:45 PM
> To: pym...@li...
> Subject: [PyMOL] Pharmacophore visualizations
>=20
> Has anyone done anything with with making PyMol able to=20
> display pharmacophores as CGOs?  Being able to align=20
> molecules in pymol with a defined pharmacophore would be nice=20
> too, but I realize that doing that would require much more=20
> effort from some developer. For the time being, it would be=20
> good to have a predefined rendering solution that I can=20
> manually align structures to for visualization.
>=20
> Thanks,
> 	Andy
>=20
> --=20
> Andrew Fant           | The lion and the calf shall lie   |=20
> Disclaimer:
> and...@tu... | down together, but the calf won't |=20
> Do you REALLY
> TCCS/USG              | get much sleep.                   |=20
> think I can
> Tufts University      |                  W. Allen         |=20
> speak for Tufts?
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Geowall Testing

[EPF \(E. P. Friis\) <EP...@no...>]

I'll try it when I get back to work tomorrow - but I'm a bit confused =
:-)  The features you mention, haven't they been part of PyMOL for some =
time already? We have active stereo glasses for our workstations, and =
use the same PyMOL version (0.99beta14) for those and the Geowall.


Cheers,

Esben


-----Original Message-----
From: Warren DeLano [mailto:wa...@de...]
Sent: Mon 2005-10-17 22:06
To: EPF (Esben Peter Friis)
Subject: RE: [PyMOL] Geowall Testing
=20
Esben,
=20
Great!
=20
Added: support for the internal gui, pop-up menus, sequence viewer, and
command line when using a passive stereo setup (versus active stereo
setups that cost about 10X more).
=20
Can you try the build at http://delsci.com/beta?
=20
Cheers,
Warren
=20
=20

--
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


________________________________

	From: EPF (Esben Peter Friis) [mailto:EP...@no...]=20
	Sent: Monday, October 17, 2005 12:58 PM
	To: Warren DeLano
	Subject: RE: [PyMOL] Geowall Testing
=09
=09


	Yep - we have one, which we use mostly for PyMOL presentations
:-)
	Stereo already works great, so I'm curious what you have in
mind. The computer connected to it is running Linux (Fedora Core 2) and
uses an Nvidia Quadro 750GLX card.
=09
=09
	Cheers,
=09
	Esben
=09
	-----Original Message-----
	From: pym...@li... on behalf of
Warren DeLano
	Sent: Mon 2005-10-17 16:27
	To: pym...@li...
	Subject: [PyMOL] Geowall Testing
=09
	PyMOL Users:
=09
	Regarding "geowalls" [also known as dual-projector passive
stereo setups
	that use polarized lenses & glasses to deliver low-cost stereo
3D to
	large audiences]...
=09
	Does anyone have one set up right now who might be able to test
a new
	PyMOL build with improved geowall stereo support?
=09
	Cheers,
	Warren
=09
	--
	Warren L. DeLano, Ph.D.                   =20
	Principal Scientist
=09
	. 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
=09
=09
=09
	-------------------------------------------------------
	This SF.Net email is sponsored by:
	Power Architecture Resource Center: Free content, downloads,
discussions,
	and more. http://solutions.newsforge.com/ibmarch.tmpl
	_______________________________________________
	PyMOL-users mailing list
	PyM...@li...
	https://lists.sourceforge.net/lists/listinfo/pymol-users
=09
=09

RE: [PyMOL] picking discrete coordinates

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

The best way to approach this is simply to build a small molecular =
object on the fly.

See examples/devel/chempy_model*.py

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
> Martin Weisel
> Sent: Monday, October 17, 2005 5:03 AM
> To: pym...@li...
> Subject: [PyMOL] picking discrete coordinates
>=20
> Hi all!  =20
> I'm trying to pick a discrete coordinate outside of the=20
> loaded protein structure (something like "create name,=20
> coord[x,y,z]") to which I can apply the "around" command.=20
> Creating an additional atom as a probe would be a makeshift=20
> solution. Is there a way to use the Fragment Builder from the API?=20
> =20
> Thanks in advance,
> Martin Weisel=20
> =20
> =20
> -------------
> Martin Weisel
> Diploma Student
> Bioinformatics Group, Frankfurt University=20
>=20
> --
> 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail
> +++ GMX - die erste Adresse f=FCr Mail, Message, More +++
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] How to raw_input() from windows Pymol?

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

Evangelos,

This is architecturally impossible in PyMOL due to clash between the
asychronous nature of GUI event handling and the synchronous nature of
script execution using the main thread.

Right now, the best thing you can do is add a new command into the
language which calls your function followed by the text provided

def my_fn(*args): print args

cmd.extend("my_fn",my_fn)

Now, the user can type...

my_fn argument-list

...to call your function.

However, I would like to understand your intended use case in greater
detail so that we can find an easier way of providing such interactivity
in the future.  Perhaps we could do this by running such scripts in a
subordinate thread and then emulating "raw_input" behavior on the main
thread.

Another approach would be a prompting mechanism which would
automatically call a provided function with the next line of input.

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
> evangelos papadopoulos
> Sent: Monday, October 17, 2005 5:03 AM
> To: pym...@li...
> Subject: [PyMOL] How to raw_input() from windows Pymol?
>=20
> Hello all,
>=20
>    I am using the windows binaries for PyMol. Whereas in=20
> Python it is easy to do a:
> a=3Draw_input()
> When I use PyMol under windows it either gets crashed or=20
> halted while I am unable to input from keybord. I searched in=20
> this email list and I found some similar questions but no answer.
> I need this for a script that I am writing to get input from=20

> the user.=20
> Is there any way to do that under windows or any other way to=20
> interactivelly input some data from the keybord into a Pymol=20
> script under windows? Has any ever done it and could it be=20
> that just I have some wrong settings in windows or in the way=20
> I run the script?  Maybe that can be done under linux/unix=20
> Pymol and be imposible under windows?
> Thank you & Best wishes
> /Cheers, Evangelos.
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

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

Michael

d/l a recent build http://delsci.com/beta

and use the "find"->"polar contacts" option under the objects Action "A"
menu in the viewer window.

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
> Michael Weber
> Sent: Monday, October 17, 2005 5:03 AM
> To: pym...@li...
> Subject: [PyMOL] automated H-bond computation & visualization=20
> in pyMOL?
>=20
> Hello everybody,
> I am new to PyMOL and I have a short question: In pyMOL - is=20
> it possible to automatically compute and visualize H-bonds in=20
> .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe=20
> there is a pyMOL script for this purpose? I need such a=20
> function for my work with catalytically active RNA molecules=20
> (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone=20
> could help me with this problem...
> =20
> All the best & thanks in advance,
> Michael.
>=20

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

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

Sebastien,

* Sebastien Moretti <seb...@ig...> [2005-10-17 08:41] wrote:
> >Sebastien,
> >
> >>I cannot 
> >>change the color for rendering modes I defined.
> >
> >I do not understand what you mean by this.
> >
> >Cheers,
> >Warren
> 
> I mean that the color, for cartoon view, is unchangeable when 'set 
> cartoon_color' is defined in the $HOME/.pymolrc file.
> Thus, when I define 'set cartoon_color' in the $HOME/.pymolrc file, I 
> cannot change the color, for the cartoons, from the GUI.
> 
> The color is kept whatever I do.

I take it that you mean that choosing the "C" box on the right-hand menu
for the object in question and then selecting a colour or colouring
scheme results in no change to your cartoon representation. In that
case, I think that what you need to do is type:

  set cartoon_color, default

Then the cartoon is not forced to be the colour that you set (slate) but
takes on the colour of the atoms in the object.

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

[PyMOL] Geowall Testing

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

PyMOL Users:

Regarding "geowalls" [also known as dual-projector passive stereo setups
that use polarized lenses & glasses to deliver low-cost stereo 3D to
large audiences]...

Does anyone have one set up right now who might be able to test a new
PyMOL build with improved geowall stereo support?

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

[PyMOL] automated H-bond computation & visualization in pyMOL?

[Michael W. <we...@st...>]

Hello everybody,
I am new to PyMOL and I have a short question: In pyMOL - is it possible =
to automatically compute and visualize H-bonds in .PDB files as it is =
e.g. possible in SWISS-PDB-VIEWER? Maybe there is a pyMOL script for =
this purpose? I need such a function for my work with catalytically =
active RNA molecules (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice =
if someone could help me with this problem...

All the best & thanks in advance,
Michael.

[PyMOL] How to raw_input() from windows Pymol?

[evangelos p. <eva...@db...>]

Hello all,

   I am using the windows binaries for PyMol. Whereas in Python it is 
easy to do a:
a=raw_input()
When I use PyMol under windows it either gets crashed or halted while I 
am unable to input from keybord. I searched in this email list and I 
found some similar questions but no answer.
I need this for a script that I am writing to get input from the user. 
Is there any way to do that under windows or any other way to 
interactivelly input some data from the keybord into a Pymol script 
under windows? Has any ever done it and could it be that just I have 
some wrong settings in windows or in the way I run the script?  Maybe 
that can be done under linux/unix Pymol and be imposible under windows?
Thank you & Best wishes
/Cheers, Evangelos.