pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] make movie without invoking GUI

[Guillaume L. <gui...@ce...>]

Qingyi Yang wrote:
> Hi,
>
> Is it possible to make a series of png without
> invoking GUI? I tries like this:
>
>   
>>> pymol -c makemovie.py
>>>       
>
> but it gave "MoviePNG-Error: Missing rendered image.".
> Thanks a lot!!
>
> Bests,
>   
You have to render the image in order to be able to write it.
Try "ray" before saving the file.

Re: [PyMOL] make movie without invoking GUI

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

You have to put:

set ray_trace_frames=1

in the script.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the jigglings and wigglings of atoms."

Richard Feynman, Nobel Laureate 1965

*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

----- Original Message -----
From: Qingyi Yang <qin...@ya...>
Date: Thursday, January 12, 2006 9:36 am
Subject: [PyMOL] make movie without invoking GUI

> Hi,
> 
> Is it possible to make a series of png without
> invoking GUI? I tries like this:
> 
> >>pymol -c makemovie.py
> 
> but it gave "MoviePNG-Error: Missing rendered image.".
> Thanks a lot!!
> 
> Bests,
> 
> Joy
> 
> 
> __________________________________________________
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> 

[PyMOL] DALI alignment visualization

[Eva V. <eva...@ms...>]

I have a set of structures that are structurally aligned to a template 
structure
by DALI. DALI provides the transformation matrices so I can transform
mol A to mol B. I was wondering if anyone had a clever
phyton script to do this for not just a pair but for many at once.

Thanks in advance,

- Eva

[PyMOL] make movie without invoking GUI

[Qingyi Y. <qin...@ya...>]

Hi,

Is it possible to make a series of png without
invoking GUI? I tries like this:

>>pymol -c makemovie.py

but it gave "MoviePNG-Error: Missing rendered image.".
Thanks a lot!!

Bests,

Joy


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Re: [PyMOL] Selecting residues on surface only

[Charlotte Habegger-P. <chp...@rs...>]

Thanks Jerome!

It worked! I also checked out your website and your tutorial in French. 
They're both great!

-Charlotte



>From: Jerome PANSANEL <j.p...@pa...>
>To: pym...@li...
>Subject: Re: [PyMOL] Selecting residues on surface only
>Date: Wed, 11 Jan 2006 17:26:55 +0100
>
>Hi,
>
>Le Mercredi 11 Janvier 2006 17:27, Charlotte Habegger-Polomat a =E9crit=A0:
>  
>
>>Hello Pymol users!
>>
>>As a fairly unexperienced user of Pymol, I have not yet found a way to
>>select all residues in one of the cavities in my protein of interest.
>>When I render the protein as a surface, I can't select and visualize the
>>individual residues in the cleft.
>>    
>>
>
>You can use the clipping planes when you want to explore the core of your=20
>protein (shift+right-button, move mouse up/down).
>Another way is to select your ligand inside your cavity, then select around
>(menu A -> around -> 6 A for your ligand selection) and then select S->=20
>surface.
>
>  
>
>>When not rendered as a surface, I=20
>>can't seem to select only residues on the surface and not those buried
>>inside.
>>
>>Is there a straightforward way to do this (select and visualize the
>>residues on the (outside) surface of a cavity, with their labels)?
>>    
>>
>
>I publish today a pre-release of a PyMOL tutorial in french :
>http://www.pansanel.net/chemistry/resources/PymolIntroduction.pdf
>
>You can take a look !
>
>Jerome Pansanel
>  
>
>  
>

[PyMOL] Re: PyMOL-users digest, Vol 1 #1103 - 3 msgs

[Seth H. <se...@gm...>]

Some options were posted along these lines but you have to know what to loo=
k
for since they are under titles like EM-izing your structure.

You can try:
set surface_quality, -3
(I think that's as low as you can go, more negative doesn't get any
blobbier).

And a bit less simple but I think you'll prefer the option quoted below fro=
m
Warren's email reply to that EM-izing question, since you are after "super
smooth" not just "smooth" (I found setting the gaussian_resolution to 13 or
so to be in the "super" realm and don't forget to add a fourth argument to
the map_new bit if you want that as mentioned below):

Quote:::
 alter all, b=3D10

 map_new can take a selection as its fourth argument, so you could
 generate an independent map for each subunit, show the surface, and
 color it independently.  It's also possible to color a surface by atomic
 proximity, but the approach is a bit convoluted:

 load some.pdb, prot
 util.cbc prot
 alter prot,b=3D10
 set gaussian_resolution, 9.0
 map_new dcalc, gaussian, 3.0
 map_double dcalc
 isosurface dsurf, dcalc, 1.0, prot


End Quote

Hope that's what you're after.
-Seth


> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>    3. Super-smooth surfaces (Stephen Graham)
> _
> Message: 3
> Date: Wed, 11 Jan 2006 22:22:15 +0000
> From: Stephen Graham <ste...@us...>
> To: pym...@li...
> Subject: [PyMOL] Super-smooth surfaces
>
> Hi there,
>
> I am making a figure in which I would like an extremely smooth
> molecular surface (I just want the protein as a blob with little to no
> definition of surface features).
>
> I tried setting the probe radius to a larger value:
> set solvent_radius, 8
> but this gives rise to ugly artefacts on the surface ('triangles' of
> surface seem to be missing).  There seems to be a whole raft of
> different settings for fine-tuning surfaces (surface_carve_*,
> surface_trim_*, etc) but I am afraid I do not know what they do and
> have been unable to find documentation on them.
>
> How can I make a surface happy (fully connected) after having set the
> probe radius way up?
>
> Thanks,
>
> Stephen
>
> --
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences
> University of Sydney
>
>
> End of PyMOL-users Digest
>

[PyMOL] Super-smooth surfaces

[Stephen G. <ste...@us...>]

Hi there,

I am making a figure in which I would like an extremely smooth
molecular surface (I just want the protein as a blob with little to no
definition of surface features).

I tried setting the probe radius to a larger value:
 set solvent_radius, 8
but this gives rise to ugly artefacts on the surface ('triangles' of
surface seem to be missing).  There seems to be a whole raft of
different settings for fine-tuning surfaces (surface_carve_*,
surface_trim_*, etc) but I am afraid I do not know what they do and
have been unable to find documentation on them.

How can I make a surface happy (fully connected) after having set the
probe radius way up?

Thanks,

Stephen

--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

Re: [PyMOL] Selecting residues on surface only

[Jerome P. <j.p...@pa...>]

Hi,

Le Mercredi 11 Janvier 2006 17:27, Charlotte Habegger-Polomat a =E9crit=A0:
> Hello Pymol users!
>
> As a fairly unexperienced user of Pymol, I have not yet found a way to
> select all residues in one of the cavities in my protein of interest.
> When I render the protein as a surface, I can't select and visualize the
> individual residues in the cleft.

You can use the clipping planes when you want to explore the core of your=20
protein (shift+right-button, move mouse up/down).
Another way is to select your ligand inside your cavity, then select around
(menu A -> around -> 6 A for your ligand selection) and then select S->=20
surface.

> When not rendered as a surface, I=20
> can't seem to select only residues on the surface and not those buried
> inside.
>
> Is there a straightforward way to do this (select and visualize the
> residues on the (outside) surface of a cavity, with their labels)?

I publish today a pre-release of a PyMOL tutorial in french :
http://www.pansanel.net/chemistry/resources/PymolIntroduction.pdf

You can take a look !

Jerome Pansanel

> Thanks!
>
> -Charlotte
>
>
>
>
> -------------------------------------------------------
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[PyMOL] Selecting residues on surface only

[Charlotte Habegger-P. <chp...@rs...>]

Hello Pymol users!

As a fairly unexperienced user of Pymol, I have not yet found a way to 
select all residues in one of the cavities in my protein of interest. 
When I render the protein as a surface, I can't select and visualize the 
individual residues in the cleft. When not rendered as a surface, I 
can't seem to select only residues on the surface and not those buried 
inside.

Is there a straightforward way to do this (select and visualize the 
residues on the (outside) surface of a cavity, with their labels)?

Thanks!

-Charlotte

RE: [PyMOL] command line and preset publication

[James K. <kni...@gm...>]

Excellent.

Thanks very much.

James

On Mon, 2006-09-01 at 13:44 -0800, Warren DeLano wrote:
> from pymol import preset
> preset.publication(object-name)
> 
> e.g.
> 
> load $TUT/1hpv.pdb
> from pymol import preset
> preset.publication("1hpv")
> 
> --
> 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 
> > James Knight
> > Sent: Monday, January 09, 2006 10:44 AM
> > To: pym...@li...
> > Subject: [PyMOL] command line and preset publication
> > 
> > Is there a way to call the preset publication command from 
> > the action menu via the command line to allow use in scripts? 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep 
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> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> > 
> > 
> > 

RE: [PyMOL] Possible to List Object Properties?

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

Alex

iterate /A///301/P, print color

Note that colors are numbers internally, so that's what you'll get...


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
> Alex Luso
> Sent: Monday, January 09, 2006 12:55 PM
> To: pym...@li...
> Subject: [PyMOL] Possible to List Object Properties?
>=20
>=20
>   Is there a way to access a list of the current properties=20
> of a given object (or atom or selection) - for instance, what=20
> is the current color, cartoon type, mode, etc of a given=20
> atom? Or more generally, something like a command that spits=20
> out the current "state" (though that might be the wrong word=20
> in the pymol context):
>=20
> something like:
> "current color , /A///301/P" or "color , /A///301/P"
> output: green
>=20
>   Thanks,
>   Alex
>=20
>=20
> 	=09
> __________________________________________
> Yahoo! DSL - Something to write home about.=20
> Just $16.99/mo. or less.=20
> dsl.yahoo.com=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Possible to List Object Properties?

[Alex L. <tap...@ya...>]

  Is there a way to access a list of the current properties
of a given object (or atom or selection) - for instance,
what is the current color, cartoon type, mode, etc of a
given atom? Or more generally, something like a command
that spits out the current "state" (though that might be
the wrong word in the pymol context):

something like:
"current color , /A///301/P" or "color , /A///301/P"
output: green

  Thanks,
  Alex


		
__________________________________________ 
Yahoo! DSL – Something to write home about. 
Just $16.99/mo. or less. 
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[PyMOL] Available fonts: Symbol? Greek characters?

[Alex L. <tap...@ya...>]

  Hi,

  I noticed in the CVS that it is now possible to manually
drag a text label independent of the atom it is attached
to. Kudos for a very nice feature. This great feature makes
me want to do as much of the text labeling work in pymol as
possible (as opposed to some outside application) - which
bring me to my question: What fonts are available for the
"label" command. I know the command
set label_font_id, 4 (etc...)
What options are available (or will be)?

  I was particularly interested in putting in some greek
symbols as labels and even tried to use unicode
(label (pk1), U"\u03B5") but I only got two square boxes
out of it. Is there an undocument way to do this? Or
Photoshop is the only way right now?

  Thanks,
  Alex


		
__________________________________________ 
Yahoo! DSL – Something to write home about. 
Just $16.99/mo. or less. 
dsl.yahoo.com 

[PyMOL] command line and preset publication

[James K. <kni...@gm...>]

Is there a way to call the preset publication command from the action
menu via the command line to allow use in scripts? 

[PyMOL] Version 0.99 betas & pending release candidates

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

PyMOL Users,

Over the next 2-6 weeks, we will be issuing a series of 0.99 release
candidates for testing.    =20

If you haven't been keeping current with PyMOL beta builds, now would be
a good time to start doing so.  The code has reached a level of
stability adequate for routine use.

Please download the latest build (beta33) for your operating system and
put it through its paces with respect to your most important tasks.  In
particular, if you have a lot of PyMOL session files saved, please try
loading them with these new builds to confirm that no unexpected
compability problems have arisen due to the changes in PyMOL.

http://delsci.com/beta

Some things that have changed recently including the lighting model,
selection naming behavior, and right-mouse zoom behavior.  Also, the
pop-up menus have been reorganized to include alignment capabilities. =20

Please let us know immediately if you encounter serious problems so that
we can attempt to resolve them before issuing the official 0.99 release.
Timing for the release will likely depend upon your experiences and
feedback.

Cheers,
Warren

PS.  There are some specific issues affecting MacPyMOL, including user
interface glitches that we are aware of but haven't yet had time to
address.  They will be fixed prior to the 0.99 release. =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

RE: [PyMOL] Can I use the mouse to control multiple windows?

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

Warren-

I never even noticed the -l option.  That's awesome!

Thanks,

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Fri, 6 Jan 2006, Warren DeLano wrote:

>
> NOTE: Bug fix for receive.py
>
> # BEGIN receive.py
>
> from pymol import cmd
> from time import sleep
> import os
>
> filename = "view.txt"
>
> while not sleep(0.2):
>    if os.path.exists(filename):
>        try:
>            cmd.set_view(eval(open(filename,'r').read()))
>            os.unlink(filename)
>        except: # if the file isn't yet complete
>            pass
>
> # END receive.py
>
>
> 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: Warren DeLano
>> Sent: Friday, January 06, 2006 2:54 PM
>> To: 'Michael George Lerner'; pym...@li...
>> Subject: RE: [PyMOL] Can I use the mouse to control multiple windows?
>>
>> Michael,
>>
>> Of course -- use ansynchrous Python threads to automate the
>> process.  For example:
>>
>> pymol test.pdb -l send.py &
>> pymol test.pdb -l receive.py
>>
>> with the scripts below.  Note use of the lowercase "L" option
>> to launch PyMOL Python scripts in their own asynchronous thread.
>>
>> Cheers,
>> Warren
>>
>> # BEGIN send.py
>>
>> from pymol import cmd
>> from time import sleep
>> import os
>>
>> last_view = cmd.get_view()
>>
>> filename = "view.txt"
>>
>> while not sleep(0.2):
>>     cur_view = cmd.get_view()
>>     if last_view != cur_view:
>>         if not os.path.exists(filename):
>>             open(filename,'w').write(str(cur_view))
>>             last_view = cur_view
>>
>> # END send.py
>>
>> # BEGIN receive.py
>>
>> from pymol import cmd
>> from time import sleep
>> import os
>>
>> filename = "view.txt"
>>
>> while not sleep(0.2):
>>     if os.path.exists(filename):
>>         try:
>>             cmd.set_view(eval(open(filename,'r').read()))
>>             os.unlink(filename)
>>         except: # if the file isn't yet complete
>>             pass
>>
>> # END receive.py
>>
>>
>> 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
>>> George Lerner
>>> Sent: Friday, January 06, 2006 1:56 PM
>>> To: pym...@li...
>>> Subject: [PyMOL] Can I use the mouse to control multiple windows?
>>>
>>>
>>> Longshot, but ..
>>>
>>> I'm looking at a structure under two different sets of
>> conditions, so
>>> I have two PyMOL windows open.  I'm constantly get_view and
>>> set_view[*] to synchronize the two windows.  Is there some
>> way to set
>>> things up so that I can drag things around in one window
>> and have the
>>> scene in the other window automatically follow along?
>>>
>>> Thanks,
>>>
>>> -michael
>>>
>>> [*] actually, I'm a bit lazier than that .. I now have this
>> run via my
>>> .pymolrc:
>>>
>>> VIEW_FILENAME = '/tmp/currentview.txt'
>>> def gv():
>>>      '''write current view to a file (default
>> /tmp/currentview.txt)'''
>>>      # '...%s...'%VIEW_FILENAME doesn't end up as gv.__doc__
>>>      f =  file(VIEW_FILENAME,'w')
>>>      f.write(str(cmd.get_view()))
>>>      f.close()
>>> def sv():
>>>      '''read current view from a file (default
>>> /tmp/currentview.txt)'''
>>>      # '...%s...'%VIEW_FILENAME doesn't end up as sv.__doc__
>>>      f = file(VIEW_FILENAME)
>>>      cmd.set_view(f.read())
>>>      f.close()
>>> cmd.extend('gv',gv)
>>> cmd.extend('sv',sv)
>>>
>>>
>>> so I can type 'gv' in one window and 'sv' in the other.
>>>
>>> --
>>> www.umich.edu/~mlerner |                        _  |Michael Lerner
>>> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
>>> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
>>> -Torrence,  Bring It On|                       / \ | mlerner@umich
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.net email is sponsored by: Splunk Inc. Do you grep
>> through log
>>> files for problems?  Stop!  Download the new AJAX search
>> engine that
>>> makes searching your log files as easy as surfing the  web.
>>  DOWNLOAD
>>> SPLUNK!
>>> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>>
>>>
>>>
>
>
> -------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

RE: [PyMOL] Python scripting for Pymol

[Jerome P. <j.p...@pa...>]

Hi,

pymol.cmd.refresh() doesn't work when the function is placed before
cmd.png(), but works when placed after.
As cmd.refresh() is much faster than time.sleep(1), the script is now
quicker (I used this function to get the 2D pictures from a sdf file
containing less than 100 structures).

here is now the corrected script :
def mol2png(ctfile,name):
    pymol.cmd.read_molstr(ctfile,name)
    pymol.cmd.set("valence",1)
    pymol.cmd.hide("all")
    pymol.cmd.show("sticks")
    pymol.cmd.set("stick_radius",1)
    pymol.cmd.color("black","elem c")
    pymol.cmd.color("red","elem o")
    pymol.cmd.color("blue","elem n")
    pymol.cmd.color("yellow","elem s")
    pymol.cmd.bg_color("white")
    pymol.cmd.zoom(name)
    pymol.cmd.ray()
    pymol.cmd.png(name)
    pymol.cmd.refresh()
    pymol.cmd.delete(name)

Works fine with a Centrino (1.6GHz) laptop and Linux Debian (sarge).

Thanks,

Jerome Pansanel


Selon Warren DeLano <wa...@de...>:

> Jerome,
>=20
> Try calling=20
>=20
>    pymol.cmd.refresh()
>=20
> before=20
>=20
>    pymol.cmd.png(name)
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
> =20
>=20
> > -----Original Message-----
> > From: pym...@li...=20
> > [mailto:pym...@li...] On Behalf Of=20
> > Jerome PANSANEL
> > Sent: Friday, January 06, 2006 5:06 AM
> > To: pym...@li...
> > Subject: [PyMOL] Python scripting for Pymol
> >=20
> > Hi,
> >=20
> > I writing a small script in python, in order to export png=20
> > picture from a MDL sdfile.
> > Here is a sample of the function :
> >=20
> > def mol2png(ctfile,name):
> >     pymol.cmd.read_molstr(ctfile,name)
> >     pymol.cmd.set("valence",1)
> >     pymol.cmd.color("black","elem c")
> >     pymol.cmd.color("red","elem o")
> >     pymol.cmd.color("blue","elem n")
> >     pymol.cmd.color("yellow","elem s")
> >     pymol.cmd.bg_color("white")
> >     pymol.cmd.zoom(name)
> >     pymol.cmd.png(name)
> >     time.sleep( 1 )
> >     pymol.cmd.delete(name)
> >=20
> >=20
> > It works fine only if I have the function time.sleep(1). If=20
> > not, I have only empty pictures. Is there another solution to=20
> > delete the molecule only when the png file has been written ?
> >=20
> > Thanks,
> >=20
> > Jerome Pansanel
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> > through log files for problems?  Stop!  Download the new AJAX=20
> > search engine that makes searching your log files as easy as=20
> > surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> >=20
> >=20
> >=20
>=20




--------------------------------------------
Mail sent through IMP: http://horde.org/imp/

RE: [PyMOL] Can I use the mouse to control multiple windows?

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

NOTE: Bug fix for receive.py=20

# BEGIN receive.py

from pymol import cmd
from time import sleep
import os

filename =3D "view.txt"

while not sleep(0.2):
    if os.path.exists(filename):
        try:
            cmd.set_view(eval(open(filename,'r').read()))
            os.unlink(filename)
        except: # if the file isn't yet complete
            pass
       =20
# END receive.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: Warren DeLano=20
> Sent: Friday, January 06, 2006 2:54 PM
> To: 'Michael George Lerner'; pym...@li...
> Subject: RE: [PyMOL] Can I use the mouse to control multiple windows?
>=20
> Michael,
>=20
> Of course -- use ansynchrous Python threads to automate the=20
> process.  For example:
>=20
> pymol test.pdb -l send.py &
> pymol test.pdb -l receive.py
>=20
> with the scripts below.  Note use of the lowercase "L" option=20
> to launch PyMOL Python scripts in their own asynchronous thread.
>=20
> Cheers,
> Warren
>=20
> # BEGIN send.py
>=20
> from pymol import cmd
> from time import sleep
> import os
>=20
> last_view =3D cmd.get_view()
>=20
> filename =3D "view.txt"
>=20
> while not sleep(0.2):
>     cur_view =3D cmd.get_view()
>     if last_view !=3D cur_view:
>         if not os.path.exists(filename):
>             open(filename,'w').write(str(cur_view))
>             last_view =3D cur_view
>=20
> # END send.py
>=20
> # BEGIN receive.py
>=20
> from pymol import cmd
> from time import sleep
> import os
>=20
> filename =3D "view.txt"
>=20
> while not sleep(0.2):
>     if os.path.exists(filename):
>         try:
>             cmd.set_view(eval(open(filename,'r').read()))
>             os.unlink(filename)
>         except: # if the file isn't yet complete
>             pass
>        =20
> # END receive.py
>=20
>=20
> Cheers,
> Warren
>=20
>=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=20
> Of Michael=20
> > George Lerner
> > Sent: Friday, January 06, 2006 1:56 PM
> > To: pym...@li...
> > Subject: [PyMOL] Can I use the mouse to control multiple windows?
> >=20
> >=20
> > Longshot, but ..
> >=20
> > I'm looking at a structure under two different sets of=20
> conditions, so=20
> > I have two PyMOL windows open.  I'm constantly get_view and=20
> > set_view[*] to synchronize the two windows.  Is there some=20
> way to set=20
> > things up so that I can drag things around in one window=20
> and have the=20
> > scene in the other window automatically follow along?
> >=20
> > Thanks,
> >=20
> > -michael
> >=20
> > [*] actually, I'm a bit lazier than that .. I now have this=20
> run via my
> > .pymolrc:
> >=20
> > VIEW_FILENAME =3D '/tmp/currentview.txt'
> > def gv():
> >      '''write current view to a file (default=20
> /tmp/currentview.txt)'''
> >      # '...%s...'%VIEW_FILENAME doesn't end up as gv.__doc__
> >      f =3D  file(VIEW_FILENAME,'w')
> >      f.write(str(cmd.get_view()))
> >      f.close()
> > def sv():
> >      '''read current view from a file (default=20
> > /tmp/currentview.txt)'''
> >      # '...%s...'%VIEW_FILENAME doesn't end up as sv.__doc__
> >      f =3D file(VIEW_FILENAME)
> >      cmd.set_view(f.read())
> >      f.close()
> > cmd.extend('gv',gv)
> > cmd.extend('sv',sv)
> >=20
> >=20
> > so I can type 'gv' in one window and 'sv' in the other.
> >=20
> > --
> > www.umich.edu/~mlerner |                        _  |Michael Lerner
> > This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
> > it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
> > -Torrence,  Bring It On|                       / \ | mlerner@umich
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log=20
> > files for problems?  Stop!  Download the new AJAX search=20
> engine that=20
> > makes searching your log files as easy as surfing the  web.=20
>  DOWNLOAD=20
> > SPLUNK!
> > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> >=20
> >=20
> >=20

RE: [PyMOL] Can I use the mouse to control multiple windows?

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

Michael,

Of course -- use ansynchrous Python threads to automate the process.
For example:

pymol test.pdb -l send.py &
pymol test.pdb -l receive.py

with the scripts below.  Note use of the lowercase "L" option to launch
PyMOL Python scripts in their own asynchronous thread.

Cheers,
Warren

# BEGIN send.py

from pymol import cmd
from time import sleep
import os

last_view =3D cmd.get_view()

filename =3D "view.txt"

while not sleep(0.2):
    cur_view =3D cmd.get_view()
    if last_view !=3D cur_view:
        if not os.path.exists(filename):
            open(filename,'w').write(str(cur_view))
            last_view =3D cur_view

# END send.py

# BEGIN receive.py

from pymol import cmd
from time import sleep
import os

filename =3D "view.txt"

while not sleep(0.2):
    if os.path.exists(filename):
        try:
            cmd.set_view(open(filename,'r').read())
            os.unlink(filename)
        except: # if the file isn't yet complete
            pass
       =20
# END receive.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
> Michael George Lerner
> Sent: Friday, January 06, 2006 1:56 PM
> To: pym...@li...
> Subject: [PyMOL] Can I use the mouse to control multiple windows?
>=20
>=20
> Longshot, but ..
>=20
> I'm looking at a structure under two different sets of=20
> conditions, so I have two PyMOL windows open.  I'm constantly=20
> get_view and set_view[*] to synchronize the two windows.  Is=20
> there some way to set things up so that I can drag things=20
> around in one window and have the scene in the other window=20
> automatically follow along?
>=20
> Thanks,
>=20
> -michael
>=20
> [*] actually, I'm a bit lazier than that .. I now have this run via my
> .pymolrc:
>=20
> VIEW_FILENAME =3D '/tmp/currentview.txt'
> def gv():
>      '''write current view to a file (default /tmp/currentview.txt)'''
>      # '...%s...'%VIEW_FILENAME doesn't end up as gv.__doc__
>      f =3D  file(VIEW_FILENAME,'w')
>      f.write(str(cmd.get_view()))
>      f.close()
> def sv():
>      '''read current view from a file (default=20
> /tmp/currentview.txt)'''
>      # '...%s...'%VIEW_FILENAME doesn't end up as sv.__doc__
>      f =3D file(VIEW_FILENAME)
>      cmd.set_view(f.read())
>      f.close()
> cmd.extend('gv',gv)
> cmd.extend('sv',sv)
>=20
>=20
> so I can type 'gv' in one window and 'sv' in the other.
>=20
> --
> www.umich.edu/~mlerner |                        _  |Michael Lerner
> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
> -Torrence,  Bring It On|                       / \ | mlerner@umich
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Can I use the mouse to control multiple windows?

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

Longshot, but ..

I'm looking at a structure under two different sets of conditions, so I 
have two PyMOL windows open.  I'm constantly get_view and set_view[*] to 
synchronize the two windows.  Is there some way to set things up so that I 
can drag things around in one window and have the scene in the other 
window automatically follow along?

Thanks,

-michael

[*] actually, I'm a bit lazier than that .. I now have this run via my 
.pymolrc:

VIEW_FILENAME = '/tmp/currentview.txt'
def gv():
     '''write current view to a file (default /tmp/currentview.txt)'''
     # '...%s...'%VIEW_FILENAME doesn't end up as gv.__doc__
     f =  file(VIEW_FILENAME,'w')
     f.write(str(cmd.get_view()))
     f.close()
def sv():
     '''read current view from a file (default /tmp/currentview.txt)'''
     # '...%s...'%VIEW_FILENAME doesn't end up as sv.__doc__
     f = file(VIEW_FILENAME)
     cmd.set_view(f.read())
     f.close()
cmd.extend('gv',gv)
cmd.extend('sv',sv)


so I can type 'gv' in one window and 'sv' in the other.

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

RE: [PyMOL] Python scripting for Pymol

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

Jerome,

Try calling=20

   pymol.cmd.refresh()

before=20

   pymol.cmd.png(name)

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
> Jerome PANSANEL
> Sent: Friday, January 06, 2006 5:06 AM
> To: pym...@li...
> Subject: [PyMOL] Python scripting for Pymol
>=20
> Hi,
>=20
> I writing a small script in python, in order to export png=20
> picture from a MDL sdfile.
> Here is a sample of the function :
>=20
> def mol2png(ctfile,name):
>     pymol.cmd.read_molstr(ctfile,name)
>     pymol.cmd.set("valence",1)
>     pymol.cmd.color("black","elem c")
>     pymol.cmd.color("red","elem o")
>     pymol.cmd.color("blue","elem n")
>     pymol.cmd.color("yellow","elem s")
>     pymol.cmd.bg_color("white")
>     pymol.cmd.zoom(name)
>     pymol.cmd.png(name)
>     time.sleep( 1 )
>     pymol.cmd.delete(name)
>=20
>=20
> It works fine only if I have the function time.sleep(1). If=20
> not, I have only empty pictures. Is there another solution to=20
> delete the molecule only when the png file has been written ?
>=20
> Thanks,
>=20
> Jerome Pansanel
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] how to extract corresponding residue pairs after alignment ?

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

Indaneel,

This isn't and won't be possible anytime soon, but you are welcome to
hack the C code in order to dump that information out for the time
being.  Eventually we will have some nice alignment management
facilities in PyMOL.

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
> Indraneel Majumdar
> Sent: Friday, January 06, 2006 12:27 PM
> To: pym...@li...
> Subject: [PyMOL] how to extract corresponding residue pairs=20
> after alignment ?
>=20
> Hi,
>=20
> Is there any way to extract corresponding residue/atom pairs=20
> after alignment?
> eg. the atoms that are used to create the cgo when "object"=20
> option is specified. (I guess this is probably in op1.ai1VLA=20
> and op2.ai1VLA in layer3/Executive.c ?)
>=20
> Thanks in advance,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Python scripting for Pymol

[gilleain t. <gil...@gm...>]

Hi,

I tried a similar, but simpler, example :

def mol2png(name):
    cmd.png(name)
    cmd.delete(name)

called as 'mol2png("1a2pA")', given that I have an object called "1a2pA"
loaded.

It works just fine on my laptop (mac).

Odd.

gilleain torrance

On 1/6/06, Jerome PANSANEL <j.p...@pa...> wrote:
>
> Hi,
>
> I writing a small script in python, in order to export png picture from a
> MDL
> sdfile.
> Here is a sample of the function :
>
> def mol2png(ctfile,name):
>     pymol.cmd.read_molstr(ctfile,name)
>     pymol.cmd.set("valence",1)
>     pymol.cmd.color("black","elem c")
>     pymol.cmd.color("red","elem o")
>     pymol.cmd.color("blue","elem n")
>     pymol.cmd.color("yellow","elem s")
>     pymol.cmd.bg_color("white")
>     pymol.cmd.zoom(name)
>     pymol.cmd.png(name)
>     time.sleep( 1 )
>     pymol.cmd.delete(name)
>
>
> It works fine only if I have the function time.sleep(1). If not, I have
> only
> empty pictures. Is there another solution to delete the molecule only whe=
n
> the png file has been written ?
>
> Thanks,
>
> Jerome Pansanel
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] Python scripting for Pymol

[Jerome P. <j.p...@pa...>]

Hi,

I writing a small script in python, in order to export png picture from a MDL
sdfile.
Here is a sample of the function :

def mol2png(ctfile,name):
    pymol.cmd.read_molstr(ctfile,name)
    pymol.cmd.set("valence",1)
    pymol.cmd.color("black","elem c")
    pymol.cmd.color("red","elem o")
    pymol.cmd.color("blue","elem n")
    pymol.cmd.color("yellow","elem s")
    pymol.cmd.bg_color("white")
    pymol.cmd.zoom(name)
    pymol.cmd.png(name)
    time.sleep( 1 )
    pymol.cmd.delete(name)


It works fine only if I have the function time.sleep(1). If not, I have only
empty pictures. Is there another solution to delete the molecule only when
the png file has been written ?

Thanks,

Jerome Pansanel

[PyMOL] Re: New spectral color pallette

[divya d. <div...@gm...>]

how can i get 300 dpi image or picture of higher resolution from pymol

On 1/5/06, Robert Campbell <rl...@po...> wrote:
> Alexander,
>
> * Ale...@bc... wrote:
> > >
> > > I would like to color my protein according to B-factor with a
> self-defined
> > > spectral palette (In this case I have put sequence conservation into =
the
> > > Bfactor this column). I found that
> > >         spectrum b, blue_white_red, minimum=3D0, maximum=3D100
> > > would do part of the job with a predefined pallette
> > >
> > > - I could not find out how to define my own new color palette like
> > > "white_red".
> > > - Is there a way to "visualize" the color palettes before applying it=
 to
> > > an object?
> > >
>
> * Seth Harris <se...@gm...> [2005-12-31 09:54] wrote:
> > This is more half an answer than the real deal, but when I had the same
> > issue I opted for the quick work around of setting the range from -100 =
to
> > 100 for the blue-white-red palette which effectively made 0-100 corresp=
ond
> > to white to red only since there were no negative B factors/conservatio=
n
> > scores.
> > e.g.
> > spectrum b, blue_white_red, minimum=3D-100, maximum=3D100
> >
> > I am curious for better answers, as you are, but haven't delved into th=
e
> > code to look for it myself, either. But perhaps this or some fine tunin=
g
> of
> > the range or other pre-defined palettes will get done what you desire.
>
> I have a script, color_b.py, available on my website that allows one
> to colour based on the value of the B-factor or occupancy columns. It
> currently has the following colour gradients:
>
>       'bgr': blue -> green   -> red
>       'rgb': red  -> green   -> blue
>       'bwr': blue -> white   -> red
>       'rwb': red  -> white   -> blue
>       'bmr': blue -> magenta -> red
>       'rmb': red  -> magenta -> blue
>       'rw' : red -> white
>       'wr' : white -> red
>       'gw' : green -> white
>       'wg' : white -> green
>       'bw' : blue -> white
>       'wb' : white -> blue
>       'gy' : green -> yellow
>       'yg' : yellow -> green
>       'gray' : black -> white
>       'reversegray' : white -> black
>
> It isn't too difficult to add more gradients by following the recipes in
> the "make_gradient" function in that script. It is also possible to set
> the minimum and maximum values to tune the exact gradient limits as well
> as to set the saturation and brightness (value) of the colours, via the
> command options.
>
> Hope this helps.
>
> 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
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
 Ms. DIVYA DUBE
 Junior Research Fellow
 C/O Dr.R.Ravishankar
 MSB Division
 CDRI
 Lucknow,INDIA