pymol-users Mailing List for PyMOL Molecular Graphics System

Tsjerk,

This will only provide a minor speedup, but the alter* and iterate* commands do take a "space" argument with a dictionary to use in lieu of PyMOL globals().

my_dict = {'L':[]}

cmd.iterate_state(1, 'all', 'L.append( (x,y,z) )', space=my_dict)

print len(my_dict['L'])

etc.

Cheers,
Warren


> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:ts...@gm...]
> Sent: Tuesday, September 29, 2009 7:40 AM
> To: Warren DeLano
> Subject: Re: [PyMOL] Iterate Script Over States
> 
> Hi Warren (e.a.),
> 
> First, as a side note, your first post had 'for state in
> cmd.count_states():' whereas it seems it should read 'for state in
> range(cmd.count_states()):'.
> 
> I find myself doing something similar to Sean now, accumulating
> coordinates over different frames for each of the atoms. The question
> is how to do that fastest. At this moment I'm doing the following,
> which is painstakingly slow (but it works :)). Aside from that it has
> a nasty hack adding to globals(), as cmd.alter executes in its own
> scope.
> 
> class AtomVar:
>     sum = None
>     ssq = None
>     N   = None
>     cov = None
>     var = None
> 
>     def __init__( self ):
>         self.sum = [ 0,0,0 ]       #  x,  y,  z
>         self.ssq = [ 0,0,0,0,0,0 ] # xx, yy, zz, xy, xz, yz
>         self.N   = 0
> 
>     def inc( self, x ):
>         self.sum = [ self.sum[i] + x[i] for i in range(3) ]
>         squares  = [ x[0]*x[0], x[1]*x[1], x[2]*x[2], x[0]*x[1],
> x[0]*x[2], x[1]*x[2] ]
>         self.ssq = [ self.ssq[i] + squares[i] for i in range(6) ]
>         self.N = self.N + 1
> 
>     def purge( self ):
>         s = self.sum
>         squares = [ s[0]*s[0], s[1]*s[1], s[2]*s[2], s[0]*s[1],
> s[0]*s[2], s[1]*s[2] ]
>         self.cov = [ (squares[i] - self.ssq[i]/self.N)/self.N for i in
> range(6) ]
>         self.var = self.cov[0] + self.cov[1] + self.cov[2]
> 
> def molVar( sele="all" ):
>     model = cmd.get_model( sele )
>     globals()["M"] = {}
>     for i in model.atom:
>         M[ i.id ] = AtomVar()
>     for state in range(cmd.count_states()):
>         cmd.iterate_state( state, sele, "M[ ID ].inc( (x,y,z) )" )
>     for i in M.keys():
>         M[ i ].purge()
>     cmd.alter( sele, "b = M[ ID ].var" )
> 
> Any suggestions are welcome :)
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Mon, Sep 28, 2009 at 9:05 PM, Warren DeLano <wa...@de...> wrote:
> > Sean,
> >
> >
> >
> > Yes, that is an alternate route.  cmd.get_model is likely slower than
> > cmd.iterate_state, but should work regardless.
> >
> >
> >
> > Cheers
> >
> > Warren
> >
> >
> >
> > ________________________________
> >
> > From: Sean Law [mailto:mag...@ho...]
> > Sent: Monday, September 28, 2009 11:58 AM
> > To: pym...@li...
> > Subject: Re: [PyMOL] Iterate Script Over States
> >
> >
> >
> > I think I figured it out (though, it wasn't documented).  What I needed
> was
> > to use:
> >
> > cmd.get_model(selection, STATE)
> >
> > I think that's the correct usage?  What I needed was to loop through a
> > selection and then to calculate the sugar pucker information.  However,
> not
> > all atoms from the selection are required for the calculation so some
> > pre-parsing of the residue is needed.  It appears that I can specify the
> > state to obtain atom objects from via the get_model command.  I hope
> that is
> > right?
> >
> > Sean
> >
> > ________________________________
> >
> > Create a cool, new character for your Windows Live(tm) Messenger. Check it
> out
> >
> > ------------------------------------------------------------------------
> ------
> > Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> > is the only developer event you need to attend this year. Jumpstart your
> > developing skills, take BlackBerry mobile applications to market and
> stay
> > ahead of the curve. Join us from November 9&#45;12, 2009. Register
> now&#33;
> > http://p.sf.net/sfu/devconf
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
> 
> 
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> 
> 
> 

Roger,

 

That's a bit odd: usually it either works or it doesn't.  Working for 20
seconds at a time may indicate defective hardware (projector, emitter,
graphics card, connector, dead battery, etc.).  

 

But as a first test, pease try using some other stereo-3D-capable
software (e.g. VMD or Chimera) in order to make certain that the problem
is not due to PyMOL itself.

 

Cheers,

Warren

 

________________________________

From: Roger Rowlett [mailto:rro...@co...] 
Sent: Tuesday, September 29, 2009 9:58 AM
To: pym...@li...
Subject: [PyMOL] DepthQ configuration in a classroom setting

 

Has anyone on the board configured a DepthQ projector for classroom use,
i.e. using a ceiling-mounted projector. Our IT department has recently
installed a DepthQ projector in a classroom-type setting, and it
displays stereo Pymol images for about 20 seconds, then loses sync. My
configuration is the following:

Intel WinXP PC with Quadro 3700 running NVidia driver 191.00
Stereo "ON" enabled in the Global settings of the Nvidia Control panel
DepthQ installed as only graphical display device (currently)
Screen resolution set to the native resolution of the DepthQ projector
I'm running a recent version (1.2) of Pymol

I assume that to get a second monitor display of the DepthQ projector I
should attach a VGA cable to the "video out" port of the DepthQ and run
that to an appropriate LCD monitor.

Am I missing anything? I'm wondering if the video cabling is too long or
inappropriate, causing the sync dropouts, or if I have missed something
really elementary in the Nvidia configuration. At this point, I'm
considering breaking down the classroom installation and testing the
computer and projector on the bench.

Cheers,



-- 

________________________________

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@co...

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
<font face="Verdana">Has anyone on the board configured a DepthQ
projector for classroom use, i.e. using a ceiling-mounted projector.
Our IT department has recently installed a DepthQ projector in a
classroom-type setting, and it displays stereo Pymol images for about
20 seconds, then loses sync. My configuration is the following:<br>
<br>
Intel WinXP PC with Quadro 3700 running NVidia driver 191.00<br>
Stereo "ON" enabled in the Global settings of the Nvidia Control panel<br>
DepthQ installed as only graphical display device (currently)<br>
Screen resolution set to the native resolution of the DepthQ projector<br>
I'm running a recent version (1.2) of Pymol<br>
<br>
I assume that to get a second monitor display of the DepthQ projector I
should attach a VGA cable to the "video out" port of the DepthQ and run
that to an appropriate LCD monitor.<br>
<br>
Am I missing anything? I'm wondering if the video cabling is too long
or inappropriate, causing the sync dropouts, or if I have missed
something really elementary in the Nvidia configuration. At this point,
I'm considering breaking down the classroom installation and testing
the computer and projector on the bench.<br>
<br>
Cheers,<br>
<br>
</font><br>
<div class="moz-signature">-- <br>
<font face="Verdana">
<hr>Roger S. Rowlett<br>
Professor<br>
Department of Chemistry<br>
Colgate University<br>
13 Oak Drive<br>
Hamilton, NY 13346<br>
<br>
tel: (315)-228-7245<br>
ofc: (315)-228-7395<br>
fax: (315)-228-7935<br>
email: <a class="moz-txt-link-abbreviated" href="mailto:rro...@co...">rro...@co...</a><br>
</font>
</div>
</body>
</html>

... This should've gone to the list ... :S

TAW

---------- Forwarded message ----------


Hi Warren (e.a.),

First, as a side note, your first post had 'for state in
cmd.count_states():' whereas it seems it should read 'for state in
range(cmd.count_states()):'.

I find myself doing something similar to Sean now, accumulating
coordinates over different frames for each of the atoms. The question
is how to do that fastest. At this moment I'm doing the following,
which is painstakingly slow (but it works :)). Aside from that it has
a nasty hack adding to globals(), as cmd.alter executes in its own
scope.

class AtomVar:
   sum = None
   ssq = None
   N   = None
   cov = None
   var = None

   def __init__( self ):
       self.sum = [ 0,0,0 ]       #  x,  y,  z
       self.ssq = [ 0,0,0,0,0,0 ] # xx, yy, zz, xy, xz, yz
       self.N   = 0

   def inc( self, x ):
       self.sum = [ self.sum[i] + x[i] for i in range(3) ]
       squares  = [ x[0]*x[0], x[1]*x[1], x[2]*x[2], x[0]*x[1],
x[0]*x[2], x[1]*x[2] ]
       self.ssq = [ self.ssq[i] + squares[i] for i in range(6) ]
       self.N = self.N + 1

   def purge( self ):
       s = self.sum
       squares = [ s[0]*s[0], s[1]*s[1], s[2]*s[2], s[0]*s[1],
s[0]*s[2], s[1]*s[2] ]
       self.cov = [ (squares[i] - self.ssq[i]/self.N)/self.N for i in
range(6) ]
       self.var = self.cov[0] + self.cov[1] + self.cov[2]

def molVar( sele="all" ):
   model = cmd.get_model( sele )
   globals()["M"] = {}
   for i in model.atom:
       M[ i.id ] = AtomVar()
   for state in range(cmd.count_states()):
       cmd.iterate_state( state, sele, "M[ ID ].inc( (x,y,z) )" )
   for i in M.keys():
       M[ i ].purge()
   cmd.alter( sele, "b = M[ ID ].var" )

Any suggestions are welcome :)

Cheers,

Tsjerk


On Mon, Sep 28, 2009 at 9:05 PM, Warren DeLano <wa...@de...> wrote:
> Sean,
>
>
>
> Yes, that is an alternate route.  cmd.get_model is likely slower than
> cmd.iterate_state, but should work regardless.
>
>
>
> Cheers
>
> Warren
>
>
>
> ________________________________
>
> From: Sean Law [mailto:mag...@ho...]
> Sent: Monday, September 28, 2009 11:58 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Iterate Script Over States
>
>
>
> I think I figured it out (though, it wasn't documented).  What I needed was
> to use:
>
> cmd.get_model(selection, STATE)
>
> I think that's the correct usage?  What I needed was to loop through a
> selection and then to calculate the sugar pucker information.  However, not
> all atoms from the selection are required for the calculation so some
> pre-parsing of the residue is needed.  It appears that I can specify the
> state to obtain atom objects from via the get_model command.  I hope that is
> right?
>
> Sean
>
> ________________________________
>
> Create a cool, new character for your Windows Live™ Messenger. Check it out
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Sean,

 

Yes, that is an alternate route.  cmd.get_model is likely slower than
cmd.iterate_state, but should work regardless.

 

Cheers

Warren

 

________________________________

From: Sean Law [mailto:mag...@ho...] 
Sent: Monday, September 28, 2009 11:58 AM
To: pym...@li...
Subject: Re: [PyMOL] Iterate Script Over States

 

I think I figured it out (though, it wasn't documented).  What I needed
was to use:

cmd.get_model(selection, STATE)

I think that's the correct usage?  What I needed was to loop through a
selection and then to calculate the sugar pucker information.  However,
not all atoms from the selection are required for the calculation so
some pre-parsing of the residue is needed.  It appears that I can
specify the state to obtain atom objects from via the get_model command.
I hope that is right?

Sean

________________________________

Create a cool, new character for your Windows Live(tm) Messenger. Check
it out <" rel="nofollow">http://go.microsoft.com/?linkid=9656621> 

I think I figured it out (though, it wasn't documented).  What I needed was to use:

cmd.get_model(selection, STATE)

I think that's the correct usage?  What I needed was to loop through a selection and then to calculate the sugar pucker information.  However, not all atoms from the selection are required for the calculation so some pre-parsing of the residue is needed.  It appears that I can specify the state to obtain atom objects from via the get_model command.  I hope that is right?

Sean
 		 	   		  
_________________________________________________________________
Create a cool, new character for your Windows Live™ Messenger. 
http://go.microsoft.com/?linkid=9656621

Sean,

I'm not sure what you have in mind other than something like (python code):

for state in cmd.count_states(): 
    cmd.iterate_state(state, selection, expression)

where expression is accumulating coordinates from multiple states

Cheers,
Warren
________________________________________
From: Sean Law [mailto:mag...@ho...] 
Sent: Monday, September 28, 2009 7:14 AM
To: pym...@li...
Subject: [PyMOL] Iterate Script Over States

Hi PyMOL Users,

I was wondering if there was a smart way of having a script iterate over all (or some) of the states.  I know that there are the usual iterate and iterate_state commands available but it appears that it makes for clumsier code.  More specifically, I'm looking to use the pucker.py script which calculates sugar dihedral angles (found under PUCKER at the PyMOL-Wiki) and have it spit values back for all states of an MD simulation rather than just only the first state.  Basically, I would like for it to behave like the distance/dihedral measurement functions available in the PyMOL wizard such that the pucker information is calculated, displayed on the screen, and changes as I run through each frame.

Thanks in advance!

Sean
________________________________________
Attention all humans. We are your photos. Free us.

I agree with Dirk - this is likely a hardware problem.  From within
PyMOL ,it can be worked around via the menu Display->Stereo->Swap Sides
or by typing "st sw" (stereo swap) at the command line.

 

Cheers,

Warren

 

________________________________

From: Dirk Kostrewa [mailto:kos...@ge...] 
Sent: Monday, September 28, 2009 7:26 AM
To: PyMOLBB
Cc: CCP4BB
Subject: Re: [PyMOL] Stereo flipping in coot and pymol

 

Dear Joachim,

 

you don't say whether its Linux, Windows or Mac OS X and which emitter
and glasses you are using. I've seen this behaviour long time ago with
very old Nvidia graphics card drivers under Linux. Sometimes, I still
see this behaviour with new drivers but with old computer hardware. Here
are a few hints that might be worth trying:

- Install the most recent Nvidia driver. If it happened after updating,
it might be worth to go back 1-2 versions.

- If you use the emitter from NuVision, you can simply invert left and
right with a small switch. 

- Sometimes, it helps to minimize the application and maximize it again.

 

Good luck,

 

Dirk.

 

Am 28.09.2009 um 15:48 schrieb Joachim Reichelt:





Dear all,
our users complain that during there graphics session front and back are

switched.
We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors.
So it seems that you see sidechains behind a sheet, that are in realety 
front of a sheet.
If they were behind it, you should not see them at all.
-- 
Joachim

------------------------------------------------------------------------
------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and
stay 
ahead of the curve. Join us from November 9-12, 2009. Register
now!
http://p.sf.net/sfu/devconf
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

 


*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:           +49-89-2180-76845
Fax:    +49-89-2180-76999
E-mail:            kos...@ge...
<mailto:kos...@lm...> 
WWW:            www.genzentrum.lmu.de
<mailto:kos...@lm...> 
*******************************************************



 

Am 28.09.2009 um 16:25 schrieb Joachim Reichelt:

> I said, we are on Linux.

Uups, yes, you are right - may fault. But you may try the new driver  
installation and the minizing/maximizing, anyway.

Good luck,

Dirk.

>

> But I did not say:
> We are using Stereographic glases  and emiter connected by 3-wire  
> cable to the DIN plug on NVIDIA Quadro FX 3000
> NVIDIA GLX Module  173.14.17  Mon Feb 23 16:04:17 PST 2009
> If of interest, this is openSUSE 11.1 on i386
>
> Am 28.09.2009 16:21, schrieb Dirk Kostrewa:
>>
>> Dear Joachim,
>>
>> you don't say whether its Linux, Windows or Mac OS X and which  
>> emitter and glasses you are using. I've seen this behaviour long  
>> time ago with very old Nvidia graphics card drivers under Linux.  
>> Sometimes, I still see this behaviour with new drivers but with old  
>> computer hardware. Here are a few hints that might be worth trying:
>> - Install the most recent Nvidia driver. If it happened after  
>> updating, it might be worth to go back 1-2 versions.
>> - If you use the emitter from NuVision, you can simply invert left  
>> and right with a small switch.
>> - Sometimes, it helps to minimize the application and maximize it  
>> again.
>>
>> Good luck,
>>
>> Dirk.
>>
>> Am 28.09.2009 um 15:48 schrieb Joachim Reichelt:
>>
>>> Dear all,
>>> our users complain that during there graphics session front and  
>>> back are
>>> switched.
>>> We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors.
>>> So it seems that you see sidechains behind a sheet, that are in  
>>> realety
>>> front of a sheet.
>>> If they were behind it, you should not see them at all.
>>> -- 
>>> Joachim
>>>
>>> ------------------------------------------------------------------------------
>>> Come build with us! The BlackBerry® Developer Conference in  
>>> SF, CA
>>> is the only developer event you need to attend this year.  
>>> Jumpstart your
>>> developing skills, take BlackBerry mobile applications to market  
>>> and stay
>>> ahead of the curve. Join us from November 9-12, 2009. Register  
>>> now!
>>> http://p.sf.net/sfu/devconf
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>> *******************************************************
>> Dirk Kostrewa
>> Gene Center, A 5.07
>> Ludwig-Maximilians-University
>> Feodor-Lynen-Str. 25
>> 81377 Munich
>> Germany
>> Phone:  +49-89-2180-76845
>> Fax:  +49-89-2180-76999
>> E-mail: kos...@ge...
>> WWW: www.genzentrum.lmu.de
>> *******************************************************
>>
>
> -- 
> <Signature_email-jr.gif>


*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: 	+49-89-2180-76845
Fax: 	+49-89-2180-76999
E-mail:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
I said, we are on Linux.<br>
But I did not say:<br>
We are using Stereographic glases  and emiter connected by 3-wire cable
to the DIN plug on NVIDIA Quadro FX 3000<br>
NVIDIA GLX Module  173.14.17  Mon Feb 23 16:04:17 PST 2009<br>
If of interest, this is openSUSE 11.1 on i386<br>
<br>
Am 28.09.2009 16:21, schrieb Dirk Kostrewa:
<blockquote
 cite="mid:647...@ge..."
 type="cite">Dear Joachim,
  <div><br>
  </div>
  <div>you don't say whether its Linux, Windows or Mac OS X and which
emitter and glasses you are using. I've seen this behaviour long time
ago with very old Nvidia graphics card drivers under Linux. Sometimes,
I still see this behaviour with new drivers but with old computer
hardware. Here are a few hints that might be worth trying:</div>
  <div>- Install the most recent Nvidia driver. If it happened after
updating, it might be worth to go back 1-2 versions.</div>
  <div>- If you use the emitter from NuVision, you can simply invert
left and right with a small switch. </div>
  <div>- Sometimes, it helps to minimize the application and maximize
it again.</div>
  <div><br>
  </div>
  <div>Good luck,</div>
  <div><br>
  </div>
  <div>Dirk.</div>
  <div><br>
  <div>
  <div>Am 28.09.2009 um 15:48 schrieb Joachim Reichelt:</div>
  <br class="Apple-interchange-newline">
  <blockquote type="cite">
    <div>Dear all,<br>
our users complain that during there graphics session front and back
are <br>
switched.<br>
We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors.<br>
So it seems that you see sidechains behind a sheet, that are in realety
    <br>
front of a sheet.<br>
If they were behind it, you should not see them at all.<br>
-- <br>
Joachim<br>
    <br>
------------------------------------------------------------------------------<br>
Come build with us! The BlackBerry&amp;reg; Developer Conference in SF,
CA<br>
is the only developer event you need to attend this year. Jumpstart your<br>
developing skills, take BlackBerry mobile applications to market and
stay <br>
ahead of the curve. Join us from November 9&amp;#45;12, 2009. Register
now&amp;#33;<br>
    <a moz-do-not-send="true" href="http://p.sf.net/sfu/devconf
" rel="nofollow">http://p.sf.net/sfu/devconf">http://p.sf.net/sfu/devconf</a><br>
_______________________________________________<br>
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 href="mailto:PyM...@li...">PyM...@li...</a>)<br>
Info Page: <a class="moz-txt-link-freetext"
 href="https://lists.sourceforge.net/lists/listinfo/pymol-users
" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users">https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a class="moz-txt-link-freetext"
 href="http://www.mail-archive.com/pym...@li...
" rel="nofollow">http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a><br>
    </div>
  </blockquote>
  </div>
  <br>
  <div> <span class="Apple-style-span"
 style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
  <div style="word-wrap: break-word;"><span class="Apple-style-span"
 style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><br
 class="Apple-interchange-newline">
*******************************************************<br>
Dirk Kostrewa<br>
Gene Center, A 5.07<br>
Ludwig-Maximilians-University<br>
Feodor-Lynen-Str. 25<br>
81377 Munich<br>
Germany<br>
Phone: <span class="Apple-tab-span" style="white-space: pre;"> </span>+49-89-2180-76845<br>
Fax: <span class="Apple-tab-span" style="white-space: pre;"> </span>+49-89-2180-76999<br>
E-mail:<span class="Apple-tab-span" style="white-space: pre;"> </span><a
 moz-do-not-send="true" href="mailto:kos...@lm...">kos...@ge...</a><br>
WWW:<span class="Apple-tab-span" style="white-space: pre;"> </span><a
 moz-do-not-send="true" href="mailto:kos...@lm...">www.genzentrum.lmu.de</a><br>
*******************************************************<br>
  </span></div>
  </span> </div>
  <br>
  </div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:par...@he..."></div>
</body>
</html>

Dear Joachim,

you don't say whether its Linux, Windows or Mac OS X and which emitter  
and glasses you are using. I've seen this behaviour long time ago with  
very old Nvidia graphics card drivers under Linux. Sometimes, I still  
see this behaviour with new drivers but with old computer hardware.  
Here are a few hints that might be worth trying:
- Install the most recent Nvidia driver. If it happened after  
updating, it might be worth to go back 1-2 versions.
- If you use the emitter from NuVision, you can simply invert left and  
right with a small switch.
- Sometimes, it helps to minimize the application and maximize it again.

Good luck,

Dirk.

Am 28.09.2009 um 15:48 schrieb Joachim Reichelt:

> Dear all,
> our users complain that during there graphics session front and back  
> are
> switched.
> We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors.
> So it seems that you see sidechains behind a sheet, that are in  
> realety
> front of a sheet.
> If they were behind it, you should not see them at all.
> -- 
> Joachim
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9-12, 2009. Register  
> now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol- 
> us...@li...


*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: 	+49-89-2180-76845
Fax: 	+49-89-2180-76999
E-mail:	kos...@ge...
WWW:	www.genzentrum.lmu.de
*******************************************************

Hi PyMOL Users,

I was wondering if there was a smart way of having a script iterate over all (or some) of the states.  I know that there are the usual iterate and iterate_state commands available but it appears that it makes for clumsier code.  More specifically, I'm looking to use the pucker.py script which calculates sugar dihedral angles (found under PUCKER at the PyMOL-Wiki) and have it spit values back for all states of an MD simulation rather than just only the first state.  Basically, I would like for it to behave like the distance/dihedral measurement functions available in the PyMOL wizard such that the pucker information is calculated, displayed on the screen, and changes as I run through each frame.

Thanks in advance!

Sean
 		 	   		  
_________________________________________________________________
Attention all humans. We are your photos. Free us.
http://go.microsoft.com/?linkid=9666046

Dear all,
our users complain that during there graphics session front and back are 
switched.
We are on Linux using NVIDA Quadro boards with 3-pin DIN connectors.
So it seems that you see sidechains behind a sheet, that are in realety 
front of a sheet.
If they were behind it, you should not see them at all.
-- 
Joachim

Hi!

You can also try bni-tools.

 http://sourceforge.net/projects/bni-tools/

It's a pymol plugin containing various little scripts i needed for 
myself which i summed up there.
Unfortunately i had no time to write a manual, and i don't know if it 
works with every pymol version.
(and it is not entirely bug-proofed)
Most of the commands work on the selection  "(sele)"  for  simplicity.
Just give it a try  and experiment with it.
Install the plugin and you will find it at Plugin-->BNI Pymol Plugin v. XX
Select the amino acids you want to convert into sequence and click on 
"get sequences" and select the format.
It also should work on multiple selections and should split the output 
into objects and chains.
Copy the sequences from the output window and paste it wherever you want.

Cheers,
Georg

Georg Steinkellner
Research Centre Applied Biocatalysis
Enzyme Development and Analytics
c/o Karl-Franzens University of Graz
    (ZMB) Centre of Molecular Biosciences

Thank you!  This was indeed the case.  I have no idea why tcl/tk 8.4 was
installed with 8.5 at the same time.  Removing 8.4 and using 8.5 seems to
have fixed the problem.

Ian

On Thu, Sep 24, 2009 at 2:38 PM, Warren DeLano <wa...@de...> wrote:

>  Ian,
>
> Based on that traceback, it looks like you have two conflicting versions of
> Tcl (8.4 as well as 8.5) linked against and running in the same
> process...that could be the source of the crash.
>
> Cheers,
> Warren
>
>  ------------------------------
> *From:* Ian Berke [mailto:ian...@ya...]
> *Sent:* Thursday, September 24, 2009 11:26 AM
> *To:* pym...@li...
> *Subject:* [PyMOL] Pymol segmentation fault
>
> Hi,
>
> I'm having an issue trying to run various plugins in pymol (apbs and
> autodock).  Whenever I select a button that should bring up a file browser
> to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol
> exits with: Segmentation fault (core dumped).  Same thing happens when I go
> to Help>About.  I can open and save files normally, and just about
> everything else works.
>
> I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin
> window to open, as well as the 1.2 trunk from svn (downloaded and compiled
> last week) which just crashes when I try to open the apbs window (I can
> install autodock.py and the window opens, but it crashes when I try to
> choose the location of files).  I'm guessing this is something to do with
> the gui and tcl/tk, but don't have any idea how to troubleshoot (see the
> catchsegv output below).  I'm running Ubuntu 9.10 on x86_64 and have  a
> GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36.
>
> Does anyone have any thoughts?
>
> Here is the backtrace portion from catchsegv:
> Backtrace:
> /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
> /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
> /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
> /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
> /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
> /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
> /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
> /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
> /usr/lib/libtcl8.5.so.0[0x7f6397793192]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x49c06f]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
> /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
> /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
> /usr/lib/libtcl8.5.so.0[0x7f639779668f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
> /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
> /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
> /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
> /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
> /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52beed]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x4d0c4d]
> /lib/libpthread.so.0[0x7f639cf69a04]
> /lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
>
> Thanks,
> Ian
>
>

> Does anyone have any thoughts?

Two things to try that may or may not help:

1. Check if the problem persists when running pymol in single-threaded 
mode ("cmd.set('max_threads',1)").  libpthread in the trace might 
indicate that one of the libraries is having issues with multiple threads.

2. On Kubuntu 8.04.3 LTS x64, I can't reproduce the problem with 1.2 
from svn trunk.  This is using Tcl/Tk 8.4 (with pymol using it's own 
source build of python 2.4.2, which may or may not be relevant); so 
installing Tcl/Tk 8.4 instead of 8.5 (source or binary) might help 
resolve the problem, or at least eliminate one possible source.

Pete

> Here is the backtrace portion from catchsegv:
> Backtrace:
> /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
> /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
> /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
> /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
> /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
> /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
> /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
> /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
> /usr/lib/libtcl8.5.so.0[0x7f6397793192]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x49c06f]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
> /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
> /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
> /usr/lib/libtcl8.5.so.0[0x7f639779668f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
> /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
> /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
> /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
> /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
> /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52beed]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x4d0c4d]
> /lib/libpthread.so.0[0x7f639cf69a04]
> /lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
> 
> Thanks,
> Ian
> 

Ian,
 
Based on that traceback, it looks like you have two conflicting versions
of Tcl (8.4 as well as 8.5) linked against and running in the same
process...that could be the source of the crash.
 
Cheers,
Warren

________________________________

	From: Ian Berke [mailto:ian...@ya...] 
	Sent: Thursday, September 24, 2009 11:26 AM
	To: pym...@li...
	Subject: [PyMOL] Pymol segmentation fault
	
	
	Hi,
	
	I'm having an issue trying to run various plugins in pymol (apbs
and autodock).  Whenever I select a button that should bring up a file
browser to choose a file (e.g. "Choose Externally generated pqr" in
apbs) Pymol exits with: Segmentation fault (core dumped).  Same thing
happens when I go to Help>About.  I can open and save files normally,
and just about everything else works.
	
	I've tried this in pymol 1.1r2pre, where I can at least get the
apbs plugin window to open, as well as the 1.2 trunk from svn
(downloaded and compiled last week) which just crashes when I try to
open the apbs window (I can install autodock.py and the window opens,
but it crashes when I try to choose the location of files).  I'm
guessing this is something to do with the gui and tcl/tk, but don't have
any idea how to troubleshoot (see the catchsegv output below).  I'm
running Ubuntu 9.10 on x86_64 and have  a GeForce 8400M GS/PCI/SSE2 with
the proprietory nvidia driver 185.18.36.
	
	Does anyone have any thoughts?
	
	Here is the backtrace portion from catchsegv:
	Backtrace:
	/usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
	
/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
	
/usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
	/usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
	/usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
	/usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
	/usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
	/usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
	/usr/lib/libtcl8.5.so.0[0x7f639777dee6]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
	
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
	/usr/lib/libtcl8.5.so.0[0x7f63977926d1]
	/usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
	/usr/lib/libtcl8.5.so.0[0x7f6397793192]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
	/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
	/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python[0x52bdf0]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python[0x4254ff]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
	/usr/bin/python[0x49c06f]
	/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python[0x52bdf0]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python[0x4254ff]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
	/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
	
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
	/usr/lib/libtcl8.5.so.0[0x7f63977527b9]
	/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
	/usr/lib/libtk8.5.so.0[0x7f6397a556f6]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
	/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
	/usr/lib/libtcl8.5.so.0[0x7f639779668f]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
	
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
	/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
	/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
	/usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
	/usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
	/usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
	/usr/lib/libtk8.5.so.0[0x7f6397a37b48]
	/usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
	/usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
	/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
	/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python[0x52beed]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
	/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
	/usr/bin/python[0x52bdf0]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python[0x4254ff]
	/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
	/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
	/usr/bin/python[0x4d0c4d]
	/lib/libpthread.so.0[0x7f639cf69a04]
	/lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
	
	Thanks, 
	Ian
	

Hi,

I'm having an issue trying to run various plugins in pymol (apbs and
autodock).  Whenever I select a button that should bring up a file browser
to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol
exits with: Segmentation fault (core dumped).  Same thing happens when I go
to Help>About.  I can open and save files normally, and just about
everything else works.

I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin
window to open, as well as the 1.2 trunk from svn (downloaded and compiled
last week) which just crashes when I try to open the apbs window (I can
install autodock.py and the window opens, but it crashes when I try to
choose the location of files).  I'm guessing this is something to do with
the gui and tcl/tk, but don't have any idea how to troubleshoot (see the
catchsegv output below).  I'm running Ubuntu 9.10 on x86_64 and have  a
GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36.

Does anyone have any thoughts?

Here is the backtrace portion from catchsegv:
Backtrace:
/usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
/usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
/usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
/usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
/usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
/usr/lib/libtcl8.5.so.0[0x7f639777dee6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtcl8.5.so.0[0x7f63977926d1]
/usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
/usr/lib/libtcl8.5.so.0[0x7f6397793192]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x49c06f]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0[0x7f63977527b9]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
/usr/lib/libtk8.5.so.0[0x7f6397a556f6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
/usr/lib/libtcl8.5.so.0[0x7f639779668f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
/usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
/usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
/usr/lib/libtk8.5.so.0[0x7f6397a37b48]
/usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
/usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52beed]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x4d0c4d]
/lib/libpthread.so.0[0x7f639cf69a04]
/lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]

Thanks,
Ian

Joachim,

 

PyMOL relies entirely upon Python's built-in proxy support (via urllib),
so if you can get a Python script configured to work properly through
your proxy, then PyMOL should work as well.

 

http://www.python.org/doc/2.5.2/lib/module-urllib.html

 

Cheers,

Warren

 

________________________________

From: Gre...@mh...
[mailto:Gre...@mh...] 
Sent: Thursday, September 24, 2009 5:51 AM
To: pym...@li...
Subject: [PyMOL] Loading PDB Files does not work with Linux

 

Hi all,

 

I can't get the functions to load pdb-data from the internet to work
under Linux. Neither "fetch" nor "load http://..." nor the plugin
remote_pdb_load.py will work (connection error - please check your
internet access). 

Under windows at least the load... method and the plugin are operable,
the fetch method does not work either.

The familiar plugin ProxyConfig.py also is of no use. The Pymol versions
are 1.0 and 1.2r1.

We have to use a http-proxy, but the proxy-url and -port are present in
the environment variable http_proxy. I would really like to use Linux,
so, do you have any hints? How should I setup pymol as to use the proxy?

 

Regards,

 

Joachim

 

 

 

 

 

Yep,

thanks Folmer

> -----Original Message-----
> From: Folmer Fredslund [mailto:fo...@gm...]
> Sent: Thursday, September 24, 2009 9:33 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Viewport dimensions query
> 
> Hi Carsten,
> 
> Is this what you are looking for?
> http://www.mail-archive.com/pymol-
> us...@li.../msg05888.html
> 
> Best regards,
> Folmer Fredslund
> 
> 2009/9/24 Schubert, Carsten [PRDUS] <CSC...@it...>:
> > Hi,
> >
> > Does anyone know how to  get a hold of the viewport dimensions from
> within a
> > script? I vaguely remember some posts about this subject, but could
> not find
> > anything in my archive.
> >
> > Thanks
> >
> >         Carsten
> >
> > ---------------------------------------------------------------------
> ---------
> > Come build with us! The BlackBerry&reg; Developer Conference in SF,
> CA
> > is the only developer event you need to attend this year. Jumpstart
> your
> > developing skills, take BlackBerry mobile applications to market and
> stay
> > ahead of the curve. Join us from November 9&#45;12, 2009. Register
> now&#33;
> > http://p.sf.net/sfu/devconf
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> us...@li...
> >
> 
> -----------------------------------------------------------------------
> -------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart
> your
> developing skills, take BlackBerry mobile applications to market and
> stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register
> now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi Carsten,

Is this what you are looking for?
http://www.mail-archive.com/pym...@li.../msg05888.html

Best regards,
Folmer Fredslund

2009/9/24 Schubert, Carsten [PRDUS] <CSC...@it...>:
> Hi,
>
> Does anyone know how to  get a hold of the viewport dimensions from within a
> script? I vaguely remember some posts about this subject, but could not find
> anything in my archive.
>
> Thanks
>
>         Carsten
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

Does anyone know how to  get a hold of the viewport dimensions from
within a script? I vaguely remember some posts about this subject, but
could not find anything in my archive.

Thanks

	Carsten

Hi all,
 
I can't get the functions to load pdb-data from the internet to work
under Linux. Neither "fetch" nor "load http://..." nor the plugin
remote_pdb_load.py will work (connection error - please check your
internet access). 
Under windows at least the load... method and the plugin are operable,
the fetch method does not work either.
The familiar plugin ProxyConfig.py also is of no use. The Pymol versions
are 1.0 and 1.2r1.
We have to use a http-proxy, but the proxy-url and -port are present in
the environment variable http_proxy. I would really like to use Linux,
so, do you have any hints? How should I setup pymol as to use the proxy?
 
Regards,
 
Joachim
 
 
 
 
 

Chandan,

 

Apologies, but PyMOL can only mutate the standard 20 amino acids.  

 

Note that you have asked that second question before:

 

http://www.mail-archive.com/pym...@li.../msg07211.h
tml

 

Again, there is no special "theory" behind PyMOL's mutagenesis wizard:
the intent behind the implementation is to simply provide geometric
substitution as per the Dunbrack rotomer library.  No optimization is
performed.  Please follow the link below for a list of related
references covering the Dunbrack library and sidechain rotamer theory:

 

http://dunbrack.fccc.edu/bbdep/bbdepdownload.php

 

Cheers,

Warren

 

________________________________

From: Chandan Choudhury [mailto:ii...@gm...] 
Sent: Tuesday, September 22, 2009 9:28 PM
To: pym...@li...
Subject: [PyMOL] mutation

 

Hello all!!

I am required to mutate one of the atom of a protein (pdb file) with
some groups of atoms. Pymol features us to mutate a residu with another
amino acid, but I cannot mutate an atom with some other group that are
not amino acids. So, how can I do it. Please help.

Also I want to know the theory behind the mutation of residue done by
pymol.
Thanks

Chandan
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA

Hello all!!

I am required to mutate one of the atom of a protein (pdb file) with some
groups of atoms. Pymol features us to mutate a residu with another amino
acid, but I cannot mutate an atom with some other group that are not amino
acids. So, how can I do it. Please help.

Also I want to know the theory behind the mutation of residue done by pymol.
Thanks

Chandan
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA