[PyMOL] slab mode fine-tuning

2011-03-29 Thread Nadine Utz
Dear pymol users,

I am looking for a way to zoom in a molecule, like the slab mode when 
you are rolling the scroll wheel. The reason why rolling the scroll 
wheel does not work in my case is that the resulting change is too 
coarse grained, i.e. either I cannot see all the atoms I want to or 
there are some atoms in front of the part I am interested in. I tried as 
well clip slab, x, but then not just atoms in front of the interesting 
part are not shown but as well behind it.

So, what I need is a cross-sectional view of my system, in which only 
everything in front of the cut is not shown (but everything behind).

Thank's a lot for any help,

Nadine


Dr. Nadine Utz
MMB - IRB Barcelona



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[PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Greipel.Joachim
Dear pymol users,
 
pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers
(260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a
result there is a kind of software OpenGL used.
The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:


Detected OpenGL version prior to 2.0.  Shaders unavailable.
OpenGL graphics engine:
GL_VENDOR: Brian Paul
GL_RENDERER: Mesa X11
GL_VERSION: 1.5 Mesa 6.4.2 



This leads to a malfunctioning hardware stereo and renders pymol 1.4
unusable for us. Earlier pymol versions do not show that strange behavior.
Other programs use the NVIDIA drivers perfectly well and allow displaying
structures in hardware stereo. I tried this thing on several machines with
the same result. Does anyone have a hint?

Regards,
 
--
Dr. rer. nat. Joachim Greipel
Med. Hochschule Hannover
Biophys. Chem. OE 4350
Carl-Neuberg-Str. 1
30625 Hannover
Germany
 
Fon: +49-511-532-3718
Fax: +49-511-532-8924
 
 


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Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Schubert, Carsten [PRDUS]
Joachim,

I'm running into the same issue on a SuSe SLED10 box. The 32bit binary
(on the 64bit OS) displays the same behavior, i.e. only the MESA libs
were used. The 64bit version actually core dumps during startup. I
opened up a bug report with Schrodinger and they were already working on
it (I suppose the crash), but wouldn't hurt to reinforce the fact that
the 32bit version only uses the MESA libs (under SuSe?). Good that your
tried the more recent drivers, I was planning to do that but haven't got
around to do this yet.

Cheers,

Carsten


 -Original Message-
 From: greipel.joac...@mh-hannover.de [mailto:Greipel.Joachim@mh-
 hannover.de]
 Sent: Tuesday, March 29, 2011 7:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4
 
 Dear pymol users,
 
 pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA
 drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version
 correctly. As a result there is a kind of software OpenGL used.
 The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:
 
 
 Detected OpenGL version prior to 2.0.  Shaders unavailable.
 OpenGL graphics engine:
 GL_VENDOR: Brian Paul
 GL_RENDERER: Mesa X11
 GL_VERSION: 1.5 Mesa 6.4.2
 
 
 
 This leads to a malfunctioning hardware stereo and renders pymol 1.4
 unusable for us. Earlier pymol versions do not show that strange
 behavior.
 Other programs use the NVIDIA drivers perfectly well and allow
 displaying
 structures in hardware stereo. I tried this thing on several machines
 with
 the same result. Does anyone have a hint?
 
 Regards,
 
 --
 Dr. rer. nat. Joachim Greipel
 Med. Hochschule Hannover
 Biophys. Chem. OE 4350
 Carl-Neuberg-Str. 1
 30625 Hannover
 Germany
 
 Fon: +49-511-532-3718
 Fax: +49-511-532-8924
 
 

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Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Schubert, Carsten [PRDUS]
Nadine,

Probably the command line is your best friend here. Look into the 'clip
near,x' and 'clip far,x' command, which allows to move the front and
back clipping planes in x increments. Positive values move towards you,
negative values of x away from you.
If that does not provide enough fine grained control you may want to
think about making a composite picture to 'fake' clipping planes per
object.

Cheers,

Carsten

 -Original Message-
 From: Nadine Utz [mailto:nad...@mmb.pcb.ub.es]
 Sent: Tuesday, March 29, 2011 6:12 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] slab mode fine-tuning
 
 Dear pymol users,
 
 I am looking for a way to zoom in a molecule, like the slab mode
when
 you are rolling the scroll wheel. The reason why rolling the scroll
 wheel does not work in my case is that the resulting change is too
 coarse grained, i.e. either I cannot see all the atoms I want to or
 there are some atoms in front of the part I am interested in. I tried
 as
 well clip slab, x, but then not just atoms in front of the
 interesting
 part are not shown but as well behind it.
 
 So, what I need is a cross-sectional view of my system, in which only
 everything in front of the cut is not shown (but everything behind).
 
 Thank's a lot for any help,
 
 Nadine
 
 
 Dr. Nadine Utz
 MMB - IRB Barcelona
 
 
 

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Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Roger Rowlett
This appears to be a common problem with 1.4 and Jason is aware of it. The
same issue exists in Ubuntu 9.04 with Nvidia 180.xx drivers, 32 bit. The Win
version works OK.

Roger Rowlett
On Mar 29, 2011 7:53 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com
wrote:
 Joachim,

 I'm running into the same issue on a SuSe SLED10 box. The 32bit binary
 (on the 64bit OS) displays the same behavior, i.e. only the MESA libs
 were used. The 64bit version actually core dumps during startup. I
 opened up a bug report with Schrodinger and they were already working on
 it (I suppose the crash), but wouldn't hurt to reinforce the fact that
 the 32bit version only uses the MESA libs (under SuSe?). Good that your
 tried the more recent drivers, I was planning to do that but haven't got
 around to do this yet.

 Cheers,

 Carsten


 -Original Message-
 From: greipel.joac...@mh-hannover.de [mailto:Greipel.Joachim@mh-
 hannover.de]
 Sent: Tuesday, March 29, 2011 7:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

 Dear pymol users,

 pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA
 drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version
 correctly. As a result there is a kind of software OpenGL used.
 The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:

 
 Detected OpenGL version prior to 2.0. Shaders unavailable.
 OpenGL graphics engine:
 GL_VENDOR: Brian Paul
 GL_RENDERER: Mesa X11
 GL_VERSION: 1.5 Mesa 6.4.2
 


 This leads to a malfunctioning hardware stereo and renders pymol 1.4
 unusable for us. Earlier pymol versions do not show that strange
 behavior.
 Other programs use the NVIDIA drivers perfectly well and allow
 displaying
 structures in hardware stereo. I tried this thing on several machines
 with
 the same result. Does anyone have a hint?

 Regards,

 --
 Dr. rer. nat. Joachim Greipel
 Med. Hochschule Hannover
 Biophys. Chem. OE 4350
 Carl-Neuberg-Str. 1
 30625 Hannover
 Germany

 Fon: +49-511-532-3718
 Fax: +49-511-532-8924




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Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Robert Campbell
Hi,

On Tue, 29 Mar 2011 6:12 AM Nadine Utz [mailto:nad...@mmb.pcb.ub.es]
wrote:

  Dear pymol users,
  
  I am looking for a way to zoom in a molecule, like the slab mode when
  you are rolling the scroll wheel. The reason why rolling the scroll
  wheel does not work in my case is that the resulting change is too
  coarse grained, i.e. either I cannot see all the atoms I want to or
  there are some atoms in front of the part I am interested in. I tried
  as
  well clip slab, x, but then not just atoms in front of the
  interesting
  part are not shown but as well behind it.
  
  So, what I need is a cross-sectional view of my system, in which only
  everything in front of the cut is not shown (but everything behind).
  
  Thank's a lot for any help,
  
On Tue, 29 Mar 2011 07:56:09 -0400 Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:

 Nadine,
 
 Probably the command line is your best friend here. Look into the 'clip
 near,x' and 'clip far,x' command, which allows to move the front and
 back clipping planes in x increments. Positive values move towards you,
 negative values of x away from you.
 If that does not provide enough fine grained control you may want to
 think about making a composite picture to 'fake' clipping planes per
 object.

You can also control the front and rear clipping planes independently by
holding down the Shift key along with the right mouse button (assuming you
are in the standard 3-button viewing mode).  Moving the mouse vertically
changes the front clipping plane and moving it horizontally changes the rear
clipping plane.

Cheers,
Rob



-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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[PyMOL] Calling pymol from python - access to global variables

2011-03-29 Thread Tsjerk Wassenaar
Hi,

I'm having some trouble accessing a function defined at top level with
alter_state in a python script launching pymol. Maybe I shouldn't be
wanting to do this, but what I'm trying, and failing to do is
exemplified by this script:

###

#!/usr/bin/env python

import pymol

if __name__ == __main__:
pymol.finish_launching()

def identity(x,y,z):
print YEAH!
return x,y,z

# Fix:
# setattr(pymol,identity,identity)

pymol.editor.build_peptide(G)
pymol.cmd.alter_state(1,all,(x,y,z)=identity(x,y,z))

###

The problem is that the function 'identity' (which may be given a more
sensical form by actually doing something with the coordinates), is
sought in the pymol namespace. I can't really figure out where I
should be looking to directly call the function. Of course, I can
register the function in the pymol module (uncomment the setattr
line), but I don't think it's proper meddling with established modules
like that. Does anyone know a better/cleaner solution?

In addition, does anyone know how to suppress the GUI stuff when
launching pymol like this?

Groetjes,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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Re: [PyMOL] Calling pymol from python - access to global variables

2011-03-29 Thread Thomas Holder
Hi Tsjerk,

use either the global pymol.stored variable or the alter_state 'space' argument.

--
#!/usr/bin/env python

if __name__ == __main__:
 import __main__
 __main__.pymol_argv = [ 'pymol', '-cq' ]
 import pymol
 pymol.finish_launching()
else:
 import pymol

def identity(x,y,z):
  print YEAH!
  return x,y,z

pymol.editor.build_peptide(G)
pymol.cmd.alter_state(1,all,(x,y,z)=identity(x,y,z),
   space={'identity':identity})

# or:
# pymol.stored.identity = identity
# pymol.cmd.alter_state(1,all,(x,y,z)=stored.identity(x,y,z))
--

Cheers,
 Thomas

On Tue, Mar 29, 2011 at 6:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi,

 I'm having some trouble accessing a function defined at top level with
 alter_state in a python script launching pymol. Maybe I shouldn't be
 wanting to do this, but what I'm trying, and failing to do is
 exemplified by this script:

 ###

 #!/usr/bin/env python

 import pymol

 if __name__ == __main__:
    pymol.finish_launching()

 def identity(x,y,z):
    print YEAH!
    return x,y,z

 # Fix:
 # setattr(pymol,identity,identity)

 pymol.editor.build_peptide(G)
 pymol.cmd.alter_state(1,all,(x,y,z)=identity(x,y,z))

 ###

 The problem is that the function 'identity' (which may be given a more
 sensical form by actually doing something with the coordinates), is
 sought in the pymol namespace. I can't really figure out where I
 should be looking to directly call the function. Of course, I can
 register the function in the pymol module (uncomment the setattr
 line), but I don't think it's proper meddling with established modules
 like that. Does anyone know a better/cleaner solution?

 In addition, does anyone know how to suppress the GUI stuff when
 launching pymol like this?

 Groetjes,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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[PyMOL] Newline character in labels

2011-03-29 Thread Andreas Spitzmüller
Hi,
I'd like to label a couple of CA atoms in with their AA code, residue
number and b-factor. Since this gets a long label, I want to split it to
get two lines.
For example, if I have the CA atom of Asn124 with a b-factor of 36.2, I
want it to be labelled as follows:

 Asn124
  36.2

However, I cannot get the line break into the label! Is there any
possibility?

I tried things like \n or unicode encoding u\u000a in combination with a
unicode font (label_font_id 15).
But I couldn't manage to get the label on two lines.

Thanks for any hints!
Andreas

PS: Please excuse if this message is posted twice, but it seems to me that  
my first attempt didn't come through to you. (This is my first posting on  
this list.)

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Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Jason Vertrees
Hi Joachim,

Sorry for the delay.  I'm spending the entire day on the floor of the
ACS meeting, showing off PyMOL.

 pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers
 (260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a
 result there is a kind of software OpenGL used.
 The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:

We're aware of this problem and we're looking into a solution.  This
bug is odd because I develop on Open SuSE 11.3 and haven't had any
problems.  We have a SLED 10.2 machine and some other Linux machines
we'll test this on.

At this point it looks like a simple initialization error with GLEW,
but we're still looking into it.

Thanks for bringing this to our attention.  I expect this to be
resolved quickly.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] Newline character in labels

2011-03-29 Thread Jason Vertrees
Hi Andreas,

This is currently not possible.  If this is a feature you'd like to
see implemented, please go here http://pymol.org/contact and leave us
a message.  It'll be tracked internally so we don't drop the ball if
we decide to implement it.

Cheers,

-- Jason

On Tue, Mar 29, 2011 at 12:03 PM, Andreas Spitzmüller
andreas.spitzmuel...@staff.uni-marburg.de wrote:
 Hi,
 I'd like to label a couple of CA atoms in with their AA code, residue
 number and b-factor. Since this gets a long label, I want to split it to
 get two lines.
 For example, if I have the CA atom of Asn124 with a b-factor of 36.2, I
 want it to be labelled as follows:

     Asn124
      36.2

 However, I cannot get the line break into the label! Is there any
 possibility?

 I tried things like \n or unicode encoding u\u000a in combination with a
 unicode font (label_font_id 15).
 But I couldn't manage to get the label on two lines.

 Thanks for any hints!
 Andreas

 PS: Please excuse if this message is posted twice, but it seems to me that
 my first attempt didn't come through to you. (This is my first posting on
 this list.)

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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] Newline character in labels

2011-03-29 Thread Tsjerk Wassenaar
Hi Andreas,

In the meantime, you can set double labels by using a pseudoatom,
labeling it with the second part, and placing the label at the spot
desired.

Cheers,

Tsjerk

On Wed, Mar 30, 2011 at 3:59 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi Andreas,

 This is currently not possible.  If this is a feature you'd like to
 see implemented, please go here http://pymol.org/contact and leave us
 a message.  It'll be tracked internally so we don't drop the ball if
 we decide to implement it.

 Cheers,

 -- Jason

 On Tue, Mar 29, 2011 at 12:03 PM, Andreas Spitzmüller
 andreas.spitzmuel...@staff.uni-marburg.de wrote:
 Hi,
 I'd like to label a couple of CA atoms in with their AA code, residue
 number and b-factor. Since this gets a long label, I want to split it to
 get two lines.
 For example, if I have the CA atom of Asn124 with a b-factor of 36.2, I
 want it to be labelled as follows:

     Asn124
      36.2

 However, I cannot get the line break into the label! Is there any
 possibility?

 I tried things like \n or unicode encoding u\u000a in combination with a
 unicode font (label_font_id 15).
 But I couldn't manage to get the label on two lines.

 Thanks for any hints!
 Andreas

 PS: Please excuse if this message is posted twice, but it seems to me that
 my first attempt didn't come through to you. (This is my first posting on
 this list.)

 --
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 growing manageability and security demands of your customers. Businesses
 are taking advantage of Intel(R) vPro (TM) technology - will your software
 be a part of the solution? Download the Intel(R) Manageability Checker
 today! http://p.sf.net/sfu/intel-dev2devmar
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120

 --
 Enable your software for Intel(R) Active Management Technology to meet the
 growing manageability and security demands of your customers. Businesses
 are taking advantage of Intel(R) vPro (TM) technology - will your software
 be a part of the solution? Download the Intel(R) Manageability Checker
 today! http://p.sf.net/sfu/intel-dev2devmar
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

--
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software 
be a part of the solution? Download the Intel(R) Manageability Checker 
today! http://p.sf.net/sfu/intel-dev2devmar
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net