Re: [PyMOL] how to get RMSD from align command

2009-10-30 Thread Warren DeLano
Tom,

Because the number of atoms in the alignment can vary with each pairwise
structure comparison, the RMS number returned by align cannot be
considered valid criterion except perhaps if presented along with the
number of atoms in each comparison.  E.g.:

RMS over X atoms

0.5 1451
0.3 1273
0.4 1343

But remember, each final RMS value will involve a different set of
atoms...and that's the root of the problem...there's no common reference
point.  

Therefore, I must recommand against using 'align' for this purpose --
it's just not the right tool for the job.

Cheers,
Warren

 -Original Message-
 From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
 Sent: Thursday, October 29, 2009 4:56 PM
 To: Warren DeLano
 Cc: Thomas Evangelidis; pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] how to get RMSD from align command
 
 Warren,
 
 before I write something incorrect into Methods section, do you think
 the overall RMSD returned by align command is a valid criterion to
 select which structure of the family is most similar?
 
 Tom
 
  Tom,
 
  Apologies for the confusion, but there really isn't any way to
  measure overall structural similarity in PyMOL other than pair_fit,
  but you have to do the work of explicitly stating which pairs are to
  be aligned.
 
  The pair_fit selections don't have to be identical, but they do have
  to correspond in a pairwise fashion.  In other words, you can
  compare any number of C-alpha positions so long as the same number
  of atomic positions are specified in each structure.
 
  Cheers,
  Warren
 
  -Original Message-
  From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
  Sent: Thu 10/29/2009 5:24 AM
  To: Warren DeLano
  Cc: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] how to get RMSD from align command
 
  Hi Warren,
 
  Now I am more confused. I used align command to measure the overall
  RMSD between homologous structures. Apparently align is not
  appropriate if not sufficient sequence similarity is present. I
later
  came across CEalign plugin, which does structure-based
  superimposition. This command also returns an RMSD value, which
  happens to be higher for the set of homologous structures I
analysed.
  Based on this I concluded that align command is more appropriate to
  measure measure structural similarity, but I'm not sure now.
 
  My objective is to select between a small set of homologous
structures
  (co-crystallized with ligands), the one with the highest structural
  similarity and use it to place a dummy ligand into one where it's
  missing. I.e. 1ebh lacks a ligand, so I compared it with 1ebg,
  1els, 1one, 2one, 5enl, 6enl, 7enl which have
  co-crystallized ligands. According to both align and cealign, 5ENL
is
  the most similar with overall RMSD 0.246 and 0.420907 respectively.
  The question is which command produces the best superimposition
  provided that these proteins belong to the enolase family and thus
  have high sequence and structural similarity? Based on the RMSD
  values, align does, but as you said this value pertains to only a
  subset of atoms after refinement.
 
  Apparently pair_fit command cannot be used for my purpose as it
  requires identical selections.
 
  Tom
 
 
  Tom,
 
  The complication with cmd.align() is that it is doing a whole lot
  more than a simple alignment.  The first number is in fact the RMS,
  but it covers only the subset of the input atoms remaining after
  refinement is completed. The count of aligned atoms is the second
  field.
 
  If you're looking for exact RMS fit values over a well-defined set
  of atoms, try using cmd.pair_fit(sele1, sele2) instead, for
example:
 
  load $TUT/1hpv.pdb
 
  create loopA, A/46-55/
 
  create loopB, B/46-55/
 
  show sticks, loop*
 
  print cmd.pair_fit(loopACA, loopBCA)
 
  Cheers,
  Warren
 
  -Original Message-
  From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
  Sent: Wed 10/28/2009 8:09 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] how to get RMSD from align command
 
  Simple question, it must have been answered before but couldn't
find
  it so far:
 
  how can I get the RMSD value from the align command in a python
  script? cmd.align() returnes a tuple of 8 numbers and none of them
is
  the actual RMSD value I get when I align these 2 structures
manually.
 
  thanks,Tom
 
 
 
---
 ---
  Come build with us! The BlackBerry(R) 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/devconference
  ___
  PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
  Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
  Archives:
http

Re: [PyMOL] how to get RMSD from align command

2009-10-29 Thread Warren DeLano
Tom,

Apologies for the confusion, but there really isn't any way to measure overall 
structural similarity in PyMOL other than pair_fit, but you have to do the work 
of explicitly stating which pairs are to be aligned.   

The pair_fit selections don't have to be identical, but they do have to 
correspond in a pairwise fashion.  In other words, you can compare any number 
of C-alpha positions so long as the same number of atomic positions are 
specified in each structure.

Cheers,
Warren

-Original Message-
From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
Sent: Thu 10/29/2009 5:24 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] how to get RMSD from align command
 
Hi Warren,

Now I am more confused. I used align command to measure the overall  
RMSD between homologous structures. Apparently align is not  
appropriate if not sufficient sequence similarity is present. I later  
came across CEalign plugin, which does structure-based  
superimposition. This command also returns an RMSD value, which  
happens to be higher for the set of homologous structures I analysed.  
Based on this I concluded that align command is more appropriate to  
measure measure structural similarity, but I'm not sure now.

My objective is to select between a small set of homologous structures  
(co-crystallized with ligands), the one with the highest structural  
similarity and use it to place a dummy ligand into one where it's  
missing. I.e. 1ebh lacks a ligand, so I compared it with 1ebg,  
1els, 1one, 2one, 5enl, 6enl, 7enl which have  
co-crystallized ligands. According to both align and cealign, 5ENL is  
the most similar with overall RMSD 0.246 and 0.420907 respectively.  
The question is which command produces the best superimposition  
provided that these proteins belong to the enolase family and thus  
have high sequence and structural similarity? Based on the RMSD  
values, align does, but as you said this value pertains to only a  
subset of atoms after refinement.

Apparently pair_fit command cannot be used for my purpose as it  
requires identical selections.

Tom


 Tom,

 The complication with cmd.align() is that it is doing a whole lot  
 more than a simple alignment.  The first number is in fact the RMS,  
 but it covers only the subset of the input atoms remaining after  
 refinement is completed. The count of aligned atoms is the second  
 field.

 If you're looking for exact RMS fit values over a well-defined set  
 of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:

 load $TUT/1hpv.pdb

 create loopA, A/46-55/

 create loopB, B/46-55/

 show sticks, loop*

 print cmd.pair_fit(loopACA, loopBCA)

 Cheers,
 Warren

 -Original Message-
 From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
 Sent: Wed 10/28/2009 8:09 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] how to get RMSD from align command

 Simple question, it must have been answered before but couldn't find
 it so far:

 how can I get the RMSD value from the align command in a python
 script? cmd.align() returnes a tuple of 8 numbers and none of them is
 the actual RMSD value I get when I align these 2 structures manually.

 thanks,Tom


 --
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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









- End message from war...@delsci.com -



--
Come build with us! The BlackBerry(R) 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/devconference
___
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






--
Come build with us! The BlackBerry(R) 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

[PyMOL] Remember, PyMOL is for visualization, not analysis.

2009-10-29 Thread Warren DeLano
Dear PyMOL-Users:

Today's questions regarding alignment RMS values suggest to me that I
should re-emphasize what PyMOL is and is not good for:

Please everyone keep in mind that PyMOL is intended to be just a
molecular graphics program, to be used for displaying, comparing, and
manipulating molecular structure in various visual and interactive ways.
PyMOL is a figure maker, a movie maker, a presentation tool -- a
molecular communications platform, if you will.

PyMOL is not intended to be, nor should it be used as, a molecular
analysis  tool.  It wasn't built with that goal in mind, and most of the
algorithms inside the program have not been rigorously validated.  As a
general rule, if the numbers matter, then you should be using other
more rigorous software for those tasks, and then loading only the final
output into PyMOL (for rendering, etc.).
 
Thank you all for keeping this in mind as you continue to apply PyMOL in
your work.  

Cheers,
Warren



--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] Replace Coordinates in State

2009-10-26 Thread Warren DeLano
Sean,

 

Unfortunately, there isn't any way at present to directly expose PyMOL's
internal C coordinate array to Python in an accessible form.  Yes,
iterate_state and alter_state are highly inefficient - it would make
more sense to provide a means of exporting and re-importing coordinate
sets via either native Python lists or, even better, NumPy arrays.  In
what form do you have the current coordinate data?

 

Cheers,

Warren

 



From: Sean Law [mailto:magic...@hotmail.com] 
Sent: Friday, October 23, 2009 4:54 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Replace Coordinates in State

 

Hi All,

I was wondering if there was a faster way to replace all coordinates.
I've used commands such as iterate_state and alter_state before but they
are far too slow since they have to iterate over each atom.  Instead, I
want to replace one set of coordinates that correspond to a specific
state with a different set.  Here's what I have to work with:

I have a list that contains x, y, z coordinates.  Of course, this list
can be manipulated and/or separated if necessary.  I'm assuming that the
coordinates for a specific state are stored somewhere in memory and I
would basically like to replace one set of coordinates with the other.
I would think that something like pointers or references would work a
lot faster than having to copy the coordinates over (which is typically
slow and is likely what alter_state is doing?). In addition, I am
dealing with 100+ states using alter_state for each state would be far
too slow.

Any suggestions would be greatly appreciated.

Thanks in advance!

Sean



Save up to 84% on Windows 7 until Jan 3-eligible CDN College or
University students only. Hurry-buy it now for $39.99!
http://go.microsoft.com/?linkid=9691631 

--
Come build with us! The BlackBerry(R) 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/devconference___
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

Re: [PyMOL] number of h-bonds

2009-10-26 Thread Warren DeLano
Hello Michael,

Unfortunately, there is no programmatic way to get this information out of 
PyMOL -- my apologies!

Cheers,
Warren

-Original Message-
From: Michael Zimmermann [mailto:micha...@iastate.edu]
Sent: Mon 10/26/2009 9:04 PM
To: pymol-users
Subject: [PyMOL] number of h-bonds
 
Dear PyMOL users,

I was using Action - find - polar interactions within selection
to get an idea about the hydrogen bonds and other polar interactions
in some molecules.  I would like to compare different conformations of
a certain molecule and one metric could be the number of pair returned
by one of these distance evaluations.  Could someone help me figure
out how to get routines like this to return the number of pairs that
they define? Alternatively, for the object that is returned, is there
a way to loop through the line objects or labels and count them?

Thank you.

--
Come build with us! The BlackBerry(R) 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/devconference
___
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






--
Come build with us! The BlackBerry(R) 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/devconference___
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

Re: [PyMOL] Pymol Align Command and RMSD Calculation ?

2009-10-25 Thread Warren DeLano
 1. What type of RMSD is calculated with align comman i.e All Atoms or
only Backbone?
 
It depends on the input selections.  If you don't restrict it to backbone 
atoms, PyMOL will perform the fit for all matched atoms.  Also, it is important 
to understand that align is a combined sequence and 3D refined structure 
alignment which, by default, iteratively discards outliers in order to achieve 
a well-matched core structure.  super is similar except that it doesn't use 
sequence.
 
 2. If I have few models/PDB stuructures of the same protein how I can
clauclate the total atoms and backbone only RMSD between these.
Actually I am confused with usuage of these commands i.e align ,
super, rms, rms_cur  etc.
 
If you're trying to calculate RMS between specific pairs of atoms :
 
If the proteins have matched identifiers (identical segment, chain, and residue 
identifier), then the command you want is fit:
 
# all atom
 
fit obj1, obj2 
 
# C-calpha only
 
fit obj1CA, obj2CA
 
If the protein do not have matched identifiers, then you must manually select 
exactly N atom pairs in each structure, and then use pair_fit:
 
# C-alpha fit for residues 10 through 80  and 100 through 120
 
pair_fit obj1///10-80+100-120/CA,  obj2///10-80+100-120/CA
 
Cheers,
Warren
 



From: Bio Brain [mailto:biobr...@gmail.com]
Sent: Sat 10/24/2009 1:11 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Pymol Align Command and RMSD Calculation ?



Dear Pymol Users,

I am looking for some very basic information about the PyMol commands.

1. What type of RMSD is calculated with align comman i.e All Atoms or
only Backbone?

2. If I have few models/PDB stuructures of the same protein how I can
clauclate the total atoms and backbone only RMSD between these.
Actually I am confused with usuage of these commands i.e align ,
super, rms, rms_cur  etc.

Regards

--
Come build with us! The BlackBerry(R) 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/devconference
___
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





--
Come build with us! The BlackBerry(R) 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/devconference___
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

Re: [PyMOL] not getting a simple translation

2009-10-22 Thread Warren DeLano
Hi David,

You have a rotate command in that script.  Did you mean to 'turn' the
camera rather than 'rotate' the atomic coordinates?

Cheers,
Warren

 -Original Message-
 From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] 
 Sent: Thursday, October 22, 2009 7:00 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] not getting a simple translation
 
 I have a 5 similar domains (struct.pdb) aligned on another 
 one (rcsb.pdb).  I made a copy of one of them and translated 
 it 37 angstroms to the right. translate [37, 0, 0 ].
 But I did not get a simple translation.  The two molecules 
 end up having a rotation between them.
 Here's the script. I need an origin command or other...?
 thanks,
 Dave
 
 #macpymol-1_1r1.tgz
 reinitialize
 bg_color white
 set antialias , 1
 set ray_trace_fog=0
 set depth_cue=0
 set direct, 0.7
 
 set ribbon_smooth, 1
 set ribbon_width, 3
 
 set_view (\
  -0.342648655,0.901220083,   -0.265300900,\
   0.939403236,0.325558662,   -0.107372068,\
  -0.010394786,   -0.286019355,   -0.958166420,\
   0.0,0.0, -128.319412231,\
  22.162364960,   43.079395294,   12.406776428,\
 101.167999268,  155.470825195,0.0 )
 
 load rcsb.pdb, rcsb2
 load rcsb.pdb, a33alone
 
 #1kcg:A
 load struct(2).pdb, 22
 #1e8i:A
 load struct(3).pdb, 33
 #1ypo:A
 load struct(4).pdb, 44
 #1B6E_dimer.pdb:A
 load struct(5).pdb, 55
 #1qo3:C
 load struct(6).pdb, 66
 
 hide lines, /rcsb2//*
 hide nonbonded, /rcsb2//*
 hide lines, /a33alone//*
 hide nonbonded, /a33alone//*
 hide lines, /22//*
 hide nonbonded, /22//*
 hide lines, /33//*
 hide nonbonded, /33//*
 hide lines, /44//*
 hide nonbonded, /44//*
 hide lines, /55//*
 hide nonbonded, /55//*
 hide lines, /66//*
 hide nonbonded, /66//*
 
 color red, /a33alone//*
 show ribbon, /a33alone//* and (name ca or name c or name n)
 
 color red, /rcsb2//*
 show ribbon, /rcsb2//* and (name ca or name c or name n)
 
 color yelloworange, /22//*
 color blue, /22//A/98-134/*
 color blue, /22//A/190-215/*
 show ribbon, /22//* and (name ca or name c or name n)
 
 color yelloworange, /33//*
 color blue, /33//A/83-121/*
 color blue, /33//A/174-199/*
 show ribbon, /33//* and (name ca or name c or name n)
 
 color yelloworange, /44//*
 color blue, /44//A/142-180/*
 color blue, /44//A/244-269/*
 show ribbon, /44//* and (name ca or name c or name n)
 
 color yelloworange, /55//*
 color blue, /55//A/60-97/*
 color blue, /55//A/153-179/*
 show ribbon, /55//* and (name ca or name c or name n)
 
 color yelloworange, /66//*
 color blue, /66//C/144-175/*
 color blue, /66//C/233-258/*
 show ribbon, /66//* and (name ca or name c or name n) hide 
 ribbon, /66//C/140-143/*
 
 rotate y, 30
 
 set_view (\
  -0.287066191,0.957891881,0.004756007,\
   0.607159078,0.178112596,0.774357498,\
   0.740909398,0.225178465,   -0.632728696,\
   0.0,0.0, -191.885284424,\
  24.745697021,   46.720252991,   14.490940094,\
 151.283813477,  232.486755371,0.0 )
 
 translate [37, 0, 0 ], a33alone
 zoom complete=1
 
 #ray 4800,4800
 #png /Users/dgarboczi/Documents/A_on_A/A_on_A_2_newview_4.png, dpi=600
 
 
 -- 
 
 --
 
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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
 
 
 
 
 

--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] real time first person camera view / control

2009-10-22 Thread Warren DeLano
Nick,
 
How would this be different from the existing Scene interpolation
capability?  
 
You can use the Scene menu to Append a series of scenes of the molecule
(views+representations) and then use Scene - Next, PAGE-DN or  the
scene command  to interpolate through them.
 
Cheers,
Warren



From: Nick Hunter [mailto:nickhunt...@googlemail.com] 
Sent: Thursday, October 22, 2009 6:24 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] real time first person camera view / control


hello -

i would like to create a first person view so that it is as if
you are walking around the scene. would this be possible through pymol's
python interface while maintaining adequate performance for real time
interaction?

if not, would it be possible/difficult to alter the source code
in such a way that the camera view control may be set up to mimic a
first person view of the scene?

thanks,
nick


--
Come build with us! The BlackBerry(R) 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/devconference___
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

Re: [PyMOL] Saving high resolution images

2009-10-22 Thread Warren DeLano
Hi Tom,
 
Actually this is how the draw command works in using the screen-based OpenGL 
renderer to create images of arbitrary size.  However, the ray-tracer isn't 
currently set up to operate that way.  Ray might work with an orthoscopic 
projection, but with perspective enabled, each frame would have a distinct 
vanishing point (if that's the correct term).
 
Cheers,
Warren



From: Thomas Stout [mailto:tst...@exelixis.com]
Sent: Thu 10/22/2009 12:36 PM
To: Tsjerk Wassenaar
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Saving high resolution images




But isn't it true that only the objects that are visible in the viewport are 
what are written to the rendered image file?  I was proposing rendering a 
poster-sized image in tiles and stitching them back together post facto to 
create a very large, high resolution image.

something like:
---
|  |  |
|  |  |
| render 1 | render 2 |
|  |  |
|  |  |
|--
|  |  |
|  |  |
| render 3 | render 4 |
|  |  |
|  |  |
---

I feel like I'm missing something important here!
-Tom

-Original Message-
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Thursday, October 22, 2009 11:45 AM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Saving high resolution images

Hi Thomas,

The viewport is not important for rendering. You can render at whatever 
resolution/dimensions you want with whatever viewport. You can even make a 
panorama using a wide angle lens if you want to have something for on your wall 
;)

Cheers,

Tsjerk

On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout tst...@exelixis.com wrote:


 Here's a crazy idea:  if someone out there were clever at both python
 and manipulating orientation matrices, I would bet that a scene
 could be quartered or cut into eighths and translated such that each
 portion filled the viewport for rendering; then the individual images
 could be spliced back together in one's favorite image handling
 program a la panoramas in photography  Is this way too complex to
 be bothered with?  I suspect parallax may be a problem...

 -Tom



 -Original Message-
 From: Eva Vanamee [mailto:eva.vana...@mssm.edu]
 Sent: Monday, October 19, 2009 1:51 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Saving high resolution images

 Hi,

 I'd like to save an image in high resolution for a poster.
 The requested size is 20 by 30. I calculated that it would
 correspond to a 6000 x 9000 pixel image.
 How can I create such a large ray traced image without crashing the
 computer?
 Many thanks in advance for the help.

 Best,

 - Eva


 --
 --
 --
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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
 This email (including any attachments) may contain material that is
 confidential and privileged and is for the sole use of the intended
 recipient. Any review, reliance or distribution by others or
 forwarding without express permission is strictly prohibited. If you
 are not the intended recipient, please contact the sender and delete
 all copies.
 Exelixis, Inc. reserves the right, to the extent and under
 circumstances permitted by applicable law, to retain, monitor and
 intercept e-mail messages to and from its systems.


 --
  Come build with us! The BlackBerry(R) 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/devconference
 ___
 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.
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
This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the 

Re: [PyMOL] Secondary Structure Matching

2009-10-21 Thread Warren DeLano
Fred,

You might try super instead of align (same syntax).

Failing that, you can use pair_fit with explicit selections -- just make sure 
the number of atoms is the same in each of the selections.

Cheers,
Warren

 -Original Message-
 From: Kerff Frédéric [mailto:fke...@ulg.ac.be] 
 Sent: Wednesday, October 21, 2009 5:51 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Secondary Structure Matching
 
 Hello,
 
 Is there a way to perform secondary structure matching with 
 Pymol. I already tried the align function with different 
 selections without any success but the 2 proteins obviously 
 share the same fold with low sequence identity.
 I know it can be done in other software like Coot but I'd 
 like to avoid having to switch from one program to another 
 all the time.
 Thank you.
 
 Fred
 
 
 --
 Frédéric Kerff
 Chargé de recherche F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège - Bat B5a
 B4000 Liège (Sart-Tilman)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772
 
 
 --
 
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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
 

--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] Saving high resolution images

2009-10-19 Thread Warren DeLano
Eva,

You may be past the limit of what PyMOL can handle.  Regardless, the
64-bit Linux builds are the best at handling large-memory tasks.

Practice with something really simple:

fragment arg

as spheres

ray 6000,9000

Also, two more things I'd suggest for such a large image (in order to
cut down on RAM usage):

set antialias,0

set hash_max, 100

ray 6000,9000

Another thing you can do is render 3000,4500 and use Photoshop to
subsample.

Cheers,
Warren

 -Original Message-
 From: Eva Vanamee [mailto:eva.vana...@mssm.edu]
 Sent: Monday, October 19, 2009 2:12 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Saving high resolution images
 
 Hi,
 
 I'd like to save an image in high resolution for a poster.
 The requested size is 20 by 30. I calculated that it would
correspond
 to a 6000 x 9000 pixel image.
 How can I create such a large ray traced image without crashing the
 computer?
 Many thanks in advance for the help.
 
 Best,
 
 - Eva
 
 


--
 
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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
 
 
 



--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] selecting multiple, non-adjacent chains

2009-10-17 Thread Warren DeLano
Sean,

There is also a more concise option:

select allothers, chain 0:4+C:J+L:Z

Or even more concise, using selection macro: chain/residue/atom

select allothers, 0:4+C:J+L:Z//

Cheers,
Warren

-Original Message-
From: Marius Retegan [mailto:marius.s.rete...@gmail.com] 
Sent: Thursday, October 15, 2009 7:13 AM
To: Sean Moore
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selecting multiple, non-adjacent chains

Try this one

select allothers, chain 0:4 or chain C:J or chain L:Z

Marius

On Thu, Oct 15, 2009 at 3:34 PM, Sean Moore semo...@mail.ucf.edu wrote:
 Hello,

 I am trying to find an easier way to select multiple chains at once in
 a large file with many chains (PDB 2i2t).  The chain assignments
 exceed z and start again at 0 at the beginning of the chain list.

 In an effort to select chain 0-4, skip chain A+B, select chain C-J,
 skip chain K, and select the remaining L-Z, I have tried (among other
 things):

 select allothers, chain 0-4 and C-J and L-Z (the dashes don't seem to
 work for select)
 select allothers, chain 0:4 and C:J and L:Z
 select allothers, chain 0:4 and chain C:J and chain L:Z
 select allothers, (chain 0:4) and (chain C:J) and (chain L:Z)

 selecting chain 0+4 works, and selecting chain 0:4 works.

 As it stands I have to click all of the chains then rename the
 selection which leads to mistakes.

 Any help is appreciated.



 --
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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


--
Come build with us! The BlackBerry(R) 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/devconference
___
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






--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] Change location of measurement label

2009-10-14 Thread Warren DeLano
Switch the mouse into editing mode, then ctrl-left-click-and-drag on  
the label to reposition.

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
war...@delsci.com

(Sent from an iPhone -- please forgive brevity and/or typos!)

On Oct 14, 2009, at 8:03 AM, Per Larsson per.lars...@sbc.su.se  
wrote:

 Hi!

 I need to make some pictures of very simple di-peptide systems, and
 need to include values (from wizard-measurement-dihedrals) of
 certain dihedral angles. However, the two labels end up very close,
 with the values almost on top of each other making them un-readable.
 Is there a way to change the location of the measurement labels?

 Thanks!
 /Per



 --- 
 --- 
 --- 
 -
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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- 
 us...@lists.sourceforge.net



--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] color functionality for mac versions

2009-10-08 Thread Warren DeLano
Mark ( indeed all Mac users)

MacPyMOL can be launched in two flavors, based on the name of the
executable:

If the executabled is named MacPyMOL, PyMOL launches in the mode you're
familiar with:  a single-window Cocoa-based interface.

If the executable is renamed PyMOLX11Hybrid, then PyMOL launches using
the Tcl/Tk/X11-based, two-window interface you're familiar with from
Windows and Linux.  That's how you can get at the color slider you seek.

Cheers,
Warren

 -Original Message-
 From: mnc2...@columbia.edu [mailto:mnc2...@columbia.edu]
 Sent: Thursday, October 08, 2009 10:50 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] color functionality for mac versions
 
 Hi
 I was talking to a fellow student about coloring different molecules
in an
 image for publication.  And one reviewer suggested the 3 colors he was
 using were different of luminocity.  He then showed me where to adjust
 this in the PC version.  Setting  Colors... , and adjust or create
new
 colors.  I'm a mac user, and both macpymol and the hybrid version have
 only red, blue and green sliders in the modify colors menu. No Lum.
slider
 or h/l/s boxes.  I am missing something?  I really like this
 functionality on the pc version.
 Thanks Mark
 
 
 
 


--
 
 Come build with us! The BlackBerry(R) 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/devconference
 ___
 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
 
 
 



--
Come build with us! The BlackBerry(R) 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/devconference
___
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


Re: [PyMOL] rmsd for multiple snaphosts

2009-10-02 Thread Warren DeLano
Dear all,

i have multiple conformations files (multi pdb) and would like to
compute for each one, the rmsd for each snapshot against the first
snapshot.
Is it possible with pymol to do such a task ?

thank you in advance for the gain of time ... :-)

nicolas floquet

Yes, using a short Python loop:

# .pml example PyMOL script

# load structure into input object

fetch 1nmr, input, async=0

# choose the reference state

create ref, input, 1, 1

# now iterate using Python

python

for i in range(cmd.count_states(input)):
cmd.create(tmp, input, i+1, 1)
print 1, i+1, cmd.fit(tmp, ref)
cmd.delete(tmp)

python end

# end example

Cheers,
Warren



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Sessions and Scope

2009-10-02 Thread Warren DeLano
Tsjerk,

Great question with a crummy answer: you can't! 

But this seems like a really good idea, at least for primitives stored
in ordinary built-in Python containers.  Saving class instances would be
problematic, since session files wouldn't necessarily be restorable in
the absence of accompanying class definitions [we do rely upon Python
pickling machinery, and are thus subject to its limitations].

Cheers,
Warren

 -Original Message-
 From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
 Sent: Friday, October 02, 2009 6:04 AM
 To: pymol-users
 Subject: [PyMOL] Sessions and Scope
 
 Hi,
 
 At present I'm setting some variables in the globals()
 dictionary/global scope, but when I save the session, these variables
 are lost. What would be the best way to preserve them? (This question
 may also be interpreted as: what does Pymol write to a session file?).
 
 Cheers,
 
 Tsjerk
 
 --
 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
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] DepthQ configuration in a classroom setting

2009-09-29 Thread Warren DeLano
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:rrowl...@colgate.edu] 
Sent: Tuesday, September 29, 2009 9:58 AM
To: pymol-users@lists.sourceforge.net
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: rrowl...@colgate.edu

--
Come build with us! The BlackBerryreg; 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 (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

Re: [PyMOL] Iterate Script Over States

2009-09-28 Thread Warren DeLano

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:magic...@hotmail.com] 
Sent: Monday, September 28, 2009 7:14 AM
To: pymol-users@lists.sourceforge.net
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.


--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Iterate Script Over States

2009-09-28 Thread Warren DeLano
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:magic...@hotmail.com] 
Sent: Monday, September 28, 2009 11:58 AM
To: pymol-users@lists.sourceforge.net
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 http://go.microsoft.com/?linkid=9656621 

--
Come build with us! The BlackBerryreg; 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 (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

Re: [PyMOL] Loading PDB Files does not work with Linux

2009-09-24 Thread Warren DeLano
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: greipel.joac...@mh-hannover.de
[mailto:greipel.joac...@mh-hannover.de] 
Sent: Thursday, September 24, 2009 5:51 AM
To: pymol-users@lists.sourceforge.net
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

 

 

 

 

 

--
Come build with us! The BlackBerryreg; 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 (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

Re: [PyMOL] Pymol segmentation fault

2009-09-24 Thread Warren DeLano
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.be...@yale.edu] 
Sent: Thursday, September 24, 2009 11:26 AM
To: pymol-users@lists.sourceforge.net
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 HelpAbout.  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]

Re: [PyMOL] mutation

2009-09-23 Thread Warren DeLano
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/pymol-users@lists.sourceforge.net/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:iitd...@gmail.com] 
Sent: Tuesday, September 22, 2009 9:28 PM
To: pymol-users@lists.sourceforge.net
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

--
Come build with us! The BlackBerryreg; 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 (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

Re: [PyMOL] dihedral angle

2009-09-22 Thread Warren DeLano
Vivek,

If there are multiple attached atoms, then there may be multiple
dihedrals present.  There is a visual indicator which shows what angle
is being measured -- do those indicator match the displayed angle? 

Cheers,
Warren

 -Original Message-
 From: Vivek Ranjan [mailto:vran...@gmail.com]
 Sent: Tuesday, September 22, 2009 1:51 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] dihedral angle
 
 Hello,
 
 When I cntrl+right-click on a bond, it is supposed to give the
 dihedral angle. However, it gives something else. E.g. the angle in
 question has actual dihedral angle of 180 degrees. However, it shows
 -56.9 degrees.
 
 Please let me know how this works ?
 
 --
 Thank you and Regards,
 
 Vivek Ranjan
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 
 



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] dash_radius

2009-09-22 Thread Warren DeLano
Craig,

In the OpenGL viewer, dashes are always drawn using line primitives, so
dash_radius has no effect until you issue the ray command.

Note that dash_width is generally preferable to dash_radius since it
controls both the OpenGL and ray-traced renditions (so long as
dash_radius is zero).

Cheers,
Warren

 -Original Message-
 From: Craig Smith [mailto:boiler...@mac.com]
 Sent: Tuesday, September 22, 2009 1:59 PM
 To: pymol-users@lists.sourceforge.net
 Cc: csmi...@lindenwood.edu
 Subject: [PyMOL] dash_radius
 
 Hello,
 
 I trying to make thicker and longer dashes for indicating distances
 for a figure I'm making.  I can make the the dashes longer with
 dash_length.  But, the dashes look very flat.  I tried making the
 dashes look rounder using dash_radius.  When I change the value I
 don't see a change in the dashes or anything else.  So, what does
 dash_radius do?  How do I make the dashes look rounder/
 
 Craig
 
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 
 



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Bond command not functioning in script

2009-09-22 Thread Warren DeLano
Stuart,
 
For what's it's worth, I'm not able to reproduce the problem:

Aside from automatic suppression of output when using the Python API,
I'm getting the exact same behavior with 

# test1.pml

cmd.pseudoatom(temp,pos=[0,0,0],name=A)
cmd.pseudoatom(temp,pos=[0,0,5],name=B)
cmd.bond(tempA,tempB)

# test2.pml

pseudoatom temp,pos=[0,0,0],name=A
pseudoatom temp,pos=[0,0,5],name=B
bond tempA,tempB

# and test3.pml

python 
cmd.pseudoatom(temp,pos=[0,0,0],name=A)
cmd.pseudoatom(temp,pos=[0,0,5],name=B)
cmd.bond(tempA,tempB)
python end

Cheers,
Warren





From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Monday, September 21, 2009 3:53 PM
To: pymol-users
Subject: [PyMOL] Bond command not functioning in script


Hello all, Warren,


I have a script which creates two pseudoatoms and a bond object
between them, but the bond step consistently fails. However, the two
pseudoatoms can be bound in the console after the script halts with the
exact same command which fails in the script:

cmd.bond(temp0A0,temp0B0)

Alternatively, cmd.do(bond temp0A0, temp0B0) fails
just the same.

The following works perfectly:
PyMOLpython
1:cmd.pseudoatom(temp,pos[0,0,0],name=A)
2:cmd.pseudoatom(temp,pos[0,0,5],name=B)
3:cmd.bond(tempA,tempB)
PyMOLpython end

So can anyone tell me why the exact same thing in a script halts
after 2?


Thanks,
Stuart Ballard
Dept. of Biochemistry
University of Wisconsin-Madison




--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Grid View of a Group

2009-09-18 Thread Warren DeLano
Yes, but it may not be the answer you want:  avoid putting those objects
into groups.  At present, groups and grids are interconnected in a
hard-coded manner.

Cheers,
Warren

 -Original Message-
 From: T. Andrew Binkowski [mailto:abinkow...@anl.gov]
 Sent: Thursday, September 17, 2009 9:18 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Grid View of a Group
 
 Hi,
 I noticed that in the Grid view that a group of objects is in each
view.
 
 For example:
 Group A has protein1, protein2 and protein 3.
 Group B has protein 4 and protein 5.
 
 In the grid view there are two views:Group A and GroupB.  Is it
 possible to have the grid view have 5 views, one of each molecule?
 
 Thanks,
 Andrew
 
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Displaying electron density from maps output by Coot.

2009-09-17 Thread Warren DeLano
To Everyone:

When posting such questions, please always indicate what specific vesion
of PyMOL you are using, since the program continues to evolve with every
release (to reflect numerous end-user suggestions, as enabled by
contributions from our sponsors.)

To Andy:

PyMOL version 1.2r1 should symmetry-expand the map assuming that density
values have been provided somewhere within the ASU.  PyMOL cannot yet
render a map straight from a reflection file.

Cheers,
Warren

 -Original Message-
 From: Andy Torelli [mailto:at...@cornell.edu]
 Sent: Thursday, September 17, 2009 11:54 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Displaying electron density from maps output by Coot.
 
 Hi everyone,
 
   I have a simple problem that has come up before (4/2/2009 post),
but
 I
 haven't found a solution yet.
   Maps written out from Coot and display in Pymol seem to be
situated
 on
 a different origin compared to the PDB coordinates.  E.g., if I:
 load my-structure.pdb
 load my-map.map, map1, 1, ccp4
 isomesh msh1,map1,1.0
   A nice electron density map is rendered (no errors), but offset
from
 the my-structure.pdb coordinates (both map and coords were output from
 Coot where they were overlaid correctly).  It sometimes works to
 explicitly indicate the residues around which to render the map:
 isomesh msh1,map1,1.0,(chain a and resi 10),carve=3.0
   In my current case however, an NCS-averaged map output from Coot
is
 not
 displaying at the desired location.  To be clear, the map can be
 displayed elsewhere in space, but it does not overlap with my
 coordinates (these are not symmetry-generated molecules, they're part
of
 the ASU).  As Robert Campbell indicated in response to the earlier
post,
 Pymol expects maps to be calculated to cover the whole molecule of
 interest.  My question is why does this map/model pair display
correctly
 in Coot while Pymol shows the map offset from the model?  Is there a
way
 to tell Pymol to place the map at a different origin (i.e. so that it
 overlays with the coordinates)?
 
   I realize this may also be a Coot question, but I'm not sure of
the
 source of the problem yet so I'm posting here.  I'll try the other bb
if
 necessary.
 
 Thanks for your help,
 -Andy Torelli
 
 ===
 Andrew T. Torelli Ph.D.
 Postdoctoral Associate
 Department of Chemistry  Chemical Biology
 Baker Laboratory, Cornell University
 Ithaca, NY 14853
 ===
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 
 



--
Come build with us! The BlackBerryreg; 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 (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


Re: [PyMOL] Pymol Symmetry Mates Naming

2009-09-17 Thread Warren DeLano
Fang,

There is no relationship between ACT and PyMOL, so one wouldn't necessarily 
expect them to match in terms of how they name the resulting objects.  However, 
I suspect there may also be a difference of intent:

Based on a quick glance at PyMOL source code, PyMOL appears to convey a 
relative cell translation (based on centers of geometries), whereas ACT may be 
returning the computation formula.

In other words, PyMOL attempts to inform the user as to whether the generated 
symmetry-related atom selection is within the same cell as the query selection 
or in one of the adjacent cells (in a translational sense).  Thus in PyMOL, the 
(overall) nearest mates (with respect to the center of geometry) will usually 
have a translation of 00 00 00, and most of the time, nearby mates will vary +1 
or -1 along a single translation. 

I'm guessing ACT simply provides the symmetry operator and the effective 
translation applied to generate the nearby mate.  That's useful for recomputing 
the mate later on, but it doesn't tell the user anything about proximity.  
PyMOL's approach is unhelpful for recomputing a mate, but one can tell from the 
object name alone which objects are likely to have the most extensive contacts 
and how they relate in a relative sense (with respect to cell translations away 
from the query selection).

Perhaps PyMOL could provide ACT-like naming through an optional setting?

Cheers,
Warren

-Original Message-
From: fangsh...@mbi.ucla.edu [mailto:fangsh...@mbi.ucla.edu]
Sent: Thu 9/17/2009 4:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Pymol Symmetry Mates Naming
 
Hi,all,

I am encountering a problem with symmetry mates generated by pymol. It
seems that the naming system in pymol and ccp4-supported ACT program are
not consistent. I have tested several pdbs in P4212 space group and
attempted to figure out the relationship between these two, but failed. I
appreciate it if you could hint me out.

Some comparisons are listed below.

ACT:NSYM ( number of symmetry operation) followed by number of
translations of one unit cell along x,y,z.

PYMOL: the first two digits are the symmetry operation. The next six
digits correspond to the relative integral unit cell translation xxyyzz.

I figured that the symmetry operation( the first two digits in pymol) is
off by 1 compared to the first digit in ACT, but have no idea how the last
six digits relates to the ACT


1em7.pdb

pymolACT
0100 21-10
0200 3220
0300 4010
0500 6000
0501 6001
---
1RH4.PDB
pymol   ACT
00-1100-1
03004000
010020-10

---
178l.pdb

0100   21-10
0001   1001
03-1   401-1
07-1   8110
0700   8111
0300   4010

Sincerely

Fang Sheng



--
Come build with us! The BlackBerryreg; 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 (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






--
Come build with us! The BlackBerryreg; 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 (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

Re: [PyMOL] movie.roll in middle of movie

2009-09-16 Thread Warren DeLano
Note that this kind of stuff is much easier in PyMOL 1.2 without any
scripting.

(ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12
under Complex Movie Creation -- login first).

Nevertheless, a possible answer is below:

Cheers,
Warren

# PyMOL .pml file (tested against PyMOL 1.2)

load $PYMOL_PATH/test/dat/1tii.pdb

unset movie_auto_interpolate
unset movie_loop

mset 1 x800 

zoom center,200 
frame 1 
mview store 

zoom center,50 
frame 120 
mview store 
frame 180 
mview store 

zoom center,15 
frame 280 
mview store 
frame 360 
mview store 

zoom center,50 
frame 400 
mview store 
frame 420 
mview store 

mview interpolate

# instead of: movie.roll 421,755 

frame 531
turn y,120
mview store

frame 642
turn y,120
mview store

frame 756 
turn y,120
mview store 
mview interpolate, power=1

zoom center,200 
frame 800 

set movie_loop
mview interpolate

mview smooth

mplay


 -Original Message-
 From: Benjamin Bobay [mailto:ben.bo...@gmail.com]
 Sent: Wednesday, September 16, 2009 8:41 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] movie.roll in middle of movie
 
 Good afternoon all -
 
 I think I have a simple question. I would like to have a series of
 zooms followed by a movie.roll and then zooming back to the start
 position. Here is what I have
 
 cmd.mset(1 x800)
 cmd.zoom(center,200)
 cmd.frame(1)
 cmd.mview(store)
 cmd.zoom(center,50)
 cmd.frame(120)
 cmd.mview(store)
 cmd.frame(180)
 cmd.mview(store)
 cmd.zoom(center,15)
 cmd.frame(280)
 cmd.mview(store)
 cmd.frame(360)
 cmd.mview(store)
 cmd.zoom(center,50)
 cmd.frame(400)
 cmd.mview(store)
 cmd.frame(420)
 cmd.mview(store)
 cmd.movie.roll(421,755)
 cmd.mview(store)
 cmd.frame(756)
 cmd.mview(store)
 cmd.zoom(center,200)
 cmd.frame(800)
 cmd.mview(reinterpolate)
 
 The problem is that is does not do the movie.roll and as the movie
 plays over and over it actually performs all the zoom actions and then
 rotates one frame and then starts the process again from that newly
 rotated frame.
 
 I would like it to perform the full rotation after the initial zoom
 and then perform the final zoom command.
 
 Any ideas where I might have messed this up?
 
 Many thanks
 Ben
 


--
 
 Come build with us! The BlackBerryreg; 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 (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
 
 
 



--
Come build with us! The BlackBerryreg; 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 (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


[PyMOL] nVidia Quadro / LCD Stereo 3D Info Link

2009-09-12 Thread Warren DeLano

For those looking to do Quadro-based stereo 3D under Windows with the new 120 
Hz LCD displays, please pay careful attention to which card you purchase if you 
expect to do stereo 3D!

nVidia has a page with the facts you need:

http://www.nvidia.com/object/quadro_pro_graphics_boards.html

Good luck!

Cheers,
Warren



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Morph Movies

2009-09-11 Thread Warren DeLano
Colin,

Can you describe what you are trying to accomplish (overall) in more
detail?

There are different approaches one could take depending on the
objective...

The simplest, but limited approach is to use the mset and madd commands
with variable numbers of frames:

# show the initial state (1) for 60 frames

mset 1 x60

# morph through to the final state (30)

madd 1 -30

# play the final state 60 times

madd 30 x60

# morph back to the initial state (1)

madd 30 -1

And so on...

Cheers,
Warren

 -Original Message-
 From: Colin Levy [mailto:c.l...@manchester.ac.uk]
 Sent: Friday, September 11, 2009 11:40 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Morph Movies
 
 Hi,
 
 Anyone know how I can include a morph in the middle of a more complex
 movie? I have generated the morph (refine_rigimol.pdb) but cant figure
 how to include this set of frames into the middle of my movie. Im
 using Macpymol 1.2 ( generated the rigimol morph in ipymol).
 
 Many thanks
 
 Colin
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Alignment Objects

2009-09-11 Thread Warren DeLano
Maia,

select all_arg_lys, resn arn+lys

Cheers,
Warren

 -Original Message-
 From: Maia Cherney [mailto:ch...@ualberta.ca]
 Sent: Friday, September 11, 2009 2:03 PM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Alignment Objects
 
 Hi,
 Is it posible in pymol to select all residues of a certain type
 automatically, like all arginines or all lysines + arginines in a
chain?
 
 Maia
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] RMS

2009-09-11 Thread Warren DeLano
Carlos, David, etc.,

From the open-source code:
  
   http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/layer4/Cmd.c

The returned rms values are as follows (in order):

return Py_BuildValue((fiififi),

  rms_info.final_rms,

  rms_info.final_n_atom,

  rms_info.n_cycles_run,

  rms_info.initial_rms,

  rms_info.initial_n_atom,

  rms_info.raw_alignment_score, 

  rms_info.n_residues_aligned);

Cheers,
Warren


From: Carlos Ríos Vera [mailto:crosv...@gmail.com] 
Sent: Saturday, August 29, 2009 4:08 PM
To: David Hall
Cc: Warren DeLano; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] RMS


2009/8/29 David Hall dwash59_2...@yahoo.com
pymol.cmd.align(%s % name_struct1, %s % name_struct2) 
oh, thanks =) 

should return a list, the first element of which is the rms, if I remember 
correctly.
Warren can probably say what the rest of the elements are.

On this note, maybe we could start documenting on the wiki what exactly all 
these commands return.  It would be very useful for scripting.
Yeah, it would be great get that information.

-David




-- 
http://crosvera.blogspot.com

Carlos Ríos V.
Estudiante de Ing. (E) en Computación e Informática.
Universidad del Bío-Bío
VIII Región, Chile

Linux user number 425502


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Rigimol

2009-09-10 Thread Warren DeLano
Colin,

Unfortunately, that is hard to do:  there is no guarantee that the
proposed (characteristic) path of motion which relates any two spacial
orientations will possess reasonable chemistry or sterics.  RigiMOL does
make an attempt to resolve simple conflicts, and the refinement step can
address minor local violations, but that is about it.

The only way to work around this problem is to manually create one or
more artificial intermediate conformations which do not exhibit such
clashes and then morph conformation 1 to the first artificial
conformation and then morph the last artificial conformation to
conformation 2.  That can be a lot of work, and it kind of misses the
point:

PyMOL (rigimol) structure morphs are only intended for visual comparison
of two or more experimentally-determined structures.  Molecular morphs
are not (and should not be portrayed as) energetically-reasonable
physiochemical paths of interconversion.

To rigorously identify reasonable (low-energy) paths of interconversion,
one must instead employ steered molecular dynamics or biased monte carlo
simulations.  Those are compute-intensive processes well beyond PyMOL's
capabilities.

Cheers,
Warren

 -Original Message-
 From: Colin Levy [mailto:c.l...@manchester.ac.uk]
 Sent: Thursday, September 10, 2009 8:59 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Rigimol
 
 Hi,
 
 I have generated a morph between two large scale domain motions using
 Rigimol . The output is fine except that the two domains pass through
 each other during their trajectory. Anyone know how to avoid this type
 of problem.
 
 Thanks
 
 Colin
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] undisplaying residues

2009-09-09 Thread Warren DeLano
Bala,
 
The trick is to leave the phosphate displayed for those residues where
the backbone should still be shown:
 
hide everything, resi 20-40 and not elem p
 
Cheers,
Warren



From: Bala subramanian [mailto:bala.biophys...@gmail.com] 
Sent: Monday, August 31, 2009 12:05 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] undisplaying residues


Friends,

I made a cartoon representation of a DNA. now i want to
undisplay the base and sugar of certain residues in the DNA. Could
someone please write me how to do the same. When i select a residue and
choose HIDE- EVERYTHING. It undisplays the cartoon of the backbone also
which i dnt want.

Regards,
Bala




--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] help about mutation

2009-09-09 Thread Warren DeLano
Chandan,
 
PyMOL's mutagenesis wizard is purely geometric, and is intended to offer
up Dunbrack rotamers as per:
 
http://dunbrack.fccc.edu/bbdep/bbdepdownload.php
 
Cheers,
Warren



From: Chandan Choudhury [mailto:iitd...@gmail.com] 
Sent: Wednesday, September 09, 2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] help about mutation



I am querious to know on what mathematical basis does the
software mutates the amino acids.
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

2009-09-09 Thread Warren DeLano
Mark,

Assuming you have one of our PyMOL 1.2r1 builds (on Mac, launch as
PyMOLX11Hybrid, not MacPyMOL), try the following command sequence:

load $TUT/1hpv.pdb

remove not (polymer or organic)

remove not byres (organic expand 4)

h_add

flag fix, not organic

show sticks, organic

orient organic

Now you can use the Builder to manipulate the ligand in the presence of
fixed protein atoms as per my previous post (see modified excerpt
below).

Everyone please keep in mind that PyMOL is just a toy modeler only
useful for setting up 3D poses that will be used as input for other
software.  If you want to do real modeling, please get Maestro,
M.O.E., Sybyl, etc.

Cheers,
Warren

Builder use:

(1) activate the builder by clicking on the Builder button on the
upper window
 
(2) click the Bumps checkbox
 
(3) click the Sculpt button
 
Now CTRL-click-and-drag (ligand) atoms (only) around in the 3D viewer.
(be careful not to click protein atoms).  You'll see the little disks
appear when the van der Waals radii overlap.  When done, click the
Clean button to minimize the structure into a nearby local minimum.   

NOTE: Ctrl-Z will actually undo conformational changes (ignore the Undo
button for now).
 
 -Original Message-
 From: Mark Benson [mailto:m...@ufl.edu] 
 Sent: Thursday, September 03, 2009 8:57 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Creating a single PDB from two PDB - ala 
 docking by hand
 
 Dear All,
 
 I am trying to build a single PDB file from two different PDB 
 files.  One PDB has a small organic ligand, and the second 
 PDB contains amino acid side chains from an active site.
 
 I load both PDB files, but I want to freeze the orientation 
 of the amino acid side chains PDB ( not move it), and then 
 place and orient the ligand PDB in a certain pose with 
 respect to the amino acid side chains.
 
 Ideally, I would then like to save the coordinates for both 
 the amino side chains and the ligand coordinates to a single PDB file.
 
 In the long run, I want to run a simple minimization on an 
 possible active site cluster and I want to get a feel for the 
 energetics of the ligand in the active site.  I don't like 
 working with MOLDEN or some of the other suites out there and 
 I wanted to try this with PyMOL.  I've gone through the 
 manual, the web, pymolwiki, the masking and protecting 
 options, and I've tried examining the use of frames and 
 split_states, but I haven't come up with anything.
 
 I've heard about a demo that Warren DeLano put on for the ACS 
 where, as part of the demo, he showed off some toy example 
 where he docked a ligand in by hand, complete with having 
 PyMOL show red/green dots for steric clashes/matches.
 
 Any ideas?
 
 -Mark
 
 
 --
 
 Let Crystal Reports handle the reporting - Free Crystal 
 Reports 2008 30-Day trial. Simplify your report design, 
 integration and deployment - and focus on what you do best, 
 core application coding. Discover what's new with Crystal 
 Reports now.  http://p.sf.net/sfu/bobj-july 
 ___
 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
 
 
 
 
 

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

2009-09-09 Thread Warren DeLano
Michael,
 
Assuming you have a PyMOL 1.2 build with the Tcl/Tk user interface
displayed:
 
Load a small-molecule or peptide structure or simply type fab 
then
 
(1) activate the builder by clicking on the Builder button on the
upper window
 
(2) click the Bumps checkbox
 
(3) click the Sculpt button
 
Now CTRL-click-and-drag atoms around in the 3D viewer.  You'll see the
little disks appear when the van der Waals radii overlap.  When done,
click the Clean button to minimize the structure into a nearby local
energy minimum.
 
Cheers,
Warren



From: Michael Lerner [mailto:mglerner+sourcefo...@gmail.com] 
Sent: Friday, September 04, 2009 6:15 AM
To: a...@artforscience.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Creating a single PDB from two PDB - ala
docking by hand


I definitely remember some mode where PyMOL would show good/bad
contacts with red/green dots, but I can't seem to figure it out now. It
was in Warren's talk as he was manually docking in a ligand. I searched,
but couldn't figure it out myself. Does anyone know how to put PyMOL
into that mode?

Cheers,

-Michael


On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg
a...@steinbergs.us wrote:


Bring up both pdb files in one session,
orient the ligand by going to editing mode and using the
shift key with
the left mouse button (3 button mouse mode) to move just
the ligand.
Once you have it in the position you want,
type select all in the command line and then hit enter,
In the A menu for the (sele) you just created pick copy
to object.
PyMOL will create a new pdb with all of the coordinates
of the two pdb
files as they are positioned on screen.
Rename it if you'd like, and save the new pdb out from
the File
menu/save molecule.



Mark Benson wrote:
 Dear All,

 I am trying to build a single PDB file from two
different PDB
 files.  One PDB has a small organic ligand, and the
second PDB
 contains amino acid side chains from an active site.

 I load both PDB files, but I want to freeze the
orientation of
 the amino acid side chains PDB ( not move it), and
then place and
 orient the ligand PDB in a certain pose with respect
to the amino
 acid side chains.

 Ideally, I would then like to save the coordinates for
both the
 amino side chains and the ligand coordinates to a
single PDB
 file.

 In the long run, I want to run a simple minimization
on an
 possible active site cluster and I want to get a feel
for the
 energetics of the ligand in the active site.  I don't
like working
 with MOLDEN or some of the other suites out there and
I wanted to
 try this with PyMOL.  I've gone through the manual,
the web,
 pymolwiki, the masking and protecting options, and
I've tried
 examining the use of frames and split_states, but I
haven't come
 up with anything.

 I've heard about a demo that Warren DeLano put on for
the ACS
 where, as part of the demo, he showed off some toy
example where
 he docked a ligand in by hand, complete with having
PyMOL show
 red/green dots for steric clashes/matches.

 Any ideas?

 -Mark




--
 Let Crystal Reports handle the reporting - Free
Crystal Reports 2008 30-Day
 trial. Simplify your report design, integration and
deployment - and focus on
 what you do best, core application coding. Discover
what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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



--
___

H. Adam Steinberg
Artist, Scientist
http://adam.steinbergs.us

Information Technology

Re: [PyMOL] broken

2009-09-02 Thread Warren DeLano
Joel,
 
When using the PyMOL launch icons, it is only possible to have one active 
version installed (registered) under Windows.  
 
However, you can (1) copy and rename the Program Files \ DeLano Scientific \ 
PyMOL folder from a correctly installed version, then (2) edit the launch.bat 
file inside the copied folder to point PYMOL_PATH at the copied location, and 
then (3) use that launch.bat to launch that copy even after removing or 
updating the main installed version.  
 
In such a situation, you can have one registered version and then any number of 
unregistered copies sitting in adjacent folders, each launchable with their own 
launch.bat script.
 
If you've got a mess at present, use the Control Panel to uninstall any 
registered copies, then delete (or rename) the Program Files \ DeLano 
Scientific \ PyMOL folder (if present) and then reinstall a fresh copy of the 
version you wish to run.
 
Cheers,
Warren
 



From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz]
Sent: Tue 9/1/2009 4:15 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] broken



Hi again folks,

 

Having tried to install both versions on my PC, then delete versions I can now 
only start pymol using the pymol.exe and any other automatic links bring the 
error:

 

Error: Pymol failed to launch Aw Shucks

 

I can get around this but it would be nice to restore to the original status 
quo.

 

Thanks for any help 

 

J

 

_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

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

 

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] APBS in pymol1.2

2009-08-27 Thread Warren DeLano
Hugo,

If building PyMOL from source, then please get APBS in source or binary form 
from the APBS sourceforge project:  http://apbs.sourceforge.net  

Cheers,
Warren

 -Original Message-
 From: Hugo G. de Teran [mailto:hugo.te...@usc.es]
 Sent: Thursday, August 27, 2009 10:06 AM
 Cc: apbs-us...@lists.sourceforge.net; pymol-users@lists.sourceforge.net
 Subject: [PyMOL] APBS in pymol1.2
 
 Hi,
 
 I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
 compiled with no problem APBS, but when I try to start a calculation I
 get the following error:
   File
 /usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py,
 line 998, in __init__
 from freemol import apbs
 ImportError: No module named freemol
 /usr/local/bin/pymol: line 2:   798 Segmentation fault
 /usr/bin/python
 /usr/local/lib64/python2.6/site-packages/pymol/__init__.py $@
 
 I have read previous posts about freemol, but I do not want to mess up
 with
 beta-versions so I only would like to make APBS work with pymol.
 
 Thanks for help,
 
 Hugo
 
 
 --
 Hugo G. de Teran, PhD.
 Parga Pondal Research fellow
 Fundación Pública Galega de Medicina Xenómica - SERGAS
 Santiago de Compostela (SPAIN)
 
 Phone +34 981563100 ext 13873
 e-mail:hugo.te...@usc.es   http://web.usc.es/~hugogdt
 
 
 
 --
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-
 Day
 trial. Simplify your report design, integration and deployment - and focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Inexplicable exception raised by cmd.color()

2009-08-26 Thread Warren DeLano
Stuart,

Hmm...it appear that QuietException is being thrown when the input pattern 
fails to match any valid object name (but without an error message being 
printed).

The easiest immediate workaround is to simply swallow the exception.

for i in range(10):
try: 
cmd.color(colors[i], sym0 + str(i) + *)
except cmd.QuietException:
pass

Cheers,
Warren


From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Wednesday, August 26, 2009 4:35 PM
To: pymol-users
Subject: [PyMOL] Inexplicable exception raised by cmd.color()

Hello Warren, all,


When attempting to execute this block of code:

    colors = 
[red,orange,yellow,green,blue,purple,salmon,grey,pink,teal,brown]
    for i in range(10):
    cmd.color(colors[i], sym0 + str(i) + *)

The following error message is displayed:

Traceback (most recent call last):
  File 
/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/parser.py,
 line 153, in parse
  File string, line 3, in module
  File 
/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/viewing.py,
 line 2425, in color
QuietException: pymol.parsing.QuietException instance at 0x104ea698

Furthermore, the object corresponding to sym00* is colored red, as expected. 
I've looked up the code in parser.py and viewing.py which generates the 
exception itself, and that has shed no light. Function color in viewing.py is 
as follows:

    # preprocess selection
    selection = selector.process(selection)
    color = _self._interpret_color(_self,str(color))
    #
    r = DEFAULT_ERROR  
    try:
    _self.lock(_self)
    r = 
_cmd.color(_self._COb,str(color),str(selection),int(flags),int(quiet))
    finally:
    _self.unlock(r,_self)
    if _self._raising(r,_self): raise QuietException
    return r

Any explanation of the bug, or an effective workaround would be greatly 
appreciated.


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] invoke ramp_new without drawing 'ramp' CGO

2009-08-25 Thread Warren DeLano
Stephen,

ramp_new ramp-name, ...

disable ramp-name

Cheers,
Warren

 -Original Message-
 From: Stephen Graham [mailto:steph...@strubi.ox.ac.uk]
 Sent: Tuesday, August 25, 2009 10:09 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO
 
 Dear all,
 
 Is it possible to invoke ramp_new and have it not draw the 'ramp' CGO?
  It's easy enough to hide the CGO when working interactively, but I've
 yet to find a way to zap it from a script (without also getting rid of
 the colour ramping itself).
 
 'hide everything, my_ramp' doesn't seem to hide the CGO, and issuing
 'delete my_ramp' from within a script kills the colour ramp before it
 gets applied (to a surface, in this case, despite the order of
 operations in the script).
 
 Thanks,
 
 Stephen
 
 --
 Dr Stephen Graham
 Division of Structural Biology
 Wellcome Trust Centre for Human Genetics
 Roosevelt Drive
 Oxford OX3 7BN
 United Kingdom
 Phone: +44 1865 287 549
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Calling scripted functions within alter_state

2009-08-24 Thread Warren DeLano
Hello Stuart,

 

By default, alter_state expressions are evaluated in the pymol
namespace of the current PyMOL instance, not the cmd (pymol.cmd)
namespace.  The reason why it works with 'run' is that run also executes
in pymol by default, and thus, includes any functions you define.

 

Try:

 

cmd.alter_state(1, copy, x,y,z = cmd.sym_partner([x,y,z],
stored.tmpOp))



instead, after using cmd.extend in your startup or GUI script.

 

Cheers,

Warren

 

 



From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Monday, August 24, 2009 3:38 PM
To: pymol-users
Subject: [PyMOL] Calling scripted functions within alter_state

 

Hello Warren, all,


I've been working on a plugin for PyMOLX11Hybrid, in which I have a few
lines of code such as:

cmd.alter_state(1, copy, x,y,z = sym_partner([x,y,z],
stored.tmpOp))

AND

cmd.alter_state(1, object, x,y,z =
cell_shift_helper([x,y,z],stored.shift))

Both those functions (sym_partner and cell_shift_helper) are extended
through cmd.extend() function, along with several others which work
perfectly well. The issue arises only when I attempt to use these
functions through a menu added to PyMOL GUI, which does not involve
issuing the run /(filepath)/(script).py command in PyMOL, but rather
initializes necessary commands on startup. I've confirmed that the
cmd.extend() calls are made properly, but I can only fix the problem by
issuing the run command independent of my initialization scripts.

Because this script is planned to be incorporated into a build of PyMOL
which will be run from a variety of file paths, I'd like to know how I
can solve this problem without simply jury rigging a run command. Is
there a way to properly make commands available within an alter_state
command without using the run command?


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Calling scripted functions within alter_state

2009-08-24 Thread Warren DeLano
Stuart,
 
Hmm...whoops, my mistake.  Cmd.extend doesn't actually add a function to
the cmd module -- only to the command keyword dictionary.
 
So, instead, set it explicitly in your .py file:
 
from pymol import cmd
 
def my_fn(...):

 
cmd.my_fn = my_fn
 
# then later on, in the menu, etc.:
 
cmd.alter_state(..., cmd.my_fn(...))
 
Cheers,
Warren
 





From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Monday, August 24, 2009 4:06 PM
To: Warren DeLano
Cc: pymol-users
Subject: Re: [PyMOL] Calling scripted functions within
alter_state


Hello Warren,


When adding in the cmd. I get these error messages:

Traceback (most recent call last):
  File string, line 1, in module
AttributeError: 'module' object has no attribute 'sym_partner'
Traceback (most recent call last):
  File string, line 1, in module
AttributeError: 'module' object has no attribute
'cell_shift_helper'

Versus the error I get with the cmd. not included:

Traceback (most recent call last):
  File string, line 1, in module
NameError: name 'sym_partner' is not defined
Traceback (most recent call last):
  File string, line 1, in module
NameError: name 'cell_shift_helper' is not defined

I'm pretty stumped at this point. Does it seem like the
pymol.cmd namespace isn't acquiring the new functions as it ought to be?


Stuart


2009/8/24 Warren DeLano war...@delsci.com


Hello Stuart,

 

By default, alter_state expressions are evaluated in the
pymol namespace of the current PyMOL instance, not the cmd
(pymol.cmd) namespace.  The reason why it works with 'run' is that run
also executes in pymol by default, and thus, includes any functions
you define.

 

Try:

 

cmd.alter_state(1, copy, x,y,z =
cmd.sym_partner([x,y,z], stored.tmpOp))



instead, after using cmd.extend in your startup or GUI
script.

 

Cheers,

Warren

 

 





From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Monday, August 24, 2009 3:38 PM
To: pymol-users
Subject: [PyMOL] Calling scripted functions within
alter_state

 

Hello Warren, all,


I've been working on a plugin for PyMOLX11Hybrid, in
which I have a few lines of code such as:

cmd.alter_state(1, copy, x,y,z =
sym_partner([x,y,z], stored.tmpOp))

AND

cmd.alter_state(1, object, x,y,z =
cell_shift_helper([x,y,z],stored.shift))

Both those functions (sym_partner and cell_shift_helper)
are extended through cmd.extend() function, along with several others
which work perfectly well. The issue arises only when I attempt to use
these functions through a menu added to PyMOL GUI, which does not
involve issuing the run /(filepath)/(script).py command in PyMOL, but
rather initializes necessary commands on startup. I've confirmed that
the cmd.extend() calls are made properly, but I can only fix the problem
by issuing the run command independent of my initialization scripts.

Because this script is planned to be incorporated into a
build of PyMOL which will be run from a variety of file paths, I'd like
to know how I can solve this problem without simply jury rigging a run
command. Is there a way to properly make commands available within an
alter_state command without using the run command?


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Zalman 3D Monitor

2009-08-24 Thread Warren DeLano
Joachim,

I think this is more an issue of driver support rather than hardware.
However, the latest drivers do not necessarily support older cards.
Please see nVidia's site for details:

http://www.nvidia.com/Download/index.aspx?lang=en-us

and click on the supported hardware tab after searching.

Cheers,
Warren


 -Original Message-
 From: Joachim Reichelt [mailto:joachim.reich...@helmholtz-hzi.de] 
 Sent: Monday, August 24, 2009 6:08 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Zalman 3D Monitor
 
 Hello,
 
 does anyone know, which Quadro card supports the Zalman mode.
 The readme states:
   Stereo options 7, 8, and 9 are only supported on G8xGL and 
 higher GPUs.
 Mode 7 is for the Zalman
 --
 Joachim
 
 --
 
 Let Crystal Reports handle the reporting - Free Crystal 
 Reports 2008 30-Day trial. Simplify your report design, 
 integration and deployment - and focus on what you do best, 
 core application coding. Discover what's new with Crystal 
 Reports now.  http://p.sf.net/sfu/bobj-july 
 ___
 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
 
 
 
 
 

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Transparent surfaces and presets

2009-08-20 Thread Warren DeLano
Jose,
 
Yes, you need to override the object-specific transparency specification from 
the preset:
 
unset transparency, object-name
 
Cheers,
Warren
 


From: Duca, Jose [mailto:jose.d...@spcorp.com]
Sent: Wed 8/19/2009 10:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Transparent surfaces and presets



Has anybody else played with presets and transparent surfaces?

When I do preset - ligand site - cartoon and then try to create a surface on 
top of it, the surface cannot be shown as transparent; while if you try other 
presets surface transparency seems to work OK.

Is there a reason for this behavior or is this a bug?

Thanks, 

José 


*
This message and any attachments are solely for the
intended recipient. If you are not the intended recipient,
disclosure, copying, use or distribution of the information 
included in this message is prohibited -- Please 
immediately and permanently delete.
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Light Command Details needed

2009-08-20 Thread Warren DeLano
The light and lightN settings are direction vectors, not coordinates.

Intensity (reflect setting) is averaged across all such directional  
sources.

It has recently been suggested that we need better control over  
lighting.

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
war...@delsci.com

(Sent from a mobile device.  Please forgive brevity and/or typos!)

On Aug 20, 2009, at 4:14 PM, Sean Moore semo...@mail.ucf.edu wrote:

 Hello,

 I could not find a way to search the archived sourceforge messages, so
 I apologize if this has been asked and answered.

 I am having trouble moving the light source before a ray command (I
 want to shine it into the crevice of a structure from behind and above
 my current view).

 I ended up using light, [1,5,-100].  I know these are X,Y,Z
 coordinates, but relative to what origin and in what units?  After
 wasting way too much time, I concluded that the values might be
 Angstroms relative to the eyes of the current view.  In examples I
 found online, the numbers are small, so this doesn't make much sense.

 Also, I see there are several light sources available.  As more and
 more lights are turned on, do the XYZ values for each additional get
 taken in order from the top of the list? Is there a way to change the
 intensity of each light in addition to its position?

 Thanks for any help.

 -Sean







 --- 
 --- 
 --- 
 -
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
 30-Day
 trial. Simplify your report design, integration and deployment - and  
 focus on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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- 
 us...@lists.sourceforge.net



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Stick Radius different for selected residues, possible?

2009-08-20 Thread Warren DeLano
Sean,

Use set_bond instead of set for per-bond properties.

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
war...@delsci.com

(Sent from a mobile device.  Please forgive brevity and/or typos!)

On Aug 20, 2009, at 4:18 PM, Sean Moore semo...@mail.ucf.edu wrote:

 Hello,
 I am trying to change the stick_radius for a few selected residues so
 they stand out relative to the surrounding mess of sticks.  If I
 command, set stick_radius, 0.75, object name, the report states
 that the stick radius was changes for the correct number of atoms in
 the file, but the displayed residues all show the original value.

 Can the stick radius be changed for a sub-set of residues and  
 rendered?

 _Sean



 --- 
 --- 
 --- 
 -
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
 30-Day
 trial. Simplify your report design, integration and deployment - and  
 focus on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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- 
 us...@lists.sourceforge.net



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] coordinate transformation

2009-08-17 Thread Warren DeLano
Vivek,
 
Create a copy of the original chain, modify the chain, and fit the copy to the 
original.  For example
 
# PyMOL 1.2 .pml input
 
fab AAA, orig
 
create copy, orig
 
set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180
 
unpick
 
fit origCA, copyCA
 
Cheers,
Warren
 


From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Mon 8/17/2009 1:44 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] coordinate transformation



Hello, 

I am trying to modify dihedral angles of a polymer chain. Once I 
perform all the required steps, I am able to orient the chain and 
align the chain along the same axis as the original chain. But 
unfortunately, pymol moves the chain to a different position. 
Basically, it changes the coordinates in a way that the center of the 
chain is at the origin. I want the chain to lie along the original 
chain with backbones coinciding with each other (almost). Is that 
possible in pymol ? 

-- 
Thank you and Regards, 

Vivek Ranjan 

-- 
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july 
___ 
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 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] Updated B-factor in trajectory

2009-08-15 Thread Warren DeLano
Oscar,
 
Use the discrete=1 option to load each PDB state as a separate set of atoms 
(instead of as a trajectory -- the default behavior).
 
load multimodel.pdb, discrete=1
 
Cheers,
Warren
 



From: S4C6Ar Chung [mailto:s4c...@gmail.com]
Sent: Sat 8/15/2009 9:44 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Updated B-factor in trajectory


Dear all,

  It seems to me that Pymol (v0.99) shows B-factor of the last frame only. How 
can I show the updated B-factor by color during trajectories. Thank you for 
your comment or help.  

Best Wishes,

Oscar

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

[PyMOL] AxPyMOL Updated: .MAE and .MOE support.

2009-08-14 Thread Warren DeLano
FYI, for Windows users who like to live on the edge...

 

AxPyMOL is the PyMOL Active Control, which makes it possible to display
live molecular content, including PyMOL PSE and PSW files inside of
PowerPoint (on Windows only).   Because we are still having trouble
getting this Windows-based component to work perfectly (i.e. without
crashing), we are continuing to give away a version of AxPyMOL as a
FREE, but UNSUPPORTED extra capability for use AT YOUR OWN RISK.

 

Today we posted an updated 1.2r1 version of AxPyMOL designed to work
with PyMOL 1.2 session and show files.  You can download it from:

 

http://delsci.com/axpymol   (file: axpymol-1_2r1-free-090814.msi)

.

Note that AxPyMOL is currently intended for use inside PowerPoint only,
with external data files stored locally in the same folder as your
presentation.  After installation, use the Control Toolbox - More
Controls button to select and drag out an AxPyMOL rectangle in your
slide, and then follow the instructions shown onscreen.  The PowerPoint
Control Toolbox can be displayed via the PowerPoint View menu -
Toolbars option.

 

By the way, one particularly useful aspect of AxPyMOL is that it can
directly read and display .MAE and .MOE files. So, if you use Chemical
Computing Group's M.O.E. or Schrodinger's Maestro, then you should be
able to load and interact with your .MOE and .MAE files directly inside
of PowerPoint using AxPyMOL.  

 

We need more feedback on how the component works out in the real-world,
so thanks in advance to those of you who try AxPyMOL and report back!

 

Cheers,

Warren

 

PS.  With Office 2007, in order to retain placeholder images, please
save your presentation in .PPT not .PPTX format.

 

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] pymol autodock plugin

2009-08-13 Thread Warren DeLano
Jed,

With the 1.2 release of PyMOL, we have completely switched over to
Numpy.  So the first thing to try is to replace:

from Numeric import *

# with

from numpy import *

Cheers,
Warren

 -Original Message-
 From: Jed Goldstone [mailto:jedg...@mit.edu]
 Sent: Thursday, August 13, 2009 1:34 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol autodock plugin
 
 The autodock plugin written by Daniel Seeliger ceased to function
(load)
 when I upgraded to Pymol 1.2r1.
 Although it is not compatible directly with Autodock 4, it did have
the
 useful functionality of
 presenting an autodock 'box' that was readily tweakable, so that the
 parameters could be exported for
 Autodock Vina. I would LOVE to have this resurrected, but I don't know
 python - can anybody help with this?
 
 The specific failures I got were:
 
 File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line
16,
 in module
 from Numeric import *
 ImportError: No module named Numeric
 Error: unable to initialize plugin 'autodock'.
 
 
 Any help would be greatly appreciated.
 
 Jed
 


--
 
 Jed Goldstone
 Research Specialist
 Woods Hole Oceanographic Institution
 Redfield 3-52 MS #32
 Woods Hole, MA  02543
 http://www.mit.edu/people/jedgold/home.html
 (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Measure surface area

2009-08-10 Thread Warren DeLano
Mirek,

PyMOL isn't the optimal tool for measuring surface area -- perhaps
others on the list can suggest good alternatives.  

The only kind of surface area PyMOL can measure well is solvent
accessible area, and it is a bit slow because all it does is sum up
partial areas associated with discrete dots on spheres (size = vdw +
solvent radius).  The basic approach is:

# (1) make sure no atoms are ignored:

flag ignore, none

# (2) delete everything except what you want to measure (important!):

remove not polymer

# (3) adjust dot settings for solvent surface area measurement:

set dot_solvent, on

set dot_density, 4

# (4) visually preview what is being measured (optional):

show dots

# (5) computer the surface area value:

print cmd.get_area()

Cheers,
Warren


 -Original Message-
 From: Mirek Cygler [mailto:mi...@bri.nrc.ca]
 Sent: Monday, August 10, 2009 11:08 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Measure surface area
 
 Hi,
   How can I get the measure in A2 of the surface area of the
surface I
 display with PyMol?
 
 Mirek
 
 


--
 
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
 Day
 trial. Simplify your report design, integration and deployment - and
focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 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
 
 
 



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] de-speculating?

2009-08-07 Thread Warren DeLano
Hi Tom,

 

set specular, 0 

 

alone should be enough to do the job if all you want to do is turn off
specular lighting -- you can ignore all those other spec_* settings.

 

However, for a more matte appearance I'd be more inclined to try:

 

set shininess,10

 

set specular_intensity, 0.2

 

# and perhaps

 

space pymol

 

# in order to lessen problems with color saturation.

 

Cheers,

Warren

 



From: Thomas Stout [mailto:tst...@exelixis.com] 
Sent: Friday, August 07, 2009 2:51 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] de-speculating?

 

 

Hi All --

 

Would anyone happen to have a recipe handy for turning down/off the
specularity (of CPK spheres especially)  in PyMOL?  I happen to be a fan
of more matte surfaces and find the highlights to be rather extreme.
I've been messing around with all of the parameters as found on
PyMOLwiki:

 

Spec direct

Spec direct power

spec power 

specular

specular intensity

 

as well as

reflect

ambient

 

et cetera

 

but haven't really found the sweet spot.

 

My current settings look like:

spec_count, 1

spec_direct, 0.0

spec_direct_power, 2000

spec_power, 2000

spec_reflect, 2

specular, 0

specular_intensity, 0.5

ambient, 0.08

reflect, 0.66


This is close, but loses some dimensionality in the CPK spheres (they
now look flat in the middle).  Oddly, the spheres look great in the GUI
(unrendered) but the ray-traced version seems to clip the shading/color
distribution badly

 

Any suggestions?

 

Thanks!

-Tom

 

 

This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] problems with apbs/pqr

2009-08-05 Thread Warren DeLano
James,

It sounds like there mayy be something other than canonical amino acids in your 
structure which might need to be removed prior to performing a calculation.  
These may be alternate conformations of amino acid side chains, ligands, or 
other unrecognized groups which cannot be processed for APBS.

Cheers,
Warren

-Original Message-
From: James Whittle [mailto:whit...@mit.edu]
Sent: Wed 8/5/2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] problems with apbs/pqr
 
Hi all,

My apologies if this has been covered by this list before, but I  
couldn't find mention of it:

I'm trying to calculate an electrostatic surface for my protein. The  
APBS Tools plug-in crashes with the message:

WARNING: 502 atoms did not have formal charges assigned
WARNING: 1051 atoms did not have properties assigned

This happens whether I use a pqr file from PDB2PQR or the PyMol  
generated PQR.

I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though  
on a linux machine, and got the same error. This plug-in works fine  
with several other coordinate files. I tried removing the chain ids  
from the pdb file, but that did not help.

Can anyone offer any advice on this?

--James

--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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






--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july___
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

Re: [PyMOL] PI-bond distance

2009-08-04 Thread Warren DeLano
 I´m desperate to get some information about PyMol, I need to know it is 
 possible to measure a distance from a middle of a pi-bond to another atom?

No, this isn't possible directly, but you can do something like the following:

# copy  paste demo snippet

load $TUT/1hpv.pdb

pseudoatom pi_cent,b/53/cg+cz

dist pi_centps1, b/met`46/ce

Cheers,
Warren


Sent: Tuesday, August 04, 2009 6:03 AM
To: info; sales
Subject: Re: PyMol

Hello,
 
I´m desperate to get some information about PyMol, I need to know it is 
possible to measure a distance from a middle of a pi-bond to another atom?
 
Hope to get answer soon as possible!
 
Best regards, E.



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Python Function with Unlimited Positional Arguments

2009-08-02 Thread Warren DeLano
Sean,

You need a keyword argument list as well, so that the effective PyMOL
class instance (_self) can be passed in by keyword (actual use of _self
is only strictly required when you have multiple PyMOLs active in a
single Python interpreter).

# pml input:

python
 
def my_fn(*arg, **kwd):
   print arg

cmd.extend(my_fn, my_fn)

python end

my_fn my_arg_1, my_arg_2

# PyMOL output:

('my_arg_1', 'my_arg_2') 

Cheers,
Warren



From: Sean Law [mailto:magic...@hotmail.com] 
Sent: Sunday, August 02, 2009 10:56 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Python Function with Unlimited Positional
Arguments


Hi PyMOLers,

I am trying to write a python script that will allow a user to
provide an unlimited number of positional arguments for a function.  I
am use to the following scheme for defining a function and its
arguments:

def some_function ( x, y, z, file=false):

#DO SOMETHING

return

Where x, y, and z are required arguments and file=false is an
optional argument.  I came across the following page pertaining to
Python:


http://www.linuxtopia.org/online_books/programming_books/python_programm
ing/python_ch15s09.html

See Unlimited Number of Positional Arguments Values

There it explains that one could use the following syntax:

def some_function ( *args):

print arg[0]

return

Now, when put this in a script and call the function in PyMOL it
spits out the following error:

Traceback (most recent call last):
  File /pymol/./modules/pymol/parser.py, line 254, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
TypeError: some_function() got an unexpected keyword argument
'_self'

Is the *args method simply not possible in PyMOL?  I tried
using **args which worked nicely for keyword arguments.

Any help would be greatly appreciated.  Thank you for your time.

Sean




Stay on top of things, check email from other accounts! Check it
out. http://go.microsoft.com/?linkid=9671350  



--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
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


Re: [PyMOL] Getting SCALE record within PyMOL

2009-07-20 Thread Warren DeLano
Stuart,

 

Sorry, there is no way to do this at present (short of manually editing
text files).  But thank you for the suggestion!


Cheers,

Warren

 



From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Saturday, July 18, 2009 1:58 PM
To: pymol-users
Subject: [PyMOL] Getting SCALE record within PyMOL

 

Hello Warren, all,


Is there any way to read the SCALE record from the PDB file of a protein
loaded into PyMOL either within PyMOL or in a script? Alternatively,
even getting the filepath from an object name so that the PDB can be
accessed directly by a script would be sufficient.


Thanks,
Stuart Ballard

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

[PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization

2009-07-17 Thread Warren DeLano
Just to make sure everyone understands:

 

Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS
ONLY due to the need of a special USB driver for the 3D Vision sync
emitter.  Unfortunately, you cannot sync a digital 120 Hz LCD using the
old stereo analog DIN sync connector - it just doesn't work.

 

Please do not waste money right now buying a 120 Hz LCD if you use Linux
or Mac OS (even if you have a Quadro card), or if you use a Windows
laptop (without a Quadro graphics chip).  You will be disappointed --
the display will not do 3D with your system, and nVidia has not promised
support for 120 Hz LCD synchronization on platforms other than Windows.
That may change, but then again, it might not.

 

Accordingly, our recommended stereo 3D solution for Mac, Linux, and for
Windows systems without Quadro cards is the Zalman M220W LCD display.
You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL
PLATFORMS (including most laptops). No special graphics hardware or
drivers are required to use the Zalman with PyMOL.
http://pymol.org/zalman

 

Cheers,

Warren

 

 

 

 

 

 

 

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

Re: [PyMOL] WARNING: No Mac or Linux support for 120 HzLCD synchronization

2009-07-17 Thread Warren DeLano
Malcolm,

 

Yes, a reasonable person might expect it to work...but we have tried on both 
Mac and Linux, and it doesn't work with either CystalEyes or NuVision hardware. 
 I don't think Modeline timings have any meaning when generating a true digital 
display signal, but regardless, the actual sync signal output is not correct.

 

My naïve guess is that this is because the analog sync signal from the Quadro 
DIN connector is based off of the SVGA vertical blanking interval and has 
nothing to do with the digital-only display signal required by these displays.  
Note that these displays do not accept an analog SVGA signal - they have only a 
pure-digital DVI-D connector - not DVI-I, and they have no HD15 SVGA input.  
They also require a full dual link DVI-D cable with all pins present.  It seems 
that the dual-link capacity is used to carry the 120 Hz signal (perhaps split 
over two regions of the display? or with the left 60Hz on one channel and the 
right 60Hz on the other?). 

 

Furthermore, even if the Quadro sync was correct, the polarization of the old 
shutter glasses conflicts with that of the liquid crystal.  I also observed 
that light from the Samsung LCD seems to interfere with the old CrystalEyes 
sync signal.  Of course, the other problem is that affordable Quadro cards do 
not even come with a sync connector.

 

So in summary, there seem to be many problems combining modern LCDs with old 
stereo 3D hardware, which presumably explains in part why nVidia decided to 
introduce a new USB emitter and glasses for use with these displays.

 

Cheers,

Warren

 



From: Davis, Malcolm [mailto:malcolm.da...@bms.com] 
Sent: Friday, July 17, 2009 2:00 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] WARNING: No Mac or Linux support for 120 HzLCD 
synchronization

 

Has anyone tried these with the old CrystalEyes glasses?  We are looking to get 
one of these to try, but it is hard to understand why there should even be a 
need for a different graphics driver or a newer Quadro card to use it that way. 
 The FX1100 cards we still have in some of our Linux workstations can be 
configured to send a 1600x1...@100hz signal to our old IBM c220p monitors and 
the 100Hz limit was from the monitor not the graphics card.  So other than 
needing to specify the Modeline manually in the X config files, why shouldn't 
this just work?

 

Malcolm

 

 

From: Warren DeLano [mailto:war...@delsci.com] 
Sent: Friday, July 17, 2009 12:23 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization

 

Just to make sure everyone understands:

 

Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due 
to the need of a special USB driver for the 3D Vision sync emitter.  
Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog 
DIN sync connector - it just doesn't work.

 

Please do not waste money right now buying a 120 Hz LCD if you use Linux or Mac 
OS (even if you have a Quadro card), or if you use a Windows laptop (without a 
Quadro graphics chip).  You will be disappointed -- the display will not do 3D 
with your system, and nVidia has not promised support for 120 Hz LCD 
synchronization on platforms other than Windows.  That may change, but then 
again, it might not.

 

Accordingly, our recommended stereo 3D solution for Mac, Linux, and for Windows 
systems without Quadro cards is the Zalman M220W LCD display.  You get fewer 
pixels for stereo 3D, but it works great with PyMOL on ALL PLATFORMS (including 
most laptops). No special graphics hardware or drivers are required to use the 
Zalman with PyMOL.  http://pymol.org/zalman

 

Cheers,

Warren

 

 

 

 

 

 

 

 



This message (including any attachments) may contain confidential, proprietary, 
privileged and/or private information. The information is intended to be for 
the use of the individual or entity designated above. If you are not the 
intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
distribution or other use of this message or any attachments by an individual 
or entity other than the intended recipient is prohibited.

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

Re: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization .

2009-07-17 Thread Warren DeLano
Minor correction, for geeks who care about technical trivia.  I
previously wrote:

 I don't think [VGA] Modeline timings have any meaning when 
 generating a true digital display signal...

Apparently the modeline timings do still have significance in terms of
digital information transport, which mimicks analog signal timing, but
there is no hard and fast correlation between data transport and what
actually happens on the screen at any moment in time.  A digital display
can in principle update whatever it wants, whenever it wants, once the
information has arrived.  

Cheers,
Warren
 


--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge
___
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


Re: [PyMOL] PyMOL 1.2r1 error report

2009-07-16 Thread Warren DeLano
Stuart,

 

Thank you for the reports, and sorry to hear you're having trouble.
Please allow me to draw your attention to the Bug Reporter link on the
PyMOL main page (www.pymol.org http://www.pymol.org/ ).  The direct
link is:

 

http://sourceforge.net/tracker/?atid=104546group_id=4546func=browse

 

One advantage of using the bug reporter system is that you can submit
accompanying script or data files which reproduce the problem.  

 

With respect to meshes, rendering of meshes is not generally broken in
1.2r1, so there must be something specific about your input which is
triggering the crash.  We may need an example file, or at least a PDB
code with associated commands, to reproduce the problem.  Likewise,
fetch is known not to be generally broken, so we may need more
information about reproducing the problem.

 

[For what it's worth, I just confirmed that:

 

fetch 1fjf, async=0

 

show mesh

 

ray

 

runs fine with 1.2r1].

 

As for selector, it is not a supported part of the supported Python
cmd API, but rather, an internal module.  In other words, you should
not ever need to be importing it.  Operationally speaking, the Python
cmd. api is defined by the file modules/pymol/api.py, and virtually
all public symbols should be accessed as methods or submethods of this
module.

 

Cheers,

Warren

 



From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Thursday, July 16, 2009 2:14 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] PyMOL 1.2r1 error report

 

Hello all, Warren,


With the new PyMOL version, myself and others at the lab have found an
issue with ray tracing of mesh representations causing memory
utilization errors.

With parameters identical to those used in previous versions of PyMOL,
1.2r1 has crashed when ray tracing isomesh generated isosurface meshes.
A memory allocation error is given, but a lack of memory does not appear
to be the real issue, as PyMOL crashes long before all RAM is consumed,
and the same error is given when we attempt to run this process on a
machine with 12GB of RAM.

There have also been a few minor issues with the fetch command. Namely,
we've seen intermitent inexplicable failure of the fetch command, while
simultaneously using it in another version of PyMOL with no issue.

Also, some older scripts now need more specific import statements to
utilize certain build-in PyMOL functionality. For example, I did not
need to state from pymol import selector to use the selector.process()
function in other versions of PyMOL, but this is not the case with the
new version. Does this reflect changes in the cmd API setup?


Regards,
Stuart Ballard

 





--

Message: 1
Date: Thu, 9 Jul 2009 13:34:53 -0700
From: Warren DeLano war...@delsci.com
Subject: [PyMOL] PyMOL 1.2r1 Released
To: pymol-users@lists.sourceforge.net
Message-ID:

896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local
Content-Type: text/plain; charset=us-ascii

Greetings,



Mac, Windows, and Linux builds for 1.2r1 were posted early this
morning.
Current subscribers can download them via



Direct download: http://delsci.com/ip/12  or via online docs:
http://delsci.info/dsc/ip



As usual, I recommend caution with upgrading.  Please don't
upgrade
right before a major talk or presentation, unless you have time
to test
everything thoroughly beforehand.  There were many last-minute
changes
made after the last beta, so some glitches are to be expected.



Please try loading your important PyMOL session and show files
into the
new version and report any serious problems.  At least one
additional
revision of the 1.2 release is anticipated before the end of the
summer.



Enabling information about the new capabilities of 1.2 will be
forthcoming over the next month, and will likely consist of a
series of
screencast demonstrations and tutorials.  There is a lot of new
stuff to
communicate!



Cheers,

Warren





 

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists

Re: [PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit

2009-07-16 Thread Warren DeLano
Valentina,

 

PyMOL has been known to work great with the Samsung 2233rz for quite
some time, but nVidia had not publicly released any of the required
190-series drivers until today.  

 

Note that, officially speaking, you will need a Quadro graphics card in
order to do OpenGL-based stereo 3D.  nVidia does not support OpenGL
stereo 3D on GeForce cards, and the required control panel options for
configuring OpenGL stereo 3D will be absent.

 

More details about today's release will be posted soon...

 

Cheers,

Warren

 



From: Valentina Corradi [mailto:valentina.corr...@gmail.com] 
Sent: Thursday, July 16, 2009 4:25 PM
To: pymol-users@lists.sourceforge.net
Subject: 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce
3D Vision Kit

 

Dear PyMOL users,

my research group is interested in using 3D stereo visualization with
PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia
GeForce GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung
SyncMaster 2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07014.h
tml ), says that only Zalman monitor can be used with PyMOL for 3D
stereo visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on
June 30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the
latest one (1.2r1) for 3D stereo visualization together with the OS and
Nvidia kit we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (Vista info)!

2009-07-16 Thread Warren DeLano
Today nVidia issued their first public beta release of their 190-series
driver.  Although this release is officially for GeForce hardware, it
seems to work fine for Quadro cards as well.  So, if you have the
following hardware setup, then you can at last now use PyMOL in Stereo
3D at full 1680x1050 resolution on a 120 Hz LCD.  Here is what you need:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows Vista 32 bit or 64 bit

 

- The driver download (warning ~230 MB ZIP file):

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.htm
l
http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.ht
ml 

 

I personally confirmed today that this download enables PyMOL to run in
Stereo 3D on a 2233RZ with a Quadro 570 graphics card and GeForce 3D
Vision hardware under Windows Vista 32 bit.  Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Extract the contents of the downloaded ZIP file.

 

3. Run the enclosed Launch.exe, click the first option to install the
graphics driver, and then reboot when prompted (essential!).

 

5. Again run Launch.exe, click the second option to install the 3D
Vision Software, and connect the USB emitter when prompted. Confirm that
the stereo 3D tests work as expected, then exit the wizard by clicking
Finish.

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to Generic active stereo (with
NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to
on, click Apply, and then close the NVIDIA control panel.

 

7. Reboot (again, essential -- OpenGL stereo 3D will not actually work
until after you reboot.)

 

8. Launch PyMOL 1.2r1 for Windows.  You should get the message: OpenGL
quad-buffer stereo 3D detected and enabled.

 

9. Now load a PDB file and issue stereo on.  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD!  

 

Cheers,

Warren

 

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (WinXP info)!

2009-07-16 Thread Warren DeLano
Continuing coverage...

 

Although GeForce 3D Vision is not officially supported for Windows XP, I
managed to get it to work with PyMOL.   Assuming you have the following
setup:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows XP 32 bit 

 

You need the 190-series graphics driver for Windows XP:

 

http://www.nvidia.com/object/winxp_190.38_beta.html

 

and the 190-series 3D Vision driver for Windows Vista:

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_190.38.html

 

Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Run the Window XP graphics driver installer and reboot.

 

3. Launch the Vista 3D Vision driver in order to extract the files you
need, but do not yet click Next on the Welcome page...just leave it open
for now...do not close the installer.

 

4. Plug in the USB emitter.  Windows should throw up the Found New
Hardware Wizard**. Choose No, not this time and go to the Next page.
Select install from a list or specific location and click Next to
continue.  Choose Search for the best driver, include this specific
location..., and click Browse.  Now comes the hard part: you must
select the folder which contains the file nvstusb.inf.  On my system,
that file was unpacked into c:\Documents and
Settings\Warren~1~000\Locals~1\Temp\pft16~tmp - your copy may be in a
similar location.  You may need to use Windows Search to find the file.
Once you've chosen the correct folder, click Ok and then Next.  You may
then be asked to locate nvstusb.sys, which should be in the same
folder.  Click Ok once you've found the file, and then Finish.  This
should complete installation of the USB driver.

 

**If Windows doesn't throw up the Found New Hardware Wizard, use the
Device Manager to locate the device and then update the driver for the
device using the same process described above.

 

5. Now allow the 3D Vision Installer to continue.  Since your on XP, not
Vista, it will complain and throw up one warning and one error message,
but it should still complete.  Reboot when prompted.  The rest of the
instructions are basically the same as for Vista:

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to Generic active stereo (with
NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to
on, click Apply, and then close the NVIDIA control panel.

 

7. Launch PyMOL 1.2r1 for Windows.  You should get the message: OpenGL
quad-buffer stereo 3D detected and enabled.

 

8. Now load a PDB file and issue stereo on.  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD using Windows XP!  

 

Cheers,

Warren

 

 

--
Enter the BlackBerry Developer Challenge  
This is your chance to win up to $100,000 in prizes! For a limited time, 
vendors submitting new applications to BlackBerry App World(TM) will have
the opportunity to enter the BlackBerry Developer Challenge. See full prize  
details at: http://p.sf.net/sfu/Challenge___
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

Re: [PyMOL] unexpected EOF while parsing

2009-07-07 Thread Warren DeLano
 To include
 blocks you have to do more than indentation. You have to put a slash
 in front of the for statement and end all but the of the blocks with a
 backslash. 

Actually, nowadays you can just wrap Python blocks with the statements: 
python and python end.  For example:

# example pymol script an embedded Python block

dele all
reset

python

for i in range(1,10):
   print i
   cmd.pseudoatom(pos=[i,i,i],color='auto')

python end

zoom (all), 10
show spheres
rock

# use box wizard to create some walls:

refresh
wizard box
cmd.get_wizard().set_mode(walls)
wizard
dele box_points

turn x,-70
turn y,-30
turn z,-10

ray

# end example

Cheers,
Warren


 -Original Message-
 From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
 Sent: Tuesday, July 07, 2009 9:16 AM
 To: jo...@uchicago.edu; pymol-users
 Subject: Re: [PyMOL] unexpected EOF while parsing
 
 Hi Jouko,
 
 You were writing a python script. Now Pymol API can handle basic
 Python, but it's not a one-to-one Python interpreter. To include
 blocks you have to do more than indentation. You have to put a slash
 in front of the for statement and end all but the of the blocks with a
 backslash. When trying to do programming, better stick to Python. Save
 the following as script.py and use run script.py from within Pymol or
 just issue 'pymol script.py':
 
 from pymol import cmd
 
 z=-7.653
 inc=0.5
 Sections=100
 FirstToLast=range(100)
 for j in FirstToLast:
   pdb=/home/jouko/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_
 + str(z) + .pdb
   cmd.load(pdb)
   cmd.do(@/home/jouko/b_color8.plm)
   cmd.png(pdb+.png)
   cmd.delete(pdb)
   z=z+inc
   print z
 
 ###
 
 Cheers,
 
 Tsjerk
 
 On Tue, Jul 7, 2009 at 5:47 PM, jo...@uchicago.edu wrote:
  Thanks to you and Gregori Gerebtzoff, I can now load the pdb,
  color the image, and save it as a picture.  However I can only
  do that for the first cross section.  I am still getting the
  unexpected EOF error.  I did have the line indented after the
  loop.  I think that maybe when I copied and pasted the script
  to the email the tab was lost, so this time I am adding the
  script file as an attachment.
 
  Thanks,
 
  Jouko
 
  P.S.  I found that @/home/jouko/b_color8.plm and
  cmd.do(@/home/jouko/b_color8.plm)  both work.
 
   Original message 
 Date: Tue, 7 Jul 2009 09:17:53 +0200
 From: Tsjerk Wassenaar tsje...@gmail.com
 Subject: Re: [PyMOL] unexpected EOF while parsing
 To: jo...@uchicago.edu
 Cc: pymol-users@lists.sourceforge.net
 
 Hi Jouko,
 
 I think you went through the Python and Pymol tutorials a bit
  too fast
 ;) You're writing a Python script to be loaded with 'run'.
  That means
 you have to adhere to Python API and can't use the Pymol specific
 language. E.g. you can't use 'png pdb', but have to use
  'cmd.png(pdb)'
 in which case pdb will be treated as a variable rather than a
  string.
 And you definitely can't use '@something.pml'.
 
 The EOF is because you violated one of the basic rules of
  Python: it
 uses indentation to structure programming. Thus after a for
  loop you
 have to start an indented line.
 
 Furthermore:
 - range by default starts from 0: range(0,Sections) is equal
  to range(Sections)
 - load will strip .pdb from the filename, so you wouldn't be
  able to
 use the variable pdb to point to it; better specify a name
 - png probably adds .png to the name, but it's good to make
  sure it does
 
 ###
 
 from pymol.cgo import *
 import colorsys,sys,re
 from pymol import cmd
 
 z=-8.153
 inc=0.5
 Sections=100
 for j in range(0, Sections):
 
  pdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-
 4a/DensityCube_Lysozyme2-4a_+
 str(z) + .pdb
     load(pdb,pdb)
     cmd.do(@c:/b_color8.plm)
     cmd.png(pdb+.png)
     cmd.delete(pdb)
     z=z+inc
 
 Hope it helps,
 
 Tsjerk
 
 On Tue, Jul 7, 2009 at 3:17 AM, jo...@uchicago.edu wrote:
  I am new to pymol and python.  I have a number of cross
  sections of lysozyme.  I want to display them one by one,
  color them using a script file that I have written earlier,
  and save the image.  I have written a script file that I had
  hoped would do this.  I have a couple problems with script
  file, but the one that is frustrating me the most is that
  immediately after the beginning of for loop pymol says that
  there in an unexpected EOF.  The other problem is that when I
  try to use the variable pdb, pymol does not use the value of
  the variable, but the variable name itself.  I have pasted my
  script file below and part of the log file.
 
  from pymol.cgo import *
  import colorsys,sys,re
  from pymol import cmd
 
  z=-8.153
  inc=0.5
  Sections=100
  for j in range(0, Sections):
 
 
  pdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-
 4a/DensityCube_Lysozyme2-4a_
  + str(z) + .pdb
       load pdb
      �...@c:/b_color8.plm
       png pdb
       delete pdb
       z=z+inc
 
 
  PyMOL@c:/Users/jouko/CrossSections.plm
  PyMOLfrom pymol.cgo import *
  

Re: [PyMOL] subversion revision for 1.2?

2009-07-04 Thread Warren DeLano
Michael,

Sorry for the confusion:  

Although 32-bit 1.2r0 Windows and Linux builds have been announced, Mac builds, 
64-bit Windows  Linux builds, as well as final updates to the open-source code 
 build scripts are still in process.   Once the complete 1.2 release is ready, 
that fact will be announced on pymol.org.

Cheers,
Warren

-Original Message-
From: Michael Banck [mailto:mba...@debian.org]
Sent: Sat 7/4/2009 7:37 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] subversion revision for 1.2?
 
Hi,

maybe I missed it in the announcement, but what is the subversion
revision for 1.2?

I can't find a tag in the repo, nor any obvious commit message.


Thanks,

Michael

--
___
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






--
___
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

Re: [PyMOL] DCD Trajectories and Movie Panel

2009-07-02 Thread Warren DeLano
Sean,

The movie panel operates on movie frames, not trajectory states, so you need to 
create a relationship between them.  A one-to-one relationship can be created 
using the Python command:

cmd.mset(1 -%d % cmd.count_states())

Or alternatively, you can use the new Movie - Program - State Loop or State 
Sweep menu items.

Cheers,
Warren

-Original Message-
From: Sean Law [mailto:magic...@hotmail.com]
Sent: Thu 7/2/2009 7:12 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] DCD Trajectories and Movie Panel
 

Hi all,

I am playing around with the new PyMOL 1.2 release and was hoping to use the 
Movie Panel in conjunction with a loaded DCD trajectory file.  However, after 
loading the MD trajectory and setting movie_panel to 1 I don't see the 
prescribed time line below the viewing area.  Of course, if I add a camera loop 
then the movie panel appears.  Is this a potential use for the movie panel or 
is this functionality not available yet?

Thank you for your time.

Sean

_
Create a cool, new character for your Windows LiveT Messenger. 
http://go.microsoft.com/?linkid=9656621


--
___
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

Re: [PyMOL] ZM-M220W and TRIMON ZM-M220W

2009-06-30 Thread Warren DeLano
The difference?  $769.99 - $354.99 = $415 exactly.

 

But seriously, this is a question for Dell, not pymol-users.

 

For what it is worth, mid $300's is the current per-unit pricing for the
ZM-M220W display - but they originally hit the market at a 2-3X higher
price, so one of those links is probably old.

 

Cheers,

Warren

 

 



From: Lihua Wang [mailto:mole...@gmail.com] 
Sent: Tuesday, June 30, 2009 11:44 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ZM-M220W and TRIMON ZM-M220W

 

Hi PyMOL users:

 

I am looking into stereo 3D on LCD monitors. What is the difference
between  ZM-M220W and TRIMON  ZM-M220W?

 

 

http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?
c=usl=ens=hiedcs=RC956904sku=A2550610
http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx
?c=usl=ens=hiedcs=RC956904sku=A2550610 

 

and

 

http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?
c=usl=ens=hiedcs=RC956904sku=A1997135
http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx
?c=usl=ens=hiedcs=RC956904sku=A1997135 

 

Thanks!

 

--
___
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

[PyMOL] Your Mom is Open Source (Fun stuff -- hey, it's Friday!)

2009-06-26 Thread Warren DeLano
Have you heard?

You Mom Is Open Source! http://winkleman.com/exhibition/view/1628 

No, that is not some veiled condemnation of maternal virtue, but rather
the provocative title of Shane Hope http://www.shanehope.info 's
latest Solo Exhibition at the Winkleman Gallery
http://www.winkleman.com  in New York City.

Shane is a modern artist (a digital surrealist?) who applies PyMOL and
other open-source tools as traditional artists employ pencil or
paintbrush. Not to be missed from his current expo are two works with
familiar titles for PyMOL users:

   ray_trace_mode=2
http://winkleman.com/artist/seriesworkview/1406/376/10324/2 

and 

   cartoon_trace_atoms=1
http://winkleman.com/artist/seriesworkview/1406/376/10326/2 

though my personal favorite is his 

   Junk DNA Sculptural Ontogenesis
http://winkleman.com/artist/seriesworkview/1406/376/10327 

 

Shane's other recent mol mods can be browsed
http://winkleman.com/artist/seriesview/1406/376  online. 

 

Congratulations to Shane Hope on this latest exhibition! 

 

Cheers,

Warren

 

http://shanehope.info http://shanehope.info/ 

 

http://www.winkleman.com http://www.winkleman.com/ 

 

--
___
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

Re: [PyMOL] is font_color universal?

2009-06-24 Thread Warren DeLano
Tom,

# per-object:

set label-color, color-name, object-name

# per-atom:

set label-color, color-name, selection

# for example

fragment arg

label all, name

set label_color, yellow, arg

set label_color, red, elem c

# note that the other label settings may not work below the per-object level

Cheers,
Warren



From: Thomas Stout [mailto:tst...@exelixis.com] 
Sent: Wednesday, June 24, 2009 10:59 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] is font_color universal?

 
Hi All -- 
 
In my reading of the documentation/wiki and experimenting with settings, it 
looks like font_color is universal, meaning that you can only have one font 
color for ALL objects in a session file -- correct? 
 
I was hoping to have different color labels for different objects, so if 
anybody knows how to manage that (without resorting to Photo$hop), I'd be very 
interested to hear!  (I'd like the labels to be the same color as the 
alpha-Carbon to which they are attached)
 
Cheers,
Tom
 
 


--
___
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


Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...

2009-06-22 Thread Warren DeLano
Hari  Others,

At this moment, the LCD flat panel to buy for use with PyMOL is the Zalman 
M220W (scan-line interleaved, passive stereo 3D).

Unfortunately, last week's nVidia driver updates do not contain the expected 
support for 120 Hz LCDs from Samsung and ViewSonic.  However, my personal 
belief and conviction is that they will be supported in the near future, and 
that they will work with PyMOL -- at least under Windows XP and Vista.

Furthermore, having personally tested the stereo 3D capabilities of both the 
Samsung and ViewSonic displays with nVidia 3D Vision emitter and glasses, the 
Samsung 2233RZ is so much better at generating a clean, nearly ghost-free 
stereo 3D effect, that I plan to strongly recommend the Samsung 2233RZ over the 
ViewSonic VX2265wm, if (when) nVidia releases their stereo-3D-capable OpenGL 
drivers for 120Hz LCDs.  

Whereas the Samsung's 3D effect is equal to, if not better than a CRT, the 
ViewSonic is clearly inferior to both -- at least in my experience, using 
nVidia 3D Vision glasses.  Hopefully ViewSonic's future 120 Hz products will be 
more competitive!

So recap:

If you need stereo 3D-capable today, then buy a Zalman M220W 
http://pymol.org/zalman .  That display will work with Mac, Windows, and Linux, 
without need of any special graphics card.  You give up half the vertical 
resolution, but hey -- it works today, and it works quite well.

However, if you expect to need a stereo 3D capable LCD in the future, then plan 
on buying a 120Hz Samsung 2233RZ with the nVidia 3D Vision glasses and an 
updated Quadro graphics card.  This will give you same high-quality, 
full-resolution 3D effect as a Crystal Eyes-based CRT setup.  But please do 
wait until the critical drivers are released before spending any money, and 
realize that you may be stuck using Windows for the time being.

Cheers,
Warren

 -Original Message-
 From: hari jayaram [mailto:hari...@gmail.com] 
 Sent: Monday, June 22, 2009 7:16 AM
 To: PyMOL-users@lists.sourceforge.net; c...@jiscmail.ac.uk
 Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
 
 Hi
 I am wondering if there is a linux nvidia driver update or 
 any other hack that allows Crystal Eyes 3 stereo products to  
 work with the LCD 120Hz flat panel monitors.
 
 I should have read Warrens warning post  (Dated Jan 23 , 2009 
 [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet) , before 
 purchasing the Viewsonic VX2265wm 120Hz LCD. But my CRT died 
 last week and since I was addicted to pymol/coot-in stereo ( 
 with Crystal Eyes 3 ) ,  I rushed out and bought this 120 Hz 
 LCD monitor.
 
 Of course things dont work . And I am wondering if there is 
 any update from nvidia or any other workaround  that allows 
 me to get stereo on this setup.
 
 Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: 
 Quadro FX 4600
 OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: 
 Crystal Eyes 3 with 3pin mini din connector
 
 
 Thanks for your help in advance
 Hari Jayaram
 Brandeis University
 
 
 
 On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano 
 war...@delsci.com wrote:
 
  Donnie,
 
  This tripped me up for a while too, but I think the stereo 
 DIN is an 
  output (for projector,  Z-screens, etc.) not an input.  
Suffice it to 
  say that the nVidia USB dongle does not work (in my hands, with or 
  without USB power) as a VESA-based emitter the way we 
 apparently both 
  hoped it would!
 
  Cheers,
  Warren
 
   -Original Message-
   From: Donnie Berkholz [mailto:dberkh...@gentoo.org]
   Sent: Tuesday, February 10, 2009 9:49 AM
   To: Warren DeLano
   Cc: PyMOL-users@lists.sourceforge.net
   Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
  
   On 23:26 Thu 22 Jan     , Warren DeLano wrote:
I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision 
bundle today ($599 for a 120 Hz LCD display with one 
 pair of glasses).
  
I was very much hoping that this new display would nevertheless 
also work with existing nVidia Quadro-based Mac or 
 Linux systems 
with existing emitters and glasses running existing 
 OpenGL software.
  Sadly,
this does not seem to be the case due at least in part 
 to the fact
  that
the phase of the sync signal coming out of the Quadro card does 
not match the update phase of the LCD display.  In 
 addition, light 
from
  the
display itself seems to corrupt the sync signal for 
 StereoGraphics 
glasses.
  
   Hi Warren,
  
   Did you happen to try the new glasses + emitter with a CRT? I am 
   particularly curious whether this works on Linux, or whether it 
   needs some sort of USB driver stubs so that Linux knows 
 what to do 
   with
  these
   devices.
  
   It comes with a stereo-DIN cable so it seems like it could work, 
   provided the emitter can get power via USB and the glasses can 
   charge via USB.
  
   If the new glasses can work with a CRT, then at least we 
 could buy 
   stereo bundles now and use

Re: [PyMOL] Animation/ Matrix Question

2009-06-19 Thread Warren DeLano
Zach,

Can you wait a week or two?   This sort of thing is about to get 100X easier in 
PyMOL...

Cheers,
Warren

-Original Message-
From: Charlop-Powers, Zachary [mailto:zachary.charlop-pow...@mssm.edu]
Sent: Thu 6/18/2009 10:11 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Animation/ Matrix Question
 
Hi,

I would like to create a movie where my molecules are moving at the same time 
that the camera is moving in/around/though them. 

I have been using Slerpy to get the movement effects that i would like but I 
would also like to make the molecules undergo translation/rotation functions 
relative to one another. Slerpy also has this capability but limited for what I 
would like to do.  Using the  Slerpy 'saction' command I can have the option to 
change elements in the scene but then Slerpy will interpolate 50 frames until 
the next shot and I don't get to coordinate my molecular movements with my 
camera movements. I can approach this if I shorten the default frame number in 
slerpy (take steps of 5 or something like that) but then I don't get to take 
advantage of Slerpy's smooth camera motion. 

Although there may be many ways to do what I would like to do, does anyone have 
any experience with outputting the view matrix  (get_view)  for each of 
slerpy's camera positions? If so,  I could do a dry run with Slerpy, use 
get_view to output the view matrix and then combine each view with a 
rotate/translate function in order to get the effect I am looking for. The only 
problem is that I haven't figured out how to do that. Perhaps someone on this 
list already has?

Hmmm. I think the most logical way would be if there were some script that 
could get_view for each frame of the final movie. Any help/suggestions would be 
greatly appreciated.

best,
zach cp

Thank You Warren; Pymol is a great program and the PyMolWiki has become a 
fantastic resource for newbies.

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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






--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects___
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

Re: [PyMOL] Disabling cartoon_highlight_color

2009-06-11 Thread Warren DeLano
set cartoon_highlight_color, default

 



From: Roger Rowlett [mailto:rrowl...@mail.colgate.edu] 
Sent: Thursday, June 11, 2009 7:17 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Disabling cartoon_highlight_color

 

How do you disable cartoon_highlight_color once it has been enabled? The
command set cartoon_highlight_color, off does not work in 1.2b3, as
suggested by the Pymol wiki. Pymol just reports that off is not a
color.

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: rrowl...@mail.colgate.edu

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects___
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

Re: [PyMOL] How to plot residu with a number 9999

2009-06-09 Thread Warren DeLano
Stephane,

Okay, I see -- you're just spilling the top digit into the chain id.  So for 
residue 10123, you can issue a selection like:

zoom chain 1 and resi 0123

Looking over the code, I note that PyMOL has a hardcoded resi field of just 
four characters plus a null.  Given how C compilers pack structs, I suspect we 
could extend that to 7 characters plus a null without adversely impacting 
PyMOL's memory use characteristics...

Cheers,
Warren

 -Original Message-
 From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr]
 Sent: Tuesday, June 09, 2009 12:34 AM
 To: Warren DeLano
 Subject: RE : [PyMOL] How to plot residu with a number  
 
 Warren,
 
 Thank you for your response
 
 Indeed, you are right and this is a well known limitation of the pdb
 format. But as you can see with the file i join in this message obtained
 from a molecular dynamics software, you can also use the field 22 - 26 to
 extend the resSeq to 9 and this with pymol and rasmol.
 
 
 
 --
 Stéphane Abel, PhD
 CEA Saclay DSV/IBITEC-S/SB2SM
 91191 Saclay, FRANCE
 website: http://www.st-abel.com
 --
 
 
 
  Message d'origine
 De: Warren DeLano [mailto:war...@delsci.com]
 Date: mar. 09/06/2009 02:01
 À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net
 Objet : RE: [PyMOL] How to plot residu with a number  
 
 Stephane,
 
 As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB
 residue identifier field is only four characters wide.
 
 So how could you possibly have a PDB file with residue identifiers
 larger than ?
 
 Cheers,
 Warren
 
  -Original Message-
  From: Stephane Abel [mailto:stephane.a...@cea.fr]
  Sent: Monday, June 08, 2009 7:30 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] How to plot residu with a number  
 
  Hi pymol users
 
 
  It seems that the command select, residue xxx to plot residue xxx
 where
  xxx is greater than  does not work in pymol version 0.99rc6
 
 
  Indeed for a pdb file with ~ 13800 residue, if i use the command:
 
 
  select water1846, residue 1846 - the water molecule with the residue
  number 1846 is plotting
 
 
  But when i use the same command (say select water11100, residue 11100)
 
 
  for plotting the residue 11100 the previous command does not work
 
 
  How to tackle this problem. Thanks in advance for your help
 
 
  Stephane
 
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] How to plot residu with a number 9999

2009-06-09 Thread Warren DeLano
Whoops, I misread my own code:

In fact, PyMOL already supports 5-character residue identifiers!  Here's how 
you use them, assuming a PDB file where the resi field spills into chain:

load your_file.pdb

alter all, resi=chain+resi

sort

# and off you go

indicate resi 1:

zoom resi 10123

Cheers,
Warren


 -Original Message-
 From: Warren DeLano 
 Sent: Tuesday, June 09, 2009 12:26 PM
 To: ABEL Stephane 175950
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] How to plot residu with a number  
 
 Stephane,
 
 Okay, I see -- you're just spilling the top digit into the 
 chain id.  So for residue 10123, you can issue a selection like:
 
 zoom chain 1 and resi 0123
 
 Looking over the code, I note that PyMOL has a hardcoded resi 
 field of just four characters plus a null.  Given how C 
 compilers pack structs, I suspect we could extend that to 7 
 characters plus a null without adversely impacting PyMOL's 
 memory use characteristics...
 
 Cheers,
 Warren
 
  -Original Message-
  From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr]
  Sent: Tuesday, June 09, 2009 12:34 AM
  To: Warren DeLano
  Subject: RE : [PyMOL] How to plot residu with a number  
  
  Warren,
  
  Thank you for your response
  
  Indeed, you are right and this is a well known limitation 
 of the pdb 
  format. But as you can see with the file i join in this message 
  obtained from a molecular dynamics software, you can also use the 
  field 22 - 26 to extend the resSeq to 9 and this with 
 pymol and rasmol.
  
  
  
  --
  Stéphane Abel, PhD
  CEA Saclay DSV/IBITEC-S/SB2SM
  91191 Saclay, FRANCE
  website: http://www.st-abel.com
  --
  
  
  
   Message d'origine
  De: Warren DeLano [mailto:war...@delsci.com]
  Date: mar. 09/06/2009 02:01
  À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net 
 Objet : RE: 
  [PyMOL] How to plot residu with a number  
  
  Stephane,
  
  As per http://www.wwpdb.org/documentation/format32/sect9.html , the 
  PDB residue identifier field is only four characters wide.
  
  So how could you possibly have a PDB file with residue identifiers 
  larger than ?
  
  Cheers,
  Warren
  
   -Original Message-
   From: Stephane Abel [mailto:stephane.a...@cea.fr]
   Sent: Monday, June 08, 2009 7:30 AM
   To: pymol-users@lists.sourceforge.net
   Subject: [PyMOL] How to plot residu with a number  
  
   Hi pymol users
  
  
   It seems that the command select, residue xxx to plot residue xxx
  where
   xxx is greater than  does not work in pymol version 0.99rc6
  
  
   Indeed for a pdb file with ~ 13800 residue, if i use the command:
  
  
   select water1846, residue 1846 - the water molecule with the 
   residue number 1846 is plotting
  
  
   But when i use the same command (say select water11100, residue 
   11100)
  
  
   for plotting the residue 11100 the previous command does not work
  
  
   How to tackle this problem. Thanks in advance for your help
  
  
   Stephane
  
  
  
 
 
 
 --
 
 Crystal Reports - New Free Runtime and 30 Day Trial Check out 
 the new simplified licensing option that enables unlimited 
 royalty-free distribution of the report engine for externally 
 facing server and web deployment.
 http://p.sf.net/sfu/businessobjects
 ___
 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
 
 
 
 
 

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] Distinct labels on white background (ray tracing)? (JimRemington)

2009-06-08 Thread Warren DeLano
Sorry, I accidentally forgot to CC the list on my response to Jim.  Yes,
the culprist is one of the 600+ settings (ray_label_specular to be
exact).  Recipe for jet-black labels below...


fragment methane
 
zoom
 
label all, name
 
bg white
 
unset depth_cue

unset ray_label_specular
 
set label_color, black
 
set label_font_id, 7
 
set label_size, 30
 
ray


Cheers,
Warren


 -Original Message-
 From: Jason Vertrees [mailto:j...@cs.dartmouth.edu]
 Sent: Monday, June 08, 2009 5:12 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Distinct labels on white background (ray tracing)?
 (JimRemington)
 
  Message: 1
  Date: Wed, 03 Jun 2009 13:52:25 -0700
  From: Jim Remington reming...@molbio.uoregon.edu
  Subject: [PyMOL] Distinct labels on white background (ray tracing)?
  To: pymol-users@lists.sourceforge.net
  Message-ID: 4a26e289.3040...@molbio.uoregon.edu
  Content-Type: text/plain; charset=ISO-8859-1; format=flowed
 
  I would like to have distinct labels for hydrogen bond lengths on a
  ball-and-stick image
  with white background (as required for publication in a particular
  journal). No matter
  what I do, the labels come out washed out and usually light grey.
This
  includes
  experimenting with label color, size and font (is there a bold
font?).
 
  For the record, I've tried the clues in the wiki and forum, for
example
  I've turned off
  ray-trace-fog, depth cueing, ray-shadowing and very high resolution
 images.
  I still get light grey labels on white background. Does anyone have
  further suggestions?
 
  Thanks much, Jim
 
 Jim,
 
 I can also reproduce this.  I think it's either a bug or one of the
600
 settings has a default that is throwing this off.  If you need this
ASAP
 and don't mind the extra steps, here's a workaround.  You make two
 photos and composite them.  Here's how (with comments):
 
 # prepare the scene; and hide your labels
 set ray_opaque_background, 1;
 bg_color white;
 hide labels;
 
 # set up your scene  ray trace it
 png layer1.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI
 
 # now hide everything but the labels and ray trace the scene
 # in mode3--which does make black labels:
 set ray_opaque_background 0;
 hide;
 show labels;
 set ray_trace_mode, 3;
 
 # do NOT move the scene in any way; ray trace it
 png layer2.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI
 
 # go into the GIMP or Photoshop and composite the images
 # (put layer2 on top of layer1) or if you have ImageMagick
 system composite layer2.png layer1.png finalImage.png
 
 # [optional] Send me $50.  :-)
 
 
 To get an idea of compositing, check out the 2nd example image/script
 from:
   http://www.pymolwiki.org/index.php/Gallery
 
 Lastly, Warren I'm sure has a one-line answer, but this should get you
 going.
 
 HTH,
 
 -- Jason
 
 --
 
 Jason Vertrees, PhD
 
 Dartmouth College : j...@cs.dartmouth.edu
 Boston University : jas...@bu.edu
 
 PyMOLWiki : http://www.pymolwiki.org/
 


--
 
 OpenSolaris 2009.06 is a cutting edge operating system for enterprises
 looking to deploy the next generation of Solaris that includes the
latest
 innovations from Sun and the OpenSource community. Download a copy and
 enjoy capabilities such as Networking, Storage and Virtualization.
 Go to: http://p.sf.net/sfu/opensolaris-get
 ___
 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
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] map smaller than in Coot

2009-06-08 Thread Warren DeLano
Greetings Michael,

I suspect this is a question PyMOL automatically normalizing the map
values, whereas the other programs might not.  For historical reasons,
PyMOL's default behavior is to normalize CCP4 map values upon loading.
To prevent this, issue:

unset normalize_ccp4_maps

before loading the map file.

Cheers,
Warren

 -Original Message-
 From: Michael Oldham [mailto:mlold...@purdue.edu]
 Sent: Monday, June 08, 2009 1:18 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] map smaller than in Coot
 
 I have a map that I generated from VOIDOO for a cavity in my protein
 structure. In Coot and O it shows up as the same size and fully covers
 a ligand visible in my structure. In PyMol it is visibly smaller and
 does not cover the ligand as well. does anyone have any idea of a
 parameter that can be changed to show the map as it looks in Coot.
 
 Thanks
 
 


--
 
 Crystal Reports - New Free Runtime and 30 Day Trial
 Check out the new simplified licensing option that enables unlimited
 royalty-free distribution of the report engine for externally facing
 server and web deployment.
 http://p.sf.net/sfu/businessobjects
 ___
 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
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] How to plot residu with a number 9999

2009-06-08 Thread Warren DeLano
Stephane,

As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB
residue identifier field is only four characters wide.  

So how could you possibly have a PDB file with residue identifiers
larger than ?  

Cheers,
Warren

 -Original Message-
 From: Stephane Abel [mailto:stephane.a...@cea.fr]
 Sent: Monday, June 08, 2009 7:30 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] How to plot residu with a number  
 
 Hi pymol users
 
 
 It seems that the command select, residue xxx to plot residue xxx
where
 xxx is greater than  does not work in pymol version 0.99rc6
 
 
 Indeed for a pdb file with ~ 13800 residue, if i use the command:
 
 
 select water1846, residue 1846 - the water molecule with the residue
 number 1846 is plotting
 
 
 But when i use the same command (say select water11100, residue 11100)
 
 
 for plotting the residue 11100 the previous command does not work
 
 
 How to tackle this problem. Thanks in advance for your help
 
 
 Stephane
 
 


--
 
 OpenSolaris 2009.06 is a cutting edge operating system for enterprises
 looking to deploy the next generation of Solaris that includes the
latest
 innovations from Sun and the OpenSource community. Download a copy and
 enjoy capabilities such as Networking, Storage and Virtualization.
 Go to: http://p.sf.net/sfu/opensolaris-get
 ___
 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
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] Hi all...

2009-06-08 Thread Warren DeLano
As for the your general question:  can you import pymol; from pymol
import cmd; pymol.finish_launching(); etc?

Answer 1: Yes, if you manually compile PyMOL open-source code into an
existing Python interpreter. 

Or 

Answer 2: Yes, if you run your Python script using PyMOL's built-in
Python interpreter (launch PyMOL as follows):

./pymol your-script.py  # with full 3D GUI
  
./pymol -qc your-script.py  # command-line only (in a terminal)

Or 

Answer 3: Yes, if you call your Python script from a PyMOL script via
the run or spawn commands inside PyMOL.

However,

Answer 4: No, if you want precompiled PyMOL build to work with an
external precompiled Python build.  This approach has proved impractical
due unavoidable application binary interface (ABI) version mismatches
between PyMOL, Python, and the host environment.
 
As for your specific question, this is something you could do with a
plain old script without even introducing the complexity of Python:


load $TUT/1hpv.pdb, query

remove not polymer

create tmp, query

set dot_solvent

get_area tmp, load_b=1

# threshold on what one considers an exposed atom (in A**2):

remove tmp and b2.5

tmp_dict = {}

iterate tmp, tmp_dict[(chain,resv)]=1

select exposed 

exposed = tmp_dict.keys()

exposed.sort()

print Solvent exposed residues (chain,residue):

for res in exposed: print res

select exposed, query in tmp

dele tmp


# visual confirmation

color white

color red, byres exposed

set sphere_solvent

as spheres

orient


Cheers,
Warren

 -Original Message-
 From: Yasser Almeida Hernandez [mailto:pedro...@fenhi.uh.cu]
 Sent: Friday, June 05, 2009 9:18 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Hi all...
 
 I want to make a python script to list the surface residues of a
 protein. The idea is import the pymol module inside the script,
 receive the pdb file to be analyzed and run the pymol's commands to do
 this task. It is possible..? the script is to tun in a classical
 terminal...
 
 Thanks...
 
 
 Correo FENHI
 
 
 
 


--
 
 OpenSolaris 2009.06 is a cutting edge operating system for enterprises
 looking to deploy the next generation of Solaris that includes the
latest
 innovations from Sun and the OpenSource community. Download a copy and
 enjoy capabilities such as Networking, Storage and Virtualization.
 Go to: http://p.sf.net/sfu/opensolaris-get
 ___
 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
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing 
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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


Re: [PyMOL] Principal Axes of Rotation

2009-06-03 Thread Warren DeLano
Sean,
 
orient selection
 
followed by a 90 degree rotation about the camera's ]X-axis should give you a 
couple of views with the desired characteristics.
 
turn x, 90
 
Cheers,
Warren
 



From: gilleain torrance [mailto:gilleain.torra...@gmail.com]
Sent: Wed 6/3/2009 5:02 AM
To: pymol-users
Subject: Re: [PyMOL] Principal Axes of Rotation



Hi,

I might be wrong, but might it be that you need the axis through the
structure that minimises the distance of all the points to it. Or, to
put it another way, the least-square-plane through the structure, the
normal to that plane, and a thir axis perpendicular to both.

If this is the case, you are in luck, as I already made such a thing:

  http://pymolwiki.org/index.php/Bounding_Box

this script was designed to make a minimal bounding box (not just an
axis-aligned one). I think that it does this, although my geometry is
not good enough to know if I am right.

Anyway, you already mention joining opposite faces of the box - well
just use the axes calculated half-way through the first function.

Hope this helps.

gilleain

On Tue, Jun 2, 2009 at 11:41 PM, Sean Law magic...@hotmail.com wrote:
 Hi,

 For the past couple of days I've been trying to find a way to rotate an
 object in order to show a front and side profile for publication.  However,
 rotating with respect to the x, y, or z axes does not produce the correct
 result (even after moving the center-of-mass of the structure to the
 origin).  What I need is a way to determine the principal axes of rotation
 for a given selection so that rotation about any one of these axes does not
 produce a wobble effect.  I've even tried drawing a rectangular box around
 the object and then drawing an axes through the centroids of opposing faces
 but I still see wobbling.  I've basically exhausted all of my attempts at
 this problem.

 Any help or suggestions would be greatly appreciated.

 Sean

 
 Create a cool, new character for your Windows Live(tm) Messenger. Check it out
 --
 OpenSolaris 2009.06 is a cutting edge operating system for enterprises
 looking to deploy the next generation of Solaris that includes the latest
 innovations from Sun and the OpenSource community. Download a copy and
 enjoy capabilities such as Networking, Storage and Virtualization.
 Go to: http://p.sf.net/sfu/opensolaris-get
 ___
 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


--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
___
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





--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] Principal Axes of Rotation

2009-06-03 Thread Warren DeLano
Sean,
 
Apologies for not understanding...
 
You definitely need orthoscopic, but there's more to it. 
 
set orthoscopic
 
fetch 1bna, async=0
 
orient 1bna
 
cmd.matrix_copy(None,1bna)
 
reset
 
from chempy.cpv import average
 
cmd.origin(position=average(*cmd.get_extent()))

 
center origin
 
# now, the maximum extent in the X Y planes should be invariant to 180 degree 
rotations about the Y or X axes respectively.
 
Cheers,
Warren
 
 
 



From: Sean Law [mailto:magic...@hotmail.com]
Sent: Wed 6/3/2009 12:28 PM
To: matthew.frank...@imclone.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Principal Axes of Rotation


Matt,

Unfortunately, as a somewhat experienced PyMOL user, I already have 
orthoscopic view turned off (along with depth cue turned off).  Thanks for 
your suggestion though.

Sean

 Subject: Re: [PyMOL] Principal Axes of Rotation
 To: magic...@hotmail.com
 CC: pymol-users@lists.sourceforge.net
 From: matthew.frank...@imclone.com
 Date: Wed, 3 Jun 2009 15:13:25 -0400
 
 
 
 Sean Law magic...@hotmail.com wrote on 06/03/2009 12:52:45 PM:
 
  Warren,
 
  After a deja vu moment, I realized that I had posed a similar
  question to you before about this (although, we didn't really have a
  resolution then). I had already tried your suggestion before I had
  posted to the mailing list but perhaps an example would be more
  appropriate in terms of what I'm seeing.
 
 
 (snip - 180 degree rotation around x axis)
 
  7) You will now see that after 2 turns that the O3' atom is situated
  well past the vertical (imaginary) line drawn by the position of
  your cursor on your screen
 
 
 This is almost certainly due to the perspective view which is on by
 default. As atoms move closer to your viewpoint, they appear bigger, and
 the inter-atomic distances also appear bigger, just as in real life. So,
 an atom which is far away and at a particular (apparent) x position, will
 be farther away from the center of the screen once you've done your 180
 degree rotation.
 
 This drawing mode was created to make structures look more realistic. If
 you don't like it, you can turn it off: under Display, choose
 Orthoscopic view. That should eliminate your wobble effect.
 
 
 Hope that helps,
 
 Matt
 
 --
 Matthew Franklin , Ph.D.
 Senior Scientist, ImClone Systems,
 a wholly owned subsidiary of Eli Lilly  Company
 180 Varick Street, 6th floor
 New York, NY 10014
 phone:(917)606-4116 fax:(212)645-2054
 
 
 Confidentiality Note: This e-mail, and any attachment to it, contains
 privileged and confidential information intended only for the use of the
 individual(s) or entity named on the e-mail. If the reader of this e-mail
 is not the intended recipient, or the employee or agent responsible for
 delivering it to the intended recipient, you are hereby notified that
 reading it is strictly prohibited. If you have received this e-mail in
 error, please immediately return it to the sender and delete it from your
 system. Thank you.
 




Attention all humans. We are your photos. Free us. 
http://go.microsoft.com/?linkid=9666044 
--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] reorienting a chain

2009-06-03 Thread Warren DeLano
Vivek,
 
Please see the example I posted today for Sean Law -- the cmd.matrix_copy 
command embedded therein (followed by reset) performs exactly the action 
you're looking for.
 
Cheers,
Warren



From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Wed 6/3/2009 9:26 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] reorienting a chain



Hello Warren,

Thank you very much for your advice.

I guess I was not being very clear. what i meant was that i would also
like to save the coordinates of this reoriented polymer. Let me be
clear:

I have a polymer aligned along y-axis. I change some of the dihedral
angles. As a result, the chain is pointing in some arbitrary
direction. So, I want to re-orient the polymer along the y-axis and
then save the coordinates of this reoriented polymer. I used the
command orient from the installed pymol on my system (version
1.0r2). But when I try to save the polymer, it still saves the same
coordinates as the one before reorientation.

Please let me know if something can be done ?

Thank you,

Vivek

On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano war...@delsci.com wrote:
 You can save a copy of the original and then superimpose the copy back onto
 it

 # using fab command from the latest 1.2 beta to create poly-ala

 fab  AAA, pol

 # create copy of the polymer

 create copy, pol

 # adjust a torsion

 set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60

 # superimpose back on the original copy

 fit pol, copy

 Cheers,
 Warren

 
 From: Vivek Ranjan [mailto:vran...@gmail.com]
 Sent: Tue 6/2/2009 10:57 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] reorienting a chain

 Hello,

 I have a long chain of polymer. Once I change some dihedral angles, it
 orients in a different direction. I would like the chain to be
 reoriented in the same direction as it initially was. Is it possible
 within pymol ? How can I achieve this ?

 --
 Thank you and Regards,

 Vivek Ranjan

 --
 OpenSolaris 2009.06 is a cutting edge operating system for enterprises
 looking to deploy the next generation of Solaris that includes the latest
 innovations from Sun and the OpenSource community. Download a copy and
 enjoy capabilities such as Networking, Storage and Virtualization.
 Go to: http://p.sf.net/sfu/opensolaris-get
 ___
 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







--
Thank you and Regards,

Vivek Ranjan

--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
___
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





--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] Selection/remove bug?

2009-06-02 Thread Warren DeLano
Hi Jim,
 
B all by itself is a selection language keyword for the b-factor property:
 
select high_b_factor, b  50
 
So just use a different selection name:
 
select chB, chain B
 
Cheers,
Warren

 


From: Jim Remington [mailto:reming...@molbio.uoregon.edu]
Sent: Tue 6/2/2009 2:08 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection/remove bug?



Dear All:

One of our crystals contains a dimer in the asymmetric unit, with chains
labeled A and B.
If I want to display chain b, I can first select chain a and remove the
atoms, using the commands:

select a, chain a
( (a) action menu: remove atoms)
Result: atoms removed

However, if after beginning anew or otherwise, I want to display chain
a, the same commands fail.

select b, chain b
( (b) action menu: remove atoms)

Result:
Selector-Error: Malformed selection.
( b )--

Any advice would be appreciated!

Thanks, Jim

--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
___
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





--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] reorienting a chain

2009-06-02 Thread Warren DeLano
You can save a copy of the original and then superimpose the copy back onto it
 
# using fab command from the latest 1.2 beta to create poly-ala
 
fab  AAA, pol
 
# create copy of the polymer
 
create copy, pol
 
# adjust a torsion
 
set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60
 
# superimpose back on the original copy
 
fit pol, copy
 
Cheers,
Warren
 



From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Tue 6/2/2009 10:57 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] reorienting a chain



Hello,

I have a long chain of polymer. Once I change some dihedral angles, it
orients in a different direction. I would like the chain to be
reoriented in the same direction as it initially was. Is it possible
within pymol ? How can I achieve this ?

--
Thank you and Regards,

Vivek Ranjan

--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
___
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





--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] wrl and dx files problem

2009-06-02 Thread Warren DeLano
Raluca,
 
PyMOL transforms the output geometry in order to deliver a default view 
matching what's seen in the viewer window.  To prevent that, you'll need to 
effectively eliminate PyMOL's camera transformation by restoring to a 
transformation-less identity matrix:
 
cmd.reset()
cmd.origin(position=[0,0,0])
cmd.center(origin)
cmd.move('z',-cmd.get_view()[11])
 
At this point, there may not be anything visible in the viewer window, but the 
output WRL file will have the same coordinate system as the input PDB, DX map, 
etc.
 
Cheers,
Warren
 



From: Raluca Mihaela ANDREI [mailto:r.and...@sns.it]
Sent: Fri 5/22/2009 10:51 AM
To: pymol-users
Subject: [PyMOL] wrl and dx files problem




Hello!
I save the surface of a protein as a .wrl, then I calculate
the electrostatic potential and I save again the surface of
the protein. I import the two surfaces in Blender (a 3D
software) and I see that they are shifted. Why does this
happen? Then I open the .wrl files and the .dx file in another
home made program and I see that the surfaces and the grid
have not the same origin. Can somebody tell me why the surface
and the grid don't have the same origin and what do I have to
do in order to fix this?

Thank you,
Raluca

--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers  brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, 
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA,  Big Spaceship. http://www.creativitycat.com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users





--
OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
looking to deploy the next generation of Solaris that includes the latest 
innovations from Sun and the OpenSource community. Download a copy and 
enjoy capabilities such as Networking, Storage and Virtualization. 
Go to: http://p.sf.net/sfu/opensolaris-get___
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

Re: [PyMOL] update mesh level to custom value after deleting map object

2009-05-28 Thread Warren DeLano
Hari,

isolevel mesh-name, level

Cheers,
Warren


From: hari jayaram [mailto:hari...@gmail.com] 
Sent: Wednesday, May 27, 2009 12:29 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] update mesh level to custom value after deleting map object

H
I have an old pymol session file .
I have a mesh object displayed whose level I can manipulate in predetermined 
ways using the Action-Level-menu. I however want to pick a level different from 
the menu options provided . 

A further complication is that I have deleted the original map object and want 
to avoid going looking for it.

Is there a way to pick a level for a mesh object that is not pre-programmed 
into the Action menu .

Thanks 
Hari


 


--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT 
is a gathering of tech-side developers  brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,  
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
Group, R/GA,  Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
___
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


Re: [PyMOL] Load Selection

2009-05-26 Thread Warren DeLano
Sean, 
 
You can save some time  a lot of memory by loading the file and
removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
 
load 1E3M.pdb; remove not A-C+F//

Cheers,
Warren
 



From: Sean Law [mailto:magic...@hotmail.com] 
Sent: Tuesday, May 26, 2009 9:10 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Load Selection


Hi PyMOLers,

I was wondering if there is a way to load part of a PDB file if
you know a priori what you want thereby saving time/memory?

Currently, I have a system that is ~160,000 atoms (protein-DNA
complex with explicit water molecules taken from an MD simulation).
When I load more than 10 structures I start running out of memory so I
was hoping that there was some way that I could specify on the command
line to only load the protein/DNA but not the water.  Right now, I have
to pre-process each pdb file before loading which seems tedious.  I was
hoping that there was already some built-in function in PyMOL that can
handle this immediately by invoking something like:

load 1E3M.pdb, selection=c. a+b or c. e+f

Thank you for your time.

Sean




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

--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT 
is a gathering of tech-side developers  brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,  
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
Group, R/GA,  Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] surface of ligand

2009-05-26 Thread Warren DeLano
set surface_mode, 1

Cheers,
Warren

 -Original Message-
 From: chaix denis [mailto:ch...@cbs.cnrs.fr]
 Sent: Tuesday, May 26, 2009 3:55 PM
 To: pymol-users@lists.sourceforge.net
 Cc: Chaix Denis; support; pymol-users@lists.sourceforge.net
 Subject: [PyMOL] surface of ligand
 
 Dear users
 
 How can I obtain the surface of a ligand in protein pdb file.
 I just need the simple surface, i doesn't need in this case, the
 electrostatic surface.
 Thanks
 


--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT 
is a gathering of tech-side developers  brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,  
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
Group, R/GA,  Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
___
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


[PyMOL] FYI: Mid-range stereo 3D projector / emitter / glasses bundle

2009-05-20 Thread Warren DeLano
Stereo-3D-enthusiasts,

 

Ad include below, just FYI -- no affiliation with DeLano Scientific --
though we have used products from these companies and found them
effective.

 

It appears that you can now set up a small conference room for
active-stereo 3D visualization with glasses for 4 people for a mere
$7,500 USD.  I suspect you could get another half dozen glasses for a
total cost under $10k (not including a stereo-3D capable PC of course).
For small groups in small or mobile settings, this bundle might make
more sense than the high-end Christie Mirage / Z-Screen / polarized
glasses solution.

 

Cheers,

Warren

--

LIGHTSPEED DESIGN AND RealD PRO INTRODUCE 3D BUNDLE

 

Offer Includes DepthQ HD 3D Projector, CrystalEyes 3 Eyewear and EXXR
Emitter

   

BELLEVUE, WA - May 20, 2009: Lightspeed Design, Inc., a developer of 3D
stereoscopic projectors, and RealD PRO, a division of leading 3D
technology and visualization equipment provider, RealD, are pleased to
announce the release of the NEW DepthQ(r)/RealD PRO Bundle.

 

The DepthQ(r)/RealD PRO Bundle consists of a DepthQ(r) HD 3D projector,
four CrystalEyes(r) 3 professional liquid crystal shutter eyewear, and
an EXXR long range wide-angle IR Theatre Emitter for a total price of
$7500. In addition, customers purchasing a DepthQ(r)/RealD PRO Bundle
from Lightspeed will be able to purchase additional CrystalEyes(r) 3
eyewear under special pricing.

 

Chris Ward, President of Lightspeed Design, Inc. said Combining these
state-of-the-art stereoscopic products into one package brings added
value to our professional customers who need high quality, stereoscopic
HD 3D technology.

 

 DepthQ(r) HD 3D Projectors offer rock-solid, 120Hz stereo 3D at
1280x720 resolution. These bright, professional-level 3D projectors can
easily display 9 ft (2.7m) wide 3D high-definition images using the
latest Texas Instruments DLP(r) and BrilliantColor(tm) technologies for
stunning colors and a 2000:1 contrast ratio.

 

CrystalEyes(r)3 is the industry standard for engineers and scientists
who develop, view and manipulate 3D computer graphics models in CAVEs,
theaters and immersive environments. CrystalEyes(r) 3 is the leader for
3D visualization in molecular modeling, virtual prototyping, and aerial
photography/mapping.

 

The EXXR Long Range Theatre Emitter offers a 130 degree infrared spread
transmitting up to 70ft (21m) making it the most powerful active eyewear
synchronization emitter in the world.

 

To order now and take advantage of this special bundle pricing, please
contact Lightspeed at http://www.depthq.com/contact.html or call our
sales department at +1-425-637-2818.

 

 Subscribe in a reader to DepthQ Latest News

 

About Lightspeed Design, Inc.

 

Lightspeed is one of the world's premiere designers of stereoscopic 3D
presentations and software technologies, with considerable technical
expertise in projection, optics and electronics. Clients include Pfizer,
Intuitive Surgical, Microsoft, Harvard  Munich Universities, US Army,
NASA, JPL, DreamWorks SKG, IMAX, and Walt Disney Animation.

 

Lightspeed's headquarters is in Bellevue, Washington, USA. For more
information, visit us at http://www.lightspeeddesign.com or contact the
company directly at sa...@lightspeeddesign.com or +1-425-637-2818.

 

About RealD PRO

 

RealD PRO is the professional division of RealD, a leading 3D technology
developer and supplier of 3D visualization equipment solutions including
3D-enabling eyewear, infrared eyewear synchronization devices, 3D-ready
DLP(r) TV kits, industrial projectors, monitor peripherals, passive 3D
solutions and 3D format converters. RealD PRO is a one-stop source for
3D information, equipment and technical support, enabling 3D for
everything from virtual prototyping to entertainment content creation.
http://www.reald.com 

 

 

Press contact:

Chris Ward

Lightspeed Design, Inc.

+1-425-637-2818

 

DepthQ(r) is a registered trademark of Lightspeed Design, Inc.
CrystalEyes(r) is a registered trademark of RealD.  Digital Light
Processing, DLP(r) and BrilliantColor(tm) are registered trademarks of
Texas Instruments. All rights reserved. 

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


[PyMOL] When in doubt, go with nVidia.

2009-05-20 Thread Warren DeLano
Folks,

 

For quite some time now, we have ourselves experienced and continued to
receive complaints regarding graphics artifacts and other glitches with
ATI/AMD Radeon HD graphics chips on multiple platforms.  Though we
haven't had time to investigate everything to our satisfaction, it is
worth noting that such issues are conspicuously absent from those using
recent nVidia and Intel graphics chips, and that they also do not occur
with older ATI chips -- only the newer HD -branded models.

 

Therefore, if you are given a choice with a new purchase today, we
strongly recommend going with nVidia-based graphics chips for running
PyMOL.  Intel chips work fine too though they aren't typically as fast.

 

Just to be clear, we don't know for certain yet whether the fault lies
with PyMOL, with the OpenGL drivers, or with the ATI graphics chips
themselves. but if you simply buy nVidia, then you can entirely avoid
having to deal with AMD/ATI-specific OpenGL problems.  Eventually these
problems will likely be worked out - the chips are just glitchy, not DOA
- but there is a lot to be said for deliberately avoiding problematic
scenarios altogether.

 

Cheers,

Warren

 

 

 

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Documentation and advice for external GUI Movies commands?

2009-05-19 Thread Warren DeLano
Jean,

 

Assuming that you are using the most recent PyMOL 1.2 beta build, first
create a Scene for each display you wish to show.  

 

(To do that, show everything the way you want and then select Append
from the Scene menu.  Repeat the process for each view / color /
representation you wish to show.  You can PgUp / PgDown through defined
Scenes.)

 

Then, to create the movie, select Program - Scene Loop - Y-Rock - #
seconds each from the Movie menu.

 

Now you can write out the movie as either a series of PNG files or an
MPEG file using Save Movie As... from the File menu.

 

Using scenes to create movies is a lot easier than messing around with
scripts : )!

 

Cheers,

Warren

 



From: Jasinski, Jean Marie [mailto:jean.jasin...@ucdenver.edu] 
Sent: Tuesday, May 19, 2009 11:06 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Documentation and advice for external GUI Movies
commands?

 

My goal is to make a simple movie from PyMol for inclusion in a
powerpoint presentation.  I understand how to use the png files to make
an avi file.

 

What I need help with is using the external GUI Movie commands to make
my movie.  I want to use the x-rock command, turn on my ligand, x-rock
again, turn off ligand, display second ligand and repeat the process.
So far, I've only used the external GUI command line to do util.mrock. I
can't find documentation for the Movie commands (Program, Update
Program, etc.).  I figure I could use a script to do all the actions I
need, but I can't figure out how to call Movie/Program/Static
Loop/X-rock,.

 

Thanks,

Jean Jasinski, Ph.D.

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] vacuum electrostatics

2009-05-18 Thread Warren DeLano
Denis,

Sorry, PyMOL only has protein charges coded at present.  Perhaps the
APBS project's pdb2pqr utility might be able to assign charges to
canonoical ligands (such as ATP)?

http://apbs.sourceforge.net

Cheers,
Warren

 -Original Message-
 From: Chaix Denis [mailto:denis.ch...@cbs.cnrs.fr]
 Sent: Monday, May 18, 2009 9:10 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] vacuum electrostatics
 
 Dear users
 
 I'm trying to compare the electrostatic charge surface of my protein
 with and without ligand, by using the command generate vacuum
 electrostatics.
 that's works fine for the protein without ATP but that doesn't work
with
 the ligand.The surface obtaine doesn't take account the ligand
 
 thanks
 
 --
 CHAIX Denis
 
 Centre de Biochimie Structurale
 INSERM U554/CNRS 5048
 29 rue de Navacelles
 F-34090 Montpellier, France
 Tel: 33 4 67 41 77 21
 Fax: 33 4 67 41 79 13
 e-mail:denis.ch...@cbs.cnrs.fr
 http://www.cbs.cnrs.fr
 
 


--
 
 Crystal Reports - New Free Runtime and 30 Day Trial
 Check out the new simplified licensing option that enables
 unlimited royalty-free distribution of the report engine
 for externally facing server and web deployment.
 http://p.sf.net/sfu/businessobjects
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 
 
 



--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] create double bonds in small molecules

2009-05-14 Thread Warren DeLano
Tom,

 

set valence

 

edit_mode

 

Ctrl-right-click on the bond

 

Ctrl-W

 

seems to do the trick.  Perhaps there's a problem with the version of
PyMOL you're using?

 

Cheers,

Warren

 



From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu] 
Sent: Thursday, May 14, 2009 10:13 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] create double bonds in small molecules

 

Hi,

 

I've been trying to get PyMOL to display a double bond at the
position of the vinyl in the attached, small-moleculePDB for some time.
The PDB was generated by converting a smiles representation of
isopentenly diphosphate (obtained from PubChem) using Corina.  The
number of attached atoms at the vinyl group is correct, but PyMOL
doesn't display the double bond.  Cycling the bond valence produces a
single-bond version (with added protons), but stops there - it won't
cycle through triple, double, single.  Downloaded a PDB of fumarate that
does display double bonds in response to Set Valence - so, my version of
PyMOL (1.1beta2, Vista environment) seems fine.

 

Thoughts?

 

Thanks,

 

Tom

--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Error: unknown type

2009-05-12 Thread Warren DeLano
Shiven,

It appears the script was flawed:

names = cmd.get_names(sel1)

should be:

names = cmd.get_names(selection=sel1)

I've updated it on the Wiki.

Cheers,
Warren

 -Original Message-
 From: Shiven Shandilya [mailto:shiven.shandi...@gmail.com]
 Sent: Monday, May 11, 2009 4:47 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Error: unknown type
 
 Hello List,
 
 Any ideas on why this script keeps failing in the newer PyMOL
builds...
 
 http://pymolwiki.org/index.php/Zero_residues
 
 I keep getting the error message:
 
 
 Error: unknown type: '1hpv'
 
 
 where 1hpv is an actual pdb file/object
 
 I am running pymol 1.2b5 rev. 3706 (compiled from svn) on Ubuntu 8.10
 
 
 Anyone else face a similar issue, or is it just me
 
 
 Thanks!
 
 --Shiven
 


--
 
 The NEW KODAK i700 Series Scanners deliver under ANY circumstances!
Your
 production scanning environment may not be a perfect world - but
thanks to
 Kodak, there's a perfect scanner to get the job done! With the NEW
KODAK
 i700
 Series Scanner you'll get full speed at 300 dpi even with all image
 processing features enabled. http://p.sf.net/sfu/kodak-com
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 
 
 



--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Vacuum electrostatics

2009-05-11 Thread Warren DeLano
Mark,

Should be fixed now (in rev 3720).

Cheers,
Wawrren


 -Original Message-
 From: Mark Wehner [mailto:mark.weh...@rub.de]
 Sent: Monday, May 11, 2009 12:11 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Vacuum electrostatics
 
 Hi everyone,
 
 in the newer version of pymol I realized it is not possible to
generate
 vacuum
 electrostatics, there's an error while assigning the formal charges.
The
 error
 message is:
 
 Alter-Error: Aborting on error. Assignment may be incomplete.
   File string, line 1
 formal_charge=0;flags=flags0x-8388609
 
 I build the source code (rev 3719) using Python 2.6.2. Is anyone
 experiencing
 similar problems at the moment?
 
 Mark
 


--
 
 The NEW KODAK i700 Series Scanners deliver under ANY circumstances!
Your
 production scanning environment may not be a perfect world - but
thanks to
 Kodak, there's a perfect scanner to get the job done! With the NEW
KODAK
 i700
 Series Scanner you'll get full speed at 300 dpi even with all image
 processing features enabled. http://p.sf.net/sfu/kodak-com
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 
 
 



--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Non-planar clipping?

2009-05-07 Thread Warren DeLano
David,
 
This is a weak area for PyMOL.  One thing to try is to switch to an animation 
with multi-layered transparency, two_sided lighting (and other tweaks) to help 
show the entire binding site volume.  The approach isn't perfect, but it may 
help:
 
fetch 1gzm, async=0
 
remove not a//
 
select my_ligand, a/ret/, enable=0
 
hide
 
show st, my_ligand
 
set transparency, 0.85
 
set transparency_mode, 1  ;# multi-layer
 
set two_sided_lighting
 
set ray_transparency_contrast, 3 ;# layer-dependent
 
set ray_transparency_oblique, 1.5 ;# normal-dependent
 
select carve_sele, my_ligand, enable=0
 
set surface_carve_selection, carve_sele
 
set surface_carve_cutoff, 4.5
 
set surface_quality, 1
 
show surface, my_ligand expand 6
 
zoom vis
 
set ray_trace_frames
 
set cache_frames
 
bg white
 
mset 1 x30
 
orient my_ligand
 
zoom my_ligand, 3
 
movie.rock
 
mplay
 
# now wait a few minutes for the movie to render and play
 
Cheers,
Warren
 



From: Margulies, David (NIH/NIAID) [E] [mailto:dmargul...@niaid.nih.gov]
Sent: Thu 5/7/2009 4:07 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Non-planar clipping?



Hi,
I would like to make a clipped illustration of a peptide-ligand binding
site, a sliced-image as it were, but because the binding site consists of
several non-linear pockets, I can't visualize all in the same clipping view.
Is there a way to make a non-planar section? Or a straightforward way of
superposing several different clipping planes with a different level of
transparency to visualize all pockets with the superposed peptide-ligand?

--
David H. Margulies, MD, PhD
Chief, Molecular Biology Section
Laboratory of Immunology, NIAID, NIH
Bldg. 10; Room 11N311
10 Center Drive
Bethesda, MD 20892-1892

email: d...@nih.gov
phone: 301-496-6429
fax: 301-496-0222

___
The information in this e-mail and any of its attachments are confidential
and may contain sensitive information.  It should not be used by anyone who
is not the original intended recipient.  If you have received this e-mail in
error please inform the sender and delete it from your mailbox or any other
storage devices.  The National Institute of Allergy and Infectious Diseases
(NIAID)  shall not accept liability for any statement made that are the
sender¹s own and not expressly made on behalf of the NIAID by one of its
representatives.



--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users





--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Vector-Based Figure Export

2009-05-06 Thread Warren DeLano
Sean,
 
We don't have vector export, but PyMOL can generate a high-resolution BW 
transparent-background raster image as illustrated below:
 
load $PYMOL_PATH/test/dat/1tii.pdb
 
as cartoon
 
set ray_trace_mode, 2
 
set ray_trace_gain, 1
 
unset antialias
 
unset opaque_background
 
unset depth_cue
 
bg white
 
ray 3600
 
That's enough pixels to fill a 8.5x11 page at over 300 dpi...
 
Cheers,
Warren



From: Sean Law [mailto:magic...@hotmail.com]
Sent: Fri 5/1/2009 6:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Vector-Based Figure Export


Hi Warren,

I know that there has been some discussion on implementing a vector-based 
figure export.  I was wondering if there were any updates on this?  I think 
that this would be an amazing feature to have.  Thanks!

Sean




Internet Explorer 8 makes surfing easier. Get it now! 
http://go.microsoft.com/?linkid=9655264 



From: Sean Law [mailto:magic...@hotmail.com]
Sent: Fri 5/1/2009 6:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Vector-Based Figure Export


Hi Warren,

I know that there has been some discussion on implementing a vector-based 
figure export.  I was wondering if there were any updates on this?  I think 
that this would be an amazing feature to have.  Thanks!

Sean




Internet Explorer 8 makes surfing easier. Get it now! 
http://go.microsoft.com/?linkid=9655264 
--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] Grid_mode - reference structure

2009-05-05 Thread Warren DeLano
Martin,

set grid_slot, -2, object-name

for the object you wish to spread across all grid slots.

Cheers,
Warren

-Original Message-
From: Höfling Martin [mailto:martin.hoefl...@gmx.de]
Sent: Tue 5/5/2009 5:02 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Grid_mode - reference structure
 
Hey Folks,

First of all: Grid Mode is awesome! Maybe I have overlooked a feature,  
but it seems to me that it is impossible to show a reference structure  
in all grids. Is there a better way than duplicating the object for  
every grid cell?

Best
Martin 

--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users






--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


Re: [PyMOL] diehedral angle

2009-05-05 Thread Warren DeLano
Vivek,
 
# new command in 1.2b5 - fabricate peptide, ALA trimer: 
 
fab AAA 
 
# set a dihedral value ro 180 degrees.
 
set_dihedral 1/C, 2/N, 2/CA, 2/C, 180
 
Cheers,
Warren
 


From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Tue 5/5/2009 12:09 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] diehedral angle



Hello,

I would like to change some of the diehedral angles in a polymer
systems. I know how to measure diehedral angle. However, I don't know
how to change it ? Any advice is greatly appreciated.

--
Thank you and Regards,

Vivek Ranjan

--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users





--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users


  1   2   3   4   5   6   >