Re: [PyMOL] writing out the surface

2012-07-15 Thread Michael Lerner
Thanks!

Apparently I'd forgotten that fetch defaults to doing a zoom (which it
obviously has to do to make things look reasonable), so I thought I didn't
need to play with the view. Too much non-PyMOL work rots the brain, it
seems.

Cheers,
-Michael

On Sun, Jul 15, 2012 at 5:35 AM, Thomas Holder 
spel...@users.sourceforge.net wrote:

 Hi Michael,

 you need to reset the camera view.

 def writeSurfaceValue(objname, wrlname='/tmp/tmp.wrl',
 ptsname='/tmp/tmp.pts', pdbname='/tmp/tmp.pdb'):

 cmd.hide('everything')
 cmd.show('surface',objname)
 view = cmd.get_view()
 cmd.set_view([1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0,
 0.0, 0.0, -50.0, 0.0, 0.0, 0.0, 40.0, 100.0, -20.0])

 cmd.save(wrlname)
 points = getIndexedFaceSet(wrlname)
 f = file(ptsname,'w')
 f.writelines(points)
 f.close()
 pts2pdb(ptsname,pdbname)
 cmd.set_view(view)

 Cheers,
   Thomas

 Michael Lerner wrote, On 07/15/12 04:05:

 I finally got back to this, and I'm still having some trouble. The
 surface I write out seems to be offset from what I'm viewing in PyMOL. I
 define the following functions:

 def getIndexedFaceSet(wrlname):
 f = file(wrlname)
 for line in f:
 if 'geometry IndexedFaceSet {' in line:
 break
 else:
 print Could not find IndexedFaceSet
 return None
 assert 'coord Coordinate' in f.next()
 assert 'point' in f.next()
 points = []
 for line in f:
 if not line.strip(): continue
 line = line.strip()
 if ']' in line:
 break
 if line.endswith(','):
 line = line[:-1]
 points.append(','.join(line.**split()) + '\n')
 return points

 def pts2pdb(ptsname,pdbname):
 f = file(pdbname,'w')
 atomid,resi = 1,1
 for line in open(ptsname):
 line = line.strip()
 if not line: continue
 c = [float(x) for x in line.split(',')]
 f.write('ATOM %06s %4s PHO  %04s%8.3f%8.3f%8.3f\n'%(atomid,**
 resi,'C',c[0],c[1],c[2]))
 atomid += 1
 f.close()
 def writeSurfaceValue(objname,**wrlname='/tmp/tmp.wrl',**
 ptsname='/tmp/tmp.pts',**pdbname='/tmp/tmp.pdb'):
 cmd.hide('everything')
 cmd.show('surface',objname)
 cmd.save(wrlname)
 points = getIndexedFaceSet(wrlname)
 f = file(ptsname,'w')
 f.writelines(points)
 f.close()
 pts2pdb(ptsname,pdbname)
 cmd.extend('write_surface_**value',writeSurfaceValue)

 and then do

 fetch 1rx1
 set surface_solvent, 1
 show surface
 run whatever file defines the above functions
 write_surface_value 1rx1
 load /tmp/tmp.pdb
 show spheres, tmp

 and the tmp object looks like it has the right shape, but is clearly
 offset from 1rx1.

 I have a feeling I'm doing something simple and obvious wrong, but I'm
 not sure what.

 Thanks,

 -Michael

 On Mon, Jun 11, 2012 at 10:47 PM, Michael Lerner mgler...@gmail.commailto:
 mgler...@gmail.com wrote:

 Hi all,

 Tsjerk- Thanks. I'm not sure how I missed that, given that it's even
 mentioned on the wiki on the surface page under the clear heading
 Exporting Surface/Mesh Coordinates to File :-|.
 (http://www.pymolwiki.org/**index.php/Surface#Exporting_**
 Surface.2FMesh_Coordinates_to_**Filehttp://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File
 ).
 I don't know anything about VRML, but I found some documentation
 online at 
 http://www.c3.hu/cryptogram/**vrmltut/part5.htmlhttp://www.c3.hu/cryptogram/vrmltut/part5.htmland
  it
 looks really straightforward. The surface will show up in the VRML
 file as an IndexedFaceSet, and the points are just XYZ triples, and
 I can safely ignore everything else.

 Darrell- Thanks. I'll build that in as an option.

 Takanori- Thanks. That's really cool. I happen to want solvent
 accessible surfaces rather than isosurfaces, but dump is
 definitely going into my bag of tricks.

 Cheers,
 -Michael

 On Mon, Jun 11, 2012 at 8:57 PM, Takanori Nakane
 
 t.nak...@mail.mfour.med.**kyoto-u.ac.jpt.nak...@mail.mfour.med.kyoto-u.ac.jp
 
 mailto:t.nakane@mail.mfour.**med.kyoto-u.ac.jpt.nak...@mail.mfour.med.kyoto-u.ac.jp
 wrote:

 Hi,

 Another way:
 There is an undocumented API called 'dump', which can
 dump coordinates of isomesh/isosurface to a file.

 For mesh, it dumps a list of vertex coordinates, which
 can be rendered as GL_LINE_STRIP.
 For surface, it dumps a list of pairs of a vertex coordinate
 and its vertex normal vector, which can be rendered as
 GL_TRIANGLES.

 Please examine my old post for a script example.
 http://www.mail-archive.com/**pymol-users@lists.sourceforge.**
 net/msg10012.htmlhttp://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html

 Best regards,

 Takanori Nakane


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Re: [PyMOL] writing out the surface

2012-07-14 Thread Michael Lerner
I finally got back to this, and I'm still having some trouble. The surface
I write out seems to be offset from what I'm viewing in PyMOL. I define the
following functions:

def getIndexedFaceSet(wrlname):
f = file(wrlname)
for line in f:
if 'geometry IndexedFaceSet {' in line:
break
else:
print Could not find IndexedFaceSet
return None
assert 'coord Coordinate' in f.next()
assert 'point' in f.next()
points = []
for line in f:
if not line.strip(): continue
line = line.strip()
if ']' in line:
break
if line.endswith(','):
line = line[:-1]
points.append(','.join(line.split()) + '\n')
return points

def pts2pdb(ptsname,pdbname):
f = file(pdbname,'w')
atomid,resi = 1,1
for line in open(ptsname):
line = line.strip()
if not line: continue
c = [float(x) for x in line.split(',')]
f.write('ATOM %06s %4s PHO  %04s
 %8.3f%8.3f%8.3f\n'%(atomid,resi,'C',c[0],c[1],c[2]))
atomid += 1
f.close()

def
writeSurfaceValue(objname,wrlname='/tmp/tmp.wrl',ptsname='/tmp/tmp.pts',pdbname='/tmp/tmp.pdb'):
cmd.hide('everything')
cmd.show('surface',objname)
cmd.save(wrlname)
points = getIndexedFaceSet(wrlname)
f = file(ptsname,'w')
f.writelines(points)
f.close()
pts2pdb(ptsname,pdbname)
cmd.extend('write_surface_value',writeSurfaceValue)

and then do

fetch 1rx1
set surface_solvent, 1
show surface
run whatever file defines the above functions
write_surface_value 1rx1
load /tmp/tmp.pdb
show spheres, tmp

and the tmp object looks like it has the right shape, but is clearly offset
from 1rx1.

I have a feeling I'm doing something simple and obvious wrong, but I'm not
sure what.

Thanks,

-Michael

On Mon, Jun 11, 2012 at 10:47 PM, Michael Lerner mgler...@gmail.com wrote:

 Hi all,

 Tsjerk- Thanks. I'm not sure how I missed that, given that it's even
 mentioned on the wiki on the surface page under the clear heading
 Exporting Surface/Mesh Coordinates to File :-|. (
 http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File).
 I don't know anything about VRML, but I found some documentation online at
 http://www.c3.hu/cryptogram/vrmltut/part5.html and it looks really
 straightforward. The surface will show up in the VRML file as an
 IndexedFaceSet, and the points are just XYZ triples, and I can safely
 ignore everything else.

 Darrell- Thanks. I'll build that in as an option.

 Takanori- Thanks. That's really cool. I happen to want solvent accessible
 surfaces rather than isosurfaces, but dump is definitely going into my
 bag of tricks.

 Cheers,
 -Michael

 On Mon, Jun 11, 2012 at 8:57 PM, Takanori Nakane 
 t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote:

 Hi,

 Another way:
 There is an undocumented API called 'dump', which can
 dump coordinates of isomesh/isosurface to a file.

 For mesh, it dumps a list of vertex coordinates, which
 can be rendered as GL_LINE_STRIP.
 For surface, it dumps a list of pairs of a vertex coordinate
 and its vertex normal vector, which can be rendered as GL_TRIANGLES.

 Please examine my old post for a script example.

 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html

 Best regards,

 Takanori Nakane


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[PyMOL] 3D printing question

2012-06-17 Thread Michael Lerner
Hi all,

I just got a MakerBot Replicator, and I'd obviously like to try my hand at
printing 3D models from PyMOL. If anybody else is doing such things, are
there any recommendations for the most straightforward way to go from PyMOL
to something that repg can read? A lot of the software I'm trying to use as
intermediates between the two is proving to be troublesome.

Cheers,
-Michael

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[PyMOL] writing out the surface

2012-06-11 Thread Michael Lerner
Hi all,

If I have a surface representation, is there currently a way to write it
out as points (perhaps with a desired spacing) to a file? I know that the
answer used to be no, but I thought I'd check just in case there was a new
function that I didn't know about.

Cheers,
-Michael

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Re: [PyMOL] writing out the surface

2012-06-11 Thread Michael Lerner
Hi all,

Tsjerk- Thanks. I'm not sure how I missed that, given that it's even
mentioned on the wiki on the surface page under the clear heading
Exporting Surface/Mesh Coordinates to File :-|. (
http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File).
I don't know anything about VRML, but I found some documentation online at
http://www.c3.hu/cryptogram/vrmltut/part5.html and it looks really
straightforward. The surface will show up in the VRML file as an
IndexedFaceSet, and the points are just XYZ triples, and I can safely
ignore everything else.

Darrell- Thanks. I'll build that in as an option.

Takanori- Thanks. That's really cool. I happen to want solvent accessible
surfaces rather than isosurfaces, but dump is definitely going into my
bag of tricks.

Cheers,
-Michael

On Mon, Jun 11, 2012 at 8:57 PM, Takanori Nakane 
t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote:

 Hi,

 Another way:
 There is an undocumented API called 'dump', which can
 dump coordinates of isomesh/isosurface to a file.

 For mesh, it dumps a list of vertex coordinates, which
 can be rendered as GL_LINE_STRIP.
 For surface, it dumps a list of pairs of a vertex coordinate
 and its vertex normal vector, which can be rendered as GL_TRIANGLES.

 Please examine my old post for a script example.
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10012.html

 Best regards,

 Takanori Nakane


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Richmond, IN   47374-4095
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Re: [PyMOL] Electrostatic calculations with ligand bound

2011-12-06 Thread Michael Lerner
Hi Andrew,

The main limitation for problems like this is that you need to have
parameters for the ligand. Making sure that you have good parameters
is often an expert-level topic, and you're probably best served by the
APBS or PDB2PQR listservs as well as the literature ... but, you can
get a decent start on things with PDB2PQR itself. See
http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization
for some good starting instructions. Once you have a PQR file that
includes both the protein and the ligand, the PyMOL/APBS plugin should
do everything that you need.

If that doesn't solve your problem, please let me know.

Cheers,
-Michael

On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew
andrew.mal...@umassmed.edu wrote:
 Hey guys,

 I am trying to calculate electrostatics with a ligand bound to my molecule 
 using ABPS.  I am not having success.  Everything I've read seems to say that 
 this is a normal limitation with APBS, and I've tried other programs to no 
 avail.  I have not been able to rebuild my molecule in the correct format 
 either.  Any help here is greatly appreciated.

 Andrew
 UMass Med School, Worcester, MA

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Re: [PyMOL] Get pymol 1.4.1 source to windows. Easy.

2011-08-25 Thread Michael Lerner

 Hi.

 I was very happy to find a post how to easy install pymol 1.4 from source
 on windows.

 1) Install python, 2.5, or 2.6 or 2.7 for windows.
 2) Download appropriate installer from:
 http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol   Select according to
 your python version.
 3) Run it
 4) PyMOL is now installed in: C:\Python2X\PyMOL

 A) C:\Python2X\PyMOL\PDB_file.reg   should be edited in a text editor, to
 match your python version. Run it.
 B) Pymol is started by clicking C:\Python27\PyMOL\pymol.cmd   which
 executes python on C:\Python27\PyMOL\pymol-launch.py

 Happy pymoling.

 Best
 Troels




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Re: [PyMOL] loading gro files

2011-08-18 Thread Michael Lerner
...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
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Re: [PyMOL] How to manage plugin dependencies

2011-07-31 Thread Michael Lerner
Hi Osvaldo,

What module? Newer versions of PyMOL ship with a much more featured set of
Python modules (scipy, numpy, matplotlib, Bio, etc.).

Cheers,

-Michael

On Sun, Jul 31, 2011 at 12:10 AM, Osvaldo Martin aloctavo...@gmail.comwrote:

 Hi Everyone,

 I`m writing a Python plug-in that depends on a certain Python module. For
 Linux users It would be easy to install this module because is available
 through the repositories (I think Mac OsX has a repositories system too, but
 I am not sure) . But for Windows this could be a little more complicated, 1)
 They don´t have a repository system and 2) Python is not installed by
 default in Windows, hence if they install any Python module this module will
 not be available to PyMol.

 I think there are at least two options.

 1) The easy one (for me): To distribute a README file with the
 instructions to install the plugin in each platform and to make my plug-in
 to check if the module if available, if not ask the user to install it.

 2) The easy one (for the user): To distribute this module with my plug-in,
 and create some installer to perform the installation in a more or less
 automatic way.

 Which option would be the better? It is option 2 to complicated to
 implement?, it is worthwhile? which are the easiest way to install Python
 modules on Windows and Mac OsX (and making them available to PyMol)?

 Thanks in advance.

 Cheers,

 Osvaldo.




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Re: [PyMOL] RMSD calculation sans alignment

2011-07-22 Thread Michael Lerner
PyMOL's rms_cur command will do what you want. E.g.

fetch 1rx1
fetch 1ra1

# reports Executive: RMS =   34.329 (159 to 159 atoms)
# because the structures still need to be translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)

# reports Executive: RMS =0.862 (159 to 159 atoms)
# because it calculates translated/rotated value, but does now
# apply the translation/rotation to the molecules
rms (1rx1 and name CA), (1ra1 and name CA)


# reports Executive: RMS =0.391 (1026 to 1026 atoms)
# standard PyMOL align, which also translates and rotates
align 1rx1, 1ra1

# both of these report Executive: RMS =0.862 (159 to 159 atoms)
# because the structures have now been translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)
rms (1rx1 and name CA), (1ra1 and name CA)

Cheers,

-Michael


On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant tgr...@hwi.buffalo.eduwrote:

 Dear all,

 I'm attempting to align a series of structures using the CEAlign plug-in in
 PyMOL due to a lack of any detectable sequence homology.  CEAlign does a
 good job of aligning and the fits are very reasonable.  However, the RMSD
 that is calculated is based only on the c-alphas that were actually aligned,
 not based on the total number of c-alphas in the structure.  After searching
 online I have been unable to find any software or servers that will simply
 calculate the RMSD of two structures as is, without aligning them first.  I
 would think this would be a relatively straightforward thing to do, just to
 calculate RMSD from two existing structures without translation or rotation
 for alignment.

 Does anyone know of a way either in PyMOL or in general to simply calculate
 the RMSD between all c-alphas of two structures?  Obviously it won't
 necessarily be a one-to-one ratio of c-alphas, but I can manually curate the
 pdb to include only the equivalent and aligned residues, even if not used
 in the CEAlign algorithm, so that there are the same number of c-alphas in
 both structures.

 Thank you for any help and suggestions,

 Tom


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Re: [PyMOL] ContactsNCONT script error

2011-05-25 Thread Michael Lerner
Hi Ivan,

There's definitely a bug in that script. It looks like most of the file has
one extra space of indentation. I don't feel comfortable changing it at the
moment, as I'm not on a machine that has ccp4, but perhaps someone else can
fix and test it. If not, I'll fix it tomorrow.

Cheers,

-Michael

On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan i.campeo...@imperial.ac.uk
 wrote:

 Dear All,


 I would like to compare the intermolecular crystal contacts in seven
 crystal forms of the same enzyme.
  I produced a list of contacts for each crystal form using the program
  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki (
 http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a
 lot of time.
  Unfortunately, when I run the ContactsNCONT script,  I always have the
 following message with different PCs running  different OS (Windows, RedHat
 or Mac):

 File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py,
 line 338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
  File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py,
 line 455, in run_file
execfile(file,global_ns,local_ns)
  File C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py, line 3
 def parseContacts( f ):
^
  IndentationError: unexpected indent


 Any suggestion will be more than appreciated.


 Thank you in advance,

 Regards

 Ivan Campeotto
 Centre for Molecular Microbiology and Infection
 Imperial College London


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Re: [PyMOL] How to construct a view showing only a single contiguous cavity

2011-05-20 Thread Michael Lerner
The last time I tried to do something similar, I found HOLLOW (
http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial
for showing a binding site, rather than an interior cavity, here:
http://hollow.sourceforge.net/binding.html .

Cheers,

-Michael

On Fri, May 20, 2011 at 7:11 PM, Ben Roberts b...@roberts.geek.nz wrote:

 Hi list,

 I'm trying to use PyMOL to construct an image of the total contiguous
 contact
 surface that starts at a particular place on the surface of a protein,
 without
 all the visual distraction and clutter that comes from other regions of the
 protein surface (not to mention internal cavities).

 I started by rendering up the whole protein as Contact surface with
 Cavities and pockets only shown. Unfortunately, this displays a large
 number
 of bubbles, some of which, despite being far away in space from the region
 of
 interest, manage to effectively obscure bits and pieces of it.

 So my next thought was to try removing the extraneous bits, however, I
 can't
 seem to select atoms in surface view; I have to display everything as lines
 or
 similar. Removing things that way gets very unwieldy, not least because of
 all
 the atoms that don't contribute anything to the surface but appear in front
 of, behind, or otherwise near to the atoms that do so.

 A third option I tried was to build the surface up, starting from the known
 points of interest, but this too is painstaking because of the need to
 guess
 where I should next expand the selection to in order to fill in the gaps.

 A remaining method of getting only the cavity of interest would, I guess,
 be
 to create a selection consisting only of those atoms that contribute
 something
 to the currently rendered surface (in this case, cavities and voids). I
 could
 then render those as spheres or something and hide unwanted contributors.
 Is
 there a way of specifying such a selection? Alternatively, is there some
 other
 smart way to achieve what I want (and by smart, I mean a way that isn't
 time-
 consuming and unusually error-prone)? I've already tried Googling, to no
 avail; I got, mostly, instructions about how to display surfaces in
 general.

 I should mention that I'm using a recent version of MacPyMol, on Mac OS X
 10.6.7.

 Any tips are welcome. Thanks!

 Best regards,
 Ben
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Re: [PyMOL] Fetching scripts

2011-05-05 Thread Michael Lerner
Hi Peter,

On Wed, May 4, 2011 at 6:56 PM, Pete Meyer pame...@mcw.edu wrote:


  - Sandboxing would be ideal, but I don't know if there's infrastructure in
 python to support it.  It might be easier to filter fetched scripts to only
 allow a restricted subset of python functions (the ast library looks like it
 might make this a bit easier).  If a script can't access the network or hard
 disk, then it doesn't need to be trusted as much.


There are a couple of issues with this

 - The last time I checked (which, admittedly, was a couple of years ago),
many people had tried and failed to set up such an environment within
Python. It turned out that there were very clever ways to get around any
sort of reasonable restrictions that people tried to impose (i.e. a
guaranteed-to-be-safe script couldn't actually do anything useful). I know
there has been a lot of desire for this, so maybe the problem has been
solved.

 - There are some plugins that need access to the hard disk. I'm not sure
about scripts. If there exists a reasonable sandboxing (or AST-based)
solution, we'll have to run those scripts in untrusted mode, which is
probably fine.



  - The wiki doesn't appear to support SSL.  So that means trusting the
 network to get to the wiki correctly, in addition to the wiki itself.  I
 don't have any good ideas for how to work around this one.


My guess is that there's just never been a real need for SSL. Jason would be
the real authority here, but I'd guess that SSL would be possible if it
there's a strong push for it.

-Michael



 Pete


 Michael Lerner wrote:

 Hi all,

 I'm considering building in a mechanism for automatically fetching scripts
 from the PyMOL Wiki. The goal is to allow users to say

 fetch findSurfaceResidues, type=script
 findSurfaceResidues doShow=True, cutoff=0.5

 The convenience benefits are obvious, especially for new users, and I
 think that lowering the barrier to script usage will greatly increase both
 the number of people who use various scripts and the incentive to place
 scripts on the wiki (especially if the fetch mechanism makes it easy for
 script authors to provide a citation/DOI/etc.).

 I've put up a tentative page about this on the wiki (
 http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments
 either via the list, private email or on the wiki, especially about

  - whether you think it's a good idea
  - security and validation
  - options you'd like
  - implementation issues

 The plan is to write this as a userland script first. If issues relating
 to security and validation can be resolved, we'll see if the official builds
 want to include it.

 Cheers,

 -Michael

 --
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 IRTA Postdoctoral Fellow
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 5635 Fishers Lane, Room T909, MSC 9314
 Rockville, MD 20852 (UPS/FedEx/Reality)
 Bethesda MD 20892-9314 (USPS)





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Re: [PyMOL] APBS Plugin: protein out of grid

2011-05-05 Thread Michael Lerner
Can you send me the files (off list) so that I can take a look?

Thanks,

-Michael

On Thu, May 5, 2011 at 5:11 PM, Ricardo O. S. Soares
ross_...@yahoo.com.brwrote:

 Dear users,

 there's a particular case where I'm using the APBS plugin and the resultant
 grid leaves a portion of the protein out of it. This portion is show in full
 white because no potential is calculated there.
 Why isnt the grid centered as usual? Changing the values by hand and them
 recaulculating does not seem to change the grid at all.

 Thanks,

 Ricardo.



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[PyMOL] Fetching scripts

2011-05-04 Thread Michael Lerner
Hi all,

I'm considering building in a mechanism for automatically fetching scripts
from the PyMOL Wiki. The goal is to allow users to say

fetch findSurfaceResidues, type=script
findSurfaceResidues doShow=True, cutoff=0.5

The convenience benefits are obvious, especially for new users, and I think
that lowering the barrier to script usage will greatly increase both the
number of people who use various scripts and the incentive to place scripts
on the wiki (especially if the fetch mechanism makes it easy for script
authors to provide a citation/DOI/etc.).

I've put up a tentative page about this on the wiki (
http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments
either via the list, private email or on the wiki, especially about

 - whether you think it's a good idea
 - security and validation
 - options you'd like
 - implementation issues

The plan is to write this as a userland script first. If issues relating to
security and validation can be resolved, we'll see if the official builds
want to include it.

Cheers,

-Michael

-- 
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] Get Protein Dimension

2011-04-26 Thread Michael Lerner
Hi Martin,

The following works for me, although I needed to change 'protein' to
'polymer'. Is 'protein' normally supported as a selection? It doesn't seem
to be in 1.4.1.

from pymol import cmd
cmd.fetch('1rx1')
a = cmd.get_extent('polymer')
print a is,a

Hope that helps,

-Michael

On Tue, Apr 26, 2011 at 7:40 AM, Martin Hediger ma@bluewin.ch wrote:

 Dear all

 I found that PyMOL offer the cmd.get_extent('protein') function, which
 returns the dimensions of the selection.
 Is it complicated to make this function available from within an
 ordinary Pythonscript?

 Thanks for hints.
 Martin



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Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

2011-04-26 Thread Michael Lerner
Hi Harry,

If they've been combined using the group command, you can ungroup them:

fetch 1rx1
# make some distance objects
dist measure01, 19/C, 20/C
dist measure02, 20/C, 21/C
dist measure03, 158/C, 159/C
dist measure04, 157/C, 159/C
# group them
group g1, measure01 or measure02
group g2, measure03 or measure04
#ungroup all of them (this leaves empty groups, which you can delete if
you'd like)
ungroup measure*

Hope that helps,

-Michael

On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb hj...@cam.ac.uk wrote:

 Hi Everyone,

 I'd like to ask for some help with dash/distance objects. I have PyMOL
 session files  which show inter-molecular interactions using PyMOL distance
 objects. These were created using a script which colours each distance
 object and merges them according to type of interaction. The problem I'm
 having is that I would prefer to visualise the interactions on a per-residue
 basis, i.e. showing all the interactions for one or more residues but not
 the others, but as the dashes are merged by interaction type I can only hide
 by that category. Extensive Googling has not led me to a solution to select
 and hide individual dashes that are merged into one UI object, so I'd like
 to ask if it is possible to do this? I'm unfortunately no longer able to run
 the script again (I am at the end of a time limited project and am preparing
 figures) and I would prefer not to replace each dash manually.

 I hope this is clear, the crux of what I am asking is if it is possible to
 select and/or hide individual distance objects in a pymol session after they
 have been merged into one object. Un-merging them would also be an
 attractive solution.

 Thanks,

 Harry

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Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

2011-04-26 Thread Michael Lerner
Hi Harry,

As far as I know, this is not currently possible in PyMOL, but perhaps
someone will correct me on this.

-Michael

On Tue, Apr 26, 2011 at 9:27 AM, Harry Jubb hj...@cam.ac.uk wrote:

 Hi Michael,

 Thank you for your response. The problem is that for types of
 inter-molecular interaction all of the visual distances are merged into one
 object in the sidebar (as if created using the measurement wizard with the
 merge with previous option on), for which unfortunately the ungroup
 command doesn't seem to work for. Left-clicking on the interaction type in
 the GUI sidebar toggles show/hide for every distance of that interaction
 type, and there are no further disclosure squares which indicates that the
 distances are grouped rather than merged. Ideally I'd like to be able to
 un-merge these objects to make each dash an object that I can hide or show
 individually so I can switch off the ones not connected to a residue of
 interest. Even better (if possible) would be to only show dashes connected
 to a residue of choice.

 I hope that makes sense. Thank you for your help,

 Harry


 On 26 Apr 2011, at 13:59, Michael Lerner wrote:

 Hi Harry,

 If they've been combined using the group command, you can ungroup them:

 fetch 1rx1
 # make some distance objects
 dist measure01, 19/C, 20/C
 dist measure02, 20/C, 21/C
 dist measure03, 158/C, 159/C
 dist measure04, 157/C, 159/C
 # group them
 group g1, measure01 or measure02
 group g2, measure03 or measure04
 #ungroup all of them (this leaves empty groups, which you can delete if
 you'd like)
 ungroup measure*

 Hope that helps,

 -Michael

 On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb hj...@cam.ac.uk wrote:

 Hi Everyone,

 I'd like to ask for some help with dash/distance objects. I have PyMOL
 session files  which show inter-molecular interactions using PyMOL distance
 objects. These were created using a script which colours each distance
 object and merges them according to type of interaction. The problem I'm
 having is that I would prefer to visualise the interactions on a per-residue
 basis, i.e. showing all the interactions for one or more residues but not
 the others, but as the dashes are merged by interaction type I can only hide
 by that category. Extensive Googling has not led me to a solution to select
 and hide individual dashes that are merged into one UI object, so I'd like
 to ask if it is possible to do this? I'm unfortunately no longer able to run
 the script again (I am at the end of a time limited project and am preparing
 figures) and I would prefer not to replace each dash manually.

 I hope this is clear, the crux of what I am asking is if it is possible to
 select and/or hide individual distance objects in a pymol session after they
 have been merged into one object. Un-merging them would also be an
 attractive solution.

 Thanks,

 Harry

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 5635 Fishers Lane, Room T909, MSC 9314
 Rockville, MD 20852 (UPS/FedEx/Reality)
 Bethesda MD 20892-9314 (USPS)


   ---

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 Part II Biochemistry
 Homerton College

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 M: 0790 813 4735




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Re: [PyMOL] Convert pml script to Pymol Python script

2011-04-08 Thread Michael Lerner
It's not elegant at all, but it's worth knowing that you can use
cmd.do(...) as a quick fix for lines that aren't immediately easy to
convert.

Even a mostly-working pml2py tool would be a useful addition to the wiki.

Cheers,

-Michael

On Fri, Apr 8, 2011 at 2:09 PM, Jason Vertrees 
jason.vertr...@schrodinger.com wrote:

 Hi Matthias,

 There is no script that I'm aware of, but writing one should be rather
 straightforward because of how the API is organized:

 commandName arg1, arg2, arg3

 becomes

 cmd.commandName(arg1, arg2, arg3)

 The hardest part would be determining when to quote strings versus not
 quoting numbers and variables.  You might be able to reflect against
 the API for a more robust script
 (http://diveintopython.org/power_of_introspection/index.html).  Java's
 great at that, not sure about Python.  Good luck.

 Cheers,

 -- Jason


 On Fri, Apr 8, 2011 at 1:01 PM, Matthias Schmidt
 matthias.rene.schm...@gmail.com wrote:
  Hi,
 
  I have a few pml scripts for pymol that I would like to rewrite
  properly in python, making use of Pymol's ability to interprete Python
  scripts.
 
  Do you know of an interpreter that converts pml scripts automatically
  to python scripts for Pymol? Since the number of tasks that you can do
  in pml is finite, this should be possible, or not?
 
  Best,
 
  Matthias
 
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Re: [PyMOL] How to save APBS-generated maps

2011-04-01 Thread Michael Lerner
Hi Cale,

After you run the APBS calculation, you will find the relevant files stored
in a temporary directory. The default location of that directory depends on
your operating system and system configuration, but you can set it
explicitly in the Plugin's Temp File Locations tab. The  name of the file
containing the map is pymol-generated.dx by default, although you can change
both the name and the location on that tab.

Cheers,

-Michael

On Fri, Apr 1, 2011 at 12:49 PM, Cale Dakwar c.dak...@gmail.com wrote:


 Hello all,

 Is there a quick way to save an APBS PyMol Plugin generated map from within
 pymol?

 Thanks in advance,
 Cale


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Re: [PyMOL] How to get pymol 1.4

2011-03-23 Thread Michael Lerner
@lists.sourceforge.net
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net



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Re: [PyMOL] Adding Hydrogens

2011-03-16 Thread Michael Lerner
I've had good results with MolProbity (
http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15)
in the past.

I had a script that would let me cycle through all of the HIS residues, add
hydrogens, and cycle between states. It's broken at the moment. The trick
was that PyMOL doesn't care about the name of the residue, so you have to
manually cycle the valences.

On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch wrote:

 Dear All
 I would like to ask if the PyMOL function to add hydrogens to an entire
 protein also has options, meaning is it possible to set the protonation
 state of individual residues specifically? Like in a list or something?
 h_add, His202:+1 or so?
 And, it can be relevant at what atom a residue gets protonated: His can
 be protonated at Nd, or Ne or both. Is there a way to control this?

 On a more general note: what other smart hydrogen adding tools are there
 out there anyway? Does anyone know a really smart tool for this? I know
 OpenBabel has a pH parameter. But on the other hand OpenBabel just
 appends the hydrogens to the PDB file, whereas PyMOL really writes them
 within the block of atoms corresponding to one residue.
 Also, AutoDock can add hydrogens and it even has an option for the
 protonation state of histidine, but it doesn't seem to work in my case.

 Thanks for your answers and input.
 martin


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Re: [PyMOL] movie with morph and electrostatics

2011-03-15 Thread Michael Lerner
If you know a bit of python, you can make a version of the Plugin that will
do this via repeated calls to self.execute('Run APBS',refocus=False).

If this would be a generally useful feature, I could add a movie button to
the plugin so that it would step through all available frames, saving PNGs
for each.

Let me know,

-Michael

On Tue, Mar 15, 2011 at 1:13 PM, Ian Slaymaker slaym...@usc.edu wrote:

 I am trying to figure out how to design a movie that will preform a morph
 between two conformations of a protein, while having each chain move as a
 rigid body, and recalculate the electrostatic surface for each midstate
 between conformations. Can anyone offer me some suggestions on how to do
 this?
 Thank you!

 Ian Slaymaker



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Re: [PyMOL] R: Re: plugin dependencies

2011-03-10 Thread Michael Lerner
I really like the fact that Jason will be including more libraries with
PyMOL in the future.

I once needed to distribute a library that depended on BioPython. It turned
out that, in my case, I only cared about a few specific files from
BioPython, so I was able to strip out the necessary functionality and just
ship that with my plugin. I don't know exactly what you're doing, but that
might be an option.

Cheers,

-Michael

On Thu, Mar 10, 2011 at 9:25 PM, rv...@libero.it rv...@libero.it wrote:

 Hi Hongbo,
 thanks for your reply.

 So, how about ship all the BioPython packages you need in your python
 code together with your plugin? Of course all dependencies should be
 included.

 Is not so simple. A library like Biopython can't be installed as a plugin.
 An
 installer (OS specific) program is needed: the official windows installer I
 checked doesn't allow the user to choose the folder (this way the
 interpreter)
 where to install. Installing manually is still tricky for a not experienced
 user.

 Cheers,
  roberto


 Messaggio originale
 Da: hongbo@biotec.tu-dresden.de
 Data: 10/03/2011 12.57
 A: pymol-users@lists.sourceforge.net
 Ogg: Re: [PyMOL] plugin dependencies
 
 Just another reminder:
 
 If the version of the external python and the python shipped with
 PyMOL are different enough on the user's computer, the package might
 still fail to work in PyMOL even if the user has installed the package
 using the external python and edited the PYTHONPATH.
 
 
 So, how about ship all the BioPython packages you need in your python
 code together with your plugin? Of course all dependencies should be
 included.
 
 On 03/10/2011 06:17 AM, rv...@libero.it wrote:
  Hello everyone,
 
  my plugin needs Biopython.
  I wish check the Biopython installation by
 
  try:
   from Bio import AlignIO   # or similar
  except ImportError:
   .. prompt the user with a msg ..
 
  The problem is:
  what the msg to the user?
 
  Downloading and installing Biopython is not enough:
  If the user downloads and installs Biopython in the external python
  interpreter still Biopython continues to be unavailable for the internal
 python
  interpreter in pyMOL.
 
  Of course the user could edit the PYTHONPATH environment variable and so
 all
  the python interpreters can read Biopython but  working with environment
  variables could be too difficult for a not experienced user.
 
  Is there a simpler way?
 
  Cheers,
 roberto
 
 

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Re: [PyMOL] Color scale changed in APBS?

2011-02-22 Thread Michael Lerner
Hi all,

On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] 
cschu...@its.jnj.com wrote:

 Hi Wataru,

 in addition to what Jason mentioned: Have you tried to look at the
 potential mapped on the solvent accessible surface and display the
 molecular surface? If you display the potential like this the colors
 will be much more muted, on the other hand this is the setting you will
 find most often displayed in the literature.


I think this is likely the case. Due to a lot of feedback, the plugin
defaults changed to showing the solvent accessible surface a while ago (see
the checkboxes in the Molecular Surface section of the Visualization panel).


 Another option is to have a look at the charge distribution of your
 molecule in the actual PQR file. The potential distribution is dependent
 on the charging algorithm used. I would recommend using/looking into
 PDQ2PQR, which is available from the APBS website and compare this to
 the homegrown charging algorithm from PyMol or GRASP for that matter.


Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting
that the current version of the plugin allows you to specify command line
arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying
out different force fields).

Cheers,

-Michael



 Hope I did not muddle the water too much

 Carsten

  -Original Message-
  From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
  Sent: Monday, February 21, 2011 10:04 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] Color scale changed in APBS?
 
  Dear PyMOL users:
 
  I recently used the APBS plugin (v1.3) to display the surface
 potential
  of a protein. I noticed that the charged surfaces were much more
  lightly colored, compared with the surface colors I have calculated in
  the past (maybe a year ago?) on the same protein, using the same
  softwares. The default settings and the same range (-10 kT to 10 kT)
  were used in both cases. Has anyone experienced this?
 
  I would appreciate any help.
 
  Wataru
 
 
 
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Re: [PyMOL] Visualizing two surfaces using APB2tools2.1

2011-02-01 Thread Michael Lerner
Thanks for the nice writeup, Jason!

There are two main ways that I know of to visualize two potentials at once.
This is one. If you're looking at, e.g., a protein-protein interface, it may
be useful to map two different electrostatic potentials to two different
PyMOL objects. Here's my overly-cautious recipe for doing that:

1. Load up PyMOL with one of your structures.
2. Fire up the plugin. Click on Choose Externally Generated PQR File and
point it at your PQR file.
3. Click on the Temp File Locations tab and change the name of the temporary
DX file to something meaningful, e.g. structure1.dx
4. Set grid and Run APBS as normal.
5. Close the plugin.
6. Type delete all
7. Load up the second structure.
8. Repeat steps 2-4, changing the name to something like structure2.dx this
time.

Now you have two correctly generated electrostatics potential maps (note:
the reason I had you do things with one structure at a time loaded in PyMOL
is so that you wouldn't have to fiddle around with the Selection to use
section of the Main options tab). Use the load command to load up the other
pqr file and the other dx map, then use the visualization panes as normal.

Cheers,

-Michael

On Tue, Feb 1, 2011 at 9:48 AM, Jason Vertrees 
jason.vertr...@schrodinger.com wrote:

 Hi Yarrow,

  Does anyone know how to visualize the surface potentials of two molecules
  simoutaneously using the APBS Tools2.1 plugin?  Thanks.

 As Michael wrote the APBS plugin, he might have more to offer, but
 here's how I'd do it.  I used this technique to look at two similar
 proteins side-by-side in PyMOL (see the 2nd image on
 http://www.pymolwiki.org/index.php/APBS).  The trick is to (1) use
 grid_mode and grid_slots; and (2) rename the maps as appropriate.
 It's not hard, but will take a couple minutes.  Here's how:

 # get two proteins; use whatever you like
 fetch 1rx1 1rx2, async=0

 # put them in the same frame of reference for grid mode
 align 1rx1, 1rx2

 # run APBS on protein #1, 1rx1
 Plugin  APBS Tools2  ...
 Under selection to use type (polymer) and 1rx1

 # rename the map
 set_name pymol-generated, 1rx1_map

 # run APBS on protein 2, 1rx2; remove the waters
 Plugin  APBS Tools2
 Under selection to use type (polymer) and 1rx2

 # rename the map
 set_name pymol-generated, 1rx2_map

 # Now, using APBS show the surfaces make sure you choose
 # 1rx1_map for 1rx1 and 1rx2_map for 1rx2; click Update if those
 # map names are not present.
 ...

 # turn on grid mode
 set grid_mode

 # assign grid slots just to be sure the right maps
 # and proteins are in the right places
 set grid_slot, 1, 1rx1
 set grid_slot, 1, 1rx1_map
 set grid_slot, 1, e_lvl_0_1

 set grid_slot, 2, 1rx2
 set grid_slot, 2, 1rx2_map
 set grid_slot, 2, e_lvl_1_1


 Now, you should be set and have an image like that I posted on the
 PyMOLWiki.

 Cheers,

 -- Jason

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Re: [PyMOL] APBS surface data export

2011-02-01 Thread Michael Lerner
Hi Matt,

PyMOL does not currently allow you to export the data mapped to the surface.
However, the dx format is very straightforward. It follows a subset of the
OpenDX standard, as described on the APBS site (
http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
).

I don't know much about surface file formats, but the PyMOL wiki mentions (
http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File)
that you can save surface coordinates to a file. It might be possible for a
developer (you?) to convince PyMOL to write out the electrostatic potential
along with whatever else it's writing to the .wrl file.

Hope that helps,

-Michael

On Mon, Jan 31, 2011 at 7:03 PM, Matteo Pendleton znfin...@gmail.comwrote:

 Greetings,

 I'm looking to use an electrostatic surface map for downstream calculations
 and was wondering whether it's currently possible (after using APBSv2 to
 calculate a surface potential map) to export a mesh of data points in a list
 format with each data point's associated potential? If not, does anyone have
 an outline of the file layout for the pymol-generated.dx file so I could
 write my own script to do it?

 Thank you kindly,

 Matt Pendleton

 Independent Researcher
 New York, NY


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Re: [PyMOL] Wiki down?

2011-01-27 Thread Michael Lerner
There's been a flood of spam to the wiki recently. Most of it has been
obvious spammy pages, but someone also deleted the main page. Cute.

On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS] 
cschu...@its.jnj.com wrote:

  I am just getting a blank page when I try to access the Pymol Wiki. Do
 other people see the same problem?

 Carsten



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Re: [PyMOL] OpenDX files from opendx.org

2010-10-18 Thread Michael Lerner
Hi David,

As far as I know, PyMOL is still using its own DX reading functions
(primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious).

I don't think it would be too much work to get PyMOL to read regular.dx. As
far as I can tell, the only problem is that PyMOL is expecting the line that
starts with object 3 to say object 3 class array type double instead of
object 3 class array float.

As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see e.g.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html),
but I'm not sure that PyMOL's DX reader supports them directly.

I have not looked into the VMD plugins. If they support non-orthogonal DX
maps out of the box, that might be a quick and easy solution.

Cheers,

-Michael

On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote:

 I have long been happy reading .dx files produced by apbs and my own
 programs into pymol.  Everything works great.

 Interestingly, when I save a .dx file from OpenDX (http://opendx.org),
 pymol seems to not be able to read it.

 I've attached two files that come from OpenDX's samples directory
 where loading into pymol gives the error ObjectMap-Error: Error
 reading map.

 Any help in what's wrong with these files (or how to patch the VMD
 plugins that I believe pymol uses to read in dx files) would be
 appreciated.

 -David


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Re: [PyMOL] Deleting and Loading multiple SDF files

2010-09-23 Thread Michael Lerner
Hi Renuka,

Please keep all PyMOL-related correspondence on the mailing list. That way,
other people can find the answers by reading the mailing list or searching
the web.

Your task is now getting a little more complicated. I think you'll probably
want to define some Python functions and use them. It's useful to know that
using the distance command with mode=2 will show polar contacts. Also,
distance objects with names starting with an underscore won't show up in the
GUI.


I'd do something like this:

1. Define some functions in a Python file that you can use via run (or
perhaps in your .pymolrc). [see
http://www.pymolwiki.org/index.php/Python_Integration and
http://www.pymolwiki.org/index.php/Script_Tutorial]. You'll need to pass the
name of your protein to these functions.

import os
from pymol import cmd

def loadclust(filename,protname):
cmd.load(filename)
dir,fname = os.path.split(filename)
# PyMOL automatically names the object by the filename
fname,extension = os.path.splitext(fname)
# cluster_4 -- 4
custernum = fname.split('_')[1]
# hidden from GUI display because it starts with _
polarname = '_polar_'+clusternum
cmd.dist(polarname,fname,protname,mode=2)
cmd.extend('loadclust',loadclust)
def delclust(filename):
dir,fname = os.path.split(filename)
# PyMOL automatically names the object by the filename
fname,extension = os.path.splitext(fname)
# cluster_4 -- 4
custernum = fname.split('_')[1]
# hidden from GUI display because it starts with _
polarname = '_polar_'+clusternum
cmd.delete(fname)
cmd.delete(polarname)
cmd.extend('delclust',delclust)

2. Then you should be able to use a similar procedure to
before. Remember that you now need to delete things and pass the name of
your protein to the functions so that polar contacts can be displayed
correctly:

for i in glob.glob(Model_1/cluster_*.sdf): loadclust(i,myprotein)

analyze things

for i in glob.glob(Model_1/cluster_*.sdf): delclust(i,myprotein)

for i in glob.glob(Model_2/cluster_*.sdf): loadclust(i,myprotein)

Unfortunately, I don't have any SD files on hand, so I haven't tested these!
Some modification may be necessary. You should also check out the script
that Jason linked.

Cheers,

-Michael

On Wed, Sep 22, 2010 at 11:52 AM, Renuka Robert renukarob...@ymail.comwrote:

 Dear Michael
 Thanks for your detailed reply. This is what exactly i needed. Now i want
 to find the hydrogen bonding between each cluster files and the protein. So
 i do the following step

 cd /home/user

 import glob


  then I load the Model_1 files with


  for i in glob.glob(Model_1/cluster_*.sdf): cmd.load(i)


  Now hydrogen bond should be displayed between protein and
 Model_1/cluster_*.sdf. Polar contacts in different colors would be more
 appreciated.


  Could you please attach your script in the above command, so that all the
 cluster_*.sdf is loaded and its polar contacts is displayed in one press.


  Thanks in advance

 Renuka.


 --- On *Wed, 22/9/10, Michael Lerner 
 mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com
 * wrote:


 From: Michael Lerner 
 mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com
 
 Subject: Re: [PyMOL] Deleting and Loading multiple SDF files
 To: Renuka Robert renukarob...@ymail.com
 Cc: PyMOL-users@lists.sourceforge.net
 Date: Wednesday, 22 September, 2010, 1:46 PM


 Hi Renuka,

 If I understand correctly, this is what you want to do:

 1. Load up all of the cluster*.sdf files in Model_1.
 2. Analyze them
 3. Delete them
 4. Load up all of the cluster*.sdf files in Model_2.
 5. Analyze them
 6. Delete them
 etc.

 If that's right, I think the easiest thing is just to change to the
 directory that contains your Model_N subdirectories. In your example, that
 would be:

 cd /home/user
 import glob

 then load the Model_1 files with

 for i in glob.glob(Model_1/cluster_*.sdf): cmd.load(i)

 then analyze them. It sounds like you're analyzing them by hand; if you're
 analyzing them by running some scripts, we can probably help to automate
 that process as well.

 After analyzing them, (and saving your results!), you'll want to delete the
 current batch of cluster files and load the new ones:

 delete cluster_*
 for i in glob.glob(Model_2/cluster_*.sdf): cmd.load(i)

 Note that you only have to type import glob once.

 Hope that helps,

 -Michael

 On Wed, Sep 22, 2010 at 9:12 AM, Renuka Robert 
 renukarob...@ymail.comhttp://mc/compose?to=renukarob...@ymail.com
  wrote:

  Dear Pymol users


  I have to do TWO jobs simultaneously in PYMOL.


  JOB 1: Load multiple *sdf files


  I have set of ligand files in *.sdf format as follows:


  /home/user/Model_1/cluster_1.sdf

 /home/user/Model_1/cluster_2.sdf

 /home/user/Model_1/cluster_3.sdf


  /home/user/Model_2/cluster_1.sdf

 /home/user/Model_2/cluster_2.sdf

 /home/user/Model_2/cluster_3.sdf


  /home/user/Model_3/cluster_1.sdf

 /home/user/Model_3/cluster_2.sdf

 /home/user/Model_3/cluster_3

Re: [PyMOL] Wizard Measurement

2010-09-05 Thread Michael Lerner
Hi Martin,

I find that the easiest way to recreate things like this is with cmd.do.
cmd.do('wizard measurement') is identical to typing 'wizard measurement'
from the command line.

In this particular case, it looks to me like just calling
cmd.wizard('measurement') works. Did you find problems when you didn't call
refresh_wizard?

Thanks,

-Michael

On Sat, Sep 4, 2010 at 12:40 PM, Martin Hediger ma@bluewin.ch wrote:

  Dear All
 I'm trying to write a littel function that allows for a short cut to
 invoke the wizard measurement. The idea is, that instead of having to
 open the GUI menueMeasurement or typing wizard measurement, I would
 like to be able to just type mes and have the measurement tool-box
 available.
 Observing what happens in the log-file when doing this shows that two
 things happen:

 wizard measurement
 refresh_wizard


 I figured out, that I can write cmd.wizard(measurement) into the
 function definition (called mes, in mes.py), and the measurement box
 appears. What I cant figure out is how to implement the refreshment of
 the wizard using the PyMOL-API.
 Can someone point this out to me?

 Thanks for any help on this, btw. the same thing would kind of be nice
 for mutagenesis.

 Martin


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Re: [PyMOL] Start PyMOL from command line

2010-09-01 Thread Michael Lerner
Hi Martin,

I know a few ways to do this:

1) If you've set your Mac up to load PDB files with PyMOL by default, you
can just type open *.pdb from the command line.

2) Instead of using OS X's open command, you can launch PyMOL directly via
/Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL *.pdb (you may
have to change that depending on where you have PyMOL installed).

3) From within PyMOL, you can type

from glob import glob
for f in glob.glob(*.pdb): cmd.load(f)

and it will load them all.


There's more information to be found on the wiki (
http://www.pymolwiki.org/index.php/Launching_PyMOL), including information
on how to set up aliases so that you can just type pymol to launch it.
It's worth noting that pymol -c will launch PyMOL in batch mode without
the GUI, which may not be what you want.

Cheers,

-Michael


On Wed, Sep 1, 2010 at 9:44 AM, Martin Hediger ma@bluewin.ch wrote:

  Dear All
 I'm using Mac OS X and would like to start PyMOL from the command line,
 so I can open up .pdb files from a command line argument by issuing $
 pymol -c /directory/*pdb (for some reason, within pymol it seems to be
 not possible to issue 'PyMOL  *pdb').
 When I enter 'pymol' in the Terminal, the Shell freezes and I have to
 kill the process.
 What is required to do so PyMOL becomes launchable from the command line.

 Thanks for suggestions.

 Martin


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Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Michael Lerner
Hi,

Which version of PyMOL, APBS and PDB2PQR are you using?

If you send me a PQR file off-list, I can take a closer look at what's going
on.

Thanks,

-Michael

On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties assigned and to either remove or fix the
 atoms.  How can I fix them?  The problem residues are just regular
 amino acids; no split confrimations etc.  I've also tried editing out
 the PDBs chain name before converting to the PDB to PQR but that
 didn't work.

 Another things I've tried is using APBSTools 2 but it errors as soon
 as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

 I really need to get this to work but I have no clue what to try next.

 Thanks in advance for any thoughts.
 -Jon


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Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Michael Lerner
On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya 
shiven.shandi...@gmail.com wrote:

 Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo
 does a stellar job as far as integrating outside programs with PyMOL goes.


I initially wrote the PyMOL/APBS plugin for my own use and I now
maintain/develop it as a community resource in my limited free time. Despite
this, several hundred users (at least) have found it quite helpful in their
research, and I've included many newer features based on their feedback. The
plugin is certainly not perfect, and I don't mind people knocking it down,
but I appreciate it when that knocking down comes with constructive
feedback.

Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as
completely free and open source suite of programs. For many reasons, I
believe that free and open source software is vital to to good science. I
would strongly urge users to consider such issues before settling on a suite
of software products, especially when you're already working with programs
like PyMOL and APBS.

Cheers,

-Michael



 Good luck!

 Best,
 Shiven



 On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties assigned and to either remove or fix the
 atoms.  How can I fix them?  The problem residues are just regular
 amino acids; no split confrimations etc.  I've also tried editing out
 the PDBs chain name before converting to the PDB to PQR but that
 didn't work.

 Another things I've tried is using APBSTools 2 but it errors as soon
 as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

 I really need to get this to work but I have no clue what to try next.

 Thanks in advance for any thoughts.
 -Jon


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[PyMOL] Some plugin development questions

2010-03-04 Thread Michael Lerner
Hi all,

I'm trying to pretty up the next version of the APBS plugin and I've
run into two issues that I'm hoping others have solved:

1. Does anyone have any experience with PMW's OptionMenu? I've been
trying something where I call an OptionMenu's setitem() and it keeps
failing no matter what I do. Perhaps someone can just point me at some
working sample code.

2. I'm having trouble launching command-line Python scripts from my
plugin on OS X. Scripts complain about things like import time
failing that work from the command line. I have a wrapper function
that works on Windows, OS X and Linux for normal binaries, and I've
included it below. It looks to me like programs launched via PyMOL
(either via os.system or via subprocess.call) just don't get a proper
environment set up, thus causing Python imports to fail, but I'm not
entirely sure.

I typically work around this in an ugly way: I mess around with
sys.path, import whatever.py and then call whatever.main() directly.
This is obviously quite fragile and depends on whatever.py to have a
nice whatever.main() defined. It gets substantially worse when
whatever.py wants lots of things in its own path.

Has anyone else experienced this? Do you know a nice workaround?

Thanks,

-Michael

def run(prog,args):
'''
wrapper to handle spaces on windows.
prog is the full path to the program.
args is a string that we will split up for you.
or a tuple.  or a list. your call.

return value is (retval,prog_out)

e.g.

(retval,prog_out) = run(/bin/ls,-al /tmp/myusername)
'''
import subprocess,tempfile

if type(args) == type(''):
args = tuple(args.split())
elif type(args) in (type([]),type(())):
args = tuple(args)
args = (prog,) + args

try:
output_file = tempfile.TemporaryFile(mode=w+)  # --
shouldn't this point to the temp dir
except IOError:
print Error opening output_file when trying to run the APBS command.

print Running:\n\tprog=%s\n\targs=%s % (prog,args)
retcode = 
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
output_file.seek(0)
#prog_out = output_file.read()
prog_out = ''.join(output_file.readlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print Results were:
print Return value:,retcode
print Output:
print prog_out
return (retcode,prog_out)

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Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

2010-02-13 Thread Michael Lerner
I don't have any MD trajectories on hand at the moment, but can DynoPlot do
this? If not, it might be an easy modification.

Cheers,
-Michael

On Sat, Feb 13, 2010 at 9:48 PM, Sean Law magic...@hotmail.com wrote:

  Hi,

 Another idea that came to mind while staring at MD trajectories all day is
 the ability to display measured values (distance, angle, dihedral, etc) in a
 localized or boxed in area (maybe even under the list of objects).  The main
 use for a measurement area would be to make it easier to monitor allosteric
 effects.  For example, from an MD simulation, if I have a protein that has
 two distant binding sites and I want to monitor the effects on site A
 (perhaps, the cavity of site a changes) when the inhibitor binds to site B.
 In PyMOL, I could measure the distance between the inhibitor and site B but
 it may simply be too far away to see the changing value as I flip through
 the frames since it is so far away from site A.  If the measurement was
 instead displayed in its own distinct area, independent of the molecule
 viewing pane then this could be helpful (or have it displayed in both a
 separate location as well as the molecule viewing area).

 Just a thought.

 Sean

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Re: [PyMOL] New Feature Ideas

2010-02-12 Thread Michael Lerner
Hi Sean,

On Fri, Feb 12, 2010 at 12:39 PM, Sean Law magic...@hotmail.com wrote:

  Hi all,

 Another feature that I find myself always wanting is a kill script button
 and/or command.  This comes in handy when I am testing a new python script
 and, accidentally, throw in an infinite loop.  It would be nice to have some
 sort of kill switch not only for python scripts but even for something as
 simple as ray-tracing.  There are times when I am ray-tracing a complicated
 scene and realize that half-way through the ray-tracing process that
 something was missing.  In that case, I normally have to kill PyMOL and
 start all over again (and hopefully, I'll have the scene/session saved).
 Having this function would greatly enhance my productivity.


You should see a button labeled Abort at the bottom right of the external
GUI window. You can click it to stop the ray tracer. It used to only work if
you started the ray tracer by clicking the Ray button in that same window,
but it appears to work no matter how you start the ray tracer now (1.2r2).

Cheers,

-Michael



 Thanks!

 Sean

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[PyMOL] Showing electric field lines

2010-02-10 Thread Michael Lerner
Hi all,

Someone recently asked me if there was a way to display field lines with
PyMOL or with an external plugin. Here's what I wrote:

It turns out that PyMOL recently grew the ability to display field lines.
After you've run APBS, you'll have a map object called pymol-generated. Try
this series of commands from the PyMOL prompt:

gradient my_grad, pymol-generated
ramp_new my_grad_ramp, pymol-generated
color my_grad_ramp, my_grad

I'm considering building this into the next version of the plugin.

Cheers,

-Michael

-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] color by element

2010-02-09 Thread Michael Lerner
have you tried:

import util
util.cbag
util.cbay
util.rainbow

etc?

after you type import util, you can type util. followed by a tab to
see the available commands.

On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols nathaniel.ech...@gmail.com
 wrote:

 On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cuwrote:

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?


 I don't think there's a single command that does this; I've always done
 something like this:

 color grey80, elem c
 color white, elem h
 color red, elem o
 color blue, elem n
 color orange, elem s

 and so on (in python, these become 'cmd.color(grey80, elem c)', etc.).
  I just discovered that there is also a separate color name for each
 element, e.g. color carbon, elem c will work, but the default coloring
 scheme seems a bit wacky sometimes (carbon is green, etc.).  If there was a
 convenient way to switch between available color sets (e.g. all of the
 options available in the menus), that would be awesome.  Currently the
 atom-name colors are hardcoded in C, unfortunately.

 Nat


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Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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[PyMOL] Pre-release version of the PyMOL-APBS plugin

2010-01-28 Thread Michael Lerner
Hi all,

I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release. There are three big advantages of
the new version:

* It's been tested modern OS X, Windows and Linux systems and fixes several
long-standing bugs.
* It allows you to call through to PDB2PQR directly.
* It has two visualization panels to aid in showing multiple potential
surfaces at once.

I've also upped the default maximum allowed memory since typical users have
bigger and faster computers these days.

The main reason that I'm sending this out now is to get bug reports. I think
it runs everywhere, but *please* let me know if you have problems with it.
Once it's shown to be stable, it'll be included in the next PyMOL release.

A slightly longer list of changes is included below.

== How to get it ==

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version
via

svn co
https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin

* You can download the it from
http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py

That should give you a file called apbsplugin.py

Once you have the plugin, you can install it via PyMOL's plugin installer:
Plugin -- Manage Plugins -- Install

Note that the plugin will be installed as APBS Tools2 so that you can
continue to use your old version.

== Longer feature list ==

* The ability to call through directly to PDB2PQR
* More modern apbs input files
* Two visualization panels. It's often quite useful to look at two different
electrostatic potentials at once. It's also quite useful to look at
electrostatic potentials mapped onto two different surfaces at once.
Multiple visualization panels makes this a snap: just set up one surface on
panel 1 and another surface on panel 2.
* Fixes several bugs that caused crashes on both OS X and Linux systems
* Increased maximum allowed memory
* Switch from os.system to subprocess for running external programs
* Deals with paths on Windows properly
* Gives better diagnostic information so that PyMOL/APBS developers can find
bugs more easily
* Lots of internal code cleanup

You can find this same information on the PyMOL wiki:
http://pymolwiki.org/index.php/User:Mglerner

Thanks,

-Michael

-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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[PyMOL] Rendering plugin

2010-01-21 Thread Michael Lerner
With all of the recent discussion about extensions to the ray command, I
thought I'd mention a little plugin I wrote several years ago. You can find
it at the bottom of

http://sitemaker.umich.edu/carlsonlab/resources.html

It's not quite as full-featured as some of the proposed ray extensions, but
it does provide a really easy way for you to say I want a 4in x 3in figure
at 600dpi.

The Ray button raytraces, and the Draw button just draws the image
without raytracing (a fast way to see that the height/width look good).

It warns you not to have the plugin window on top of your main PyMOL window
when you click Ray. That doesn't seem to be necessary anymore, at least on
my MacBook Pro.

[image:
?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw]

Cheers,

-Michael

-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

2010-01-21 Thread Michael Lerner
The ray command bugs me, so I'll take a stab at improving it this afternoon.

Can someone tell me how to get the size of the current viewport?

This solution:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

width,height = cmd.get_session()['main'][0:2]


doesn't seem to work for me:

PyMOLprint sorted(cmd.get_session().keys())
['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
'version', 'view', 'view_dict', 'wizard']

-Michael

On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established companies.
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-- 
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

2010-01-21 Thread Michael Lerner
I think this works. It handles different units (in and cm). If you leave out
width or height, it gets scaled correctly. If you  leave them both out, you
get whatever the current viewport size is (is there something better?).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):

Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.

rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600

Extra keyword arguments get passed on to the normal ray command.

if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x:   units = 'in'
elif 'cm' in x: units = 'cm'
x = float(x.replace(units,'').strip())
if units ==   'cm':   x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print x,units,dpi
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us.
try:
height,width = todots(height,units,dpi),todots(width,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
#cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)

On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner 
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 The ray command bugs me, so I'll take a stab at improving it this
 afternoon.

 Can someone tell me how to get the size of the current viewport?

 This solution:
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

 width,height = cmd.get_session()['main'][0:2]


 doesn't seem to work for me:

 PyMOLprint sorted(cmd.get_session().keys())
 ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
 'version', 'view', 'view_dict', 'wizard']

 -Michael

 On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established
 companies.
 http://p.sf.net/sfu/rsaconf-dev2dev
 ___
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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 --
 Michael Lerner, Ph.D.
 IRTA Postdoctoral Fellow
 Laboratory of Computational Biology NIH/NHLBI
 5635 Fishers Lane, Room T909, MSC 9314
 Rockville, MD 20852 (UPS/FedEx/Reality)
 Bethesda MD 20892-9314 (USPS)




-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

2010-01-21 Thread Michael Lerner
Here's a slightly improved version. It only kicks in if dpi is specified. I
think that you could make the obvious modifications to the help message and
argument list and use it as a replacement for cmd.ray (as long as you're
aware of the fact that the argument list will be different).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=-1,units='in',**kwargs):

Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.

rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600

Extra keyword arguments get passed on to the normal ray command.

Units can be 'in' or 'cm'.

For backwards compatibility, the conversion to dpi (or dots per
centimeter) is only performed when dpi is specified.

if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x:
units = 'in'
elif 'cm' in x:
units = 'cm'
x = float(x.replace(units,'').strip())
if (dpi == -1):
return x
if units ==   'cm':   x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print '%s%s at %sdpi'%(x,units,dpi)
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us when
given -1.
try:
width,height = todots(width,units,dpi),todots(height,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)


On Thu, Jan 21, 2010 at 2:39 PM, Michael Lerner 
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 I think this works. It handles different units (in and cm). If you leave
 out width or height, it gets scaled correctly. If you  leave them both out,
 you get whatever the current viewport size is (is there something better?).

 #!/usr/bin/env pymol

 from pymol import cmd

 def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
 
 Slightly better version of the ray command.
 You can specify width and height in the units of your choice, e.g.

 rayy 3,2,units=in,dpi=300
 rayy 3in,2in
 rayy 1in, 2 cm, dpi=600

 Extra keyword arguments get passed on to the normal ray command.
 
 if type(dpi) in [type('')]: dpi = int(dpi)
 in_per_cm = 0.393700787
 def todots(x,units,dpi):
 if type(x) in [type('')]:
 x = x.lower()
 if 'in' in x:   units = 'in'
 elif 'cm' in x: units = 'cm'
 x = float(x.replace(units,'').strip())
 if units ==   'cm':   x = x * in_per_cm
 elif units == 'in': pass
 else: raise ValueError('Unknown units (%s)'%units)
 print x,units,dpi
 return int(x * dpi)
 # How do we get current width/height of viewport? MainSceneGetSize
 perhaps
 # But it doesn't matter, as PyMOL will autoscale internally for us.
 try:
 height,width = todots(height,units,dpi),todots(width,units,dpi)
 except ValueError:
 print Unknown units
 return
 print 'width',width,'height',height
 cmd.ray(width=width,height=height,**kwargs)
 #cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
 cmd.extend('rayy',rayy)

 On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner 
 mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 The ray command bugs me, so I'll take a stab at improving it this
 afternoon.

 Can someone tell me how to get the size of the current viewport?

 This solution:

 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

 width,height = cmd.get_session()['main'][0:2]


 doesn't seem to work for me:

 PyMOLprint sorted(cmd.get_session().keys())
 ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
 'version', 'view', 'view_dict', 'wizard']

 -Michael

 On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues

Re: [PyMOL] Rendering plugin

2010-01-21 Thread Michael Lerner
In keeping with the modern way of doing things, I've

1. put the rendering plugin up on the wiki (
http://pymolwiki.org/index.php/Rendering_Plugin )
2. put a metric version of the plugin on the same page
3. put the rayy code on my userpage on the wiki ( see my .pymolrc here:
http://pymolwiki.org/index.php/User:Mglerner ). If you add it to your
.pymolrc, you will be able to type rayy 3 in, 2 in, dpi=300 from the PyMOL
command line
4. Followed Luca Jovine's suggestion to change the order of rayy's
arguments.

Cheers,

-Michael

On Thu, Jan 21, 2010 at 11:29 AM, Michael Lerner mgler...@gmail.com wrote:

 With all of the recent discussion about extensions to the ray command, I
 thought I'd mention a little plugin I wrote several years ago. You can find
 it at the bottom of

 http://sitemaker.umich.edu/carlsonlab/resources.html

 It's not quite as full-featured as some of the proposed ray extensions, but
 it does provide a really easy way for you to say I want a 4in x 3in figure
 at 600dpi.

 The Ray button raytraces, and the Draw button just draws the image
 without raytracing (a fast way to see that the height/width look good).

 It warns you not to have the plugin window on top of your main PyMOL window
 when you click Ray. That doesn't seem to be necessary anymore, at least on
 my MacBook Pro.

 [image:
 ?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw]

 Cheers,

 -Michael

 --
 Michael Lerner, Ph.D.
 IRTA Postdoctoral Fellow
 Laboratory of Computational Biology NIH/NHLBI
 5635 Fishers Lane, Room T909, MSC 9314
 Rockville, MD 20852 (UPS/FedEx/Reality)
 Bethesda MD 20892-9314 (USPS)




-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
ishot-10.png--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

2010-01-20 Thread Michael Lerner
Several more votes for one of these from lots of people in my lab.

On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established companies.
 http://p.sf.net/sfu/rsaconf-dev2dev
 ___
 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




-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
Throughout its 18-year history, RSA Conference consistently attracts the
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Re: [PyMOL] select atoms near electron density

2010-01-11 Thread Michael Lerner
Yes, I believe this is the case.

-Michael

On Sat, Jan 9, 2010 at 4:20 AM, Jason Vertrees jason.vertr...@gmail.comwrote:

 Michael,

 I don't think this is possible with PyMOL.  Distance measures are
 calculated from objects.

 -- Jason

 --
 Jason Vertrees, PhD
 jason.vertr...@schrodinger.com

 PyMOL Product Manager
 Schrodinger, Inc.



 On Fri, Jan 8, 2010 at 7:05 PM, Michael Zimmermann micha...@iastate.edu
 wrote:
  Dear PyMol users,
 
  I wonder if anyone knows a way to select atoms that are near a region
  of electron density.
 
  Say I have a binding pocket in atomic detail, but the ligand binds
  transiently and non-specifically, so I just have an approximate
  electron density could for it.  Is it possible to select atoms in an
  object that are near to these density levels?  Alternatively, can you
  turn a map into an object that can be used in this way (fill it with
  dummy atoms)?
 
  Thank you,
 
  Michael Zimmermann
 
 
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Re: [PyMOL] unable to initialize plugin

2010-01-08 Thread Michael Lerner
This sounds familiar. I think I ran into the same thing with the APBS plugin
when upgrading PyMOL at one point.

On Fri, Jan 8, 2010 at 11:51 AM, Jason Vertrees jason.vertr...@gmail.comwrote:

 Ilaria,

 Which plugin are you trying to use?  Also, please beware that scripts
 and plugins are different and have different methods of install.
 Lastly are you using PyMOL 0.99, 1.x?

 -- Jason

 --
 Jason Vertrees, PhD

 PyMOLWiki -- http://www.pymolwiki.org



 On Fri, Jan 8, 2010 at 9:21 AM, ilaria carlone
 ilariacarl...@hotmail.com wrote:
  Hi all,
 
  I have some problems after the installation of plugins in PyMOL.
  I downloaded some plugins from the pymol wiki and copied them in the
  indicated directory (such as C:\Programs\DeLano
  Scientific\PyMOL\modules\pmg_tk\startup). I installed them by the PyMOL
  interface and restarted the program, but, after lauching PyMOL, it
 returned
  the following message:
 
  Traceback (most recent call last):
File /home/scivis/pymol/modules/pmg_tk/PMGApp.py, line 227, in
  initializePlugins
  mod.__init__(self)
  TypeError: module.__init__() argument 1 must be string, not instance
  Error: unable to initialize plugin (and the name of the plugin...)
 
  Can you help me? Maybe it is a trivial problem...
 
  Thanks,
 
  Ila
 
  
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Re: [PyMOL] dynamic bonding

2009-12-14 Thread Michael Lerner
I remember this posting from a while ago:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06885.html

which may have some clues.

--- begin ---

Whoops, my bad -- I duped the approval before seeing your repost!

Answer:


# first create a phony molecular trajectory

load $PYMOL_PATH/test/dat/pept.pdb, obj

for a in range(2,31): cmd.create(obj,obj,1,a)

unbond 5/c, 6/n

protect not ((5/c or 6/n) extend 4)

sculpt_activate obj, 30

sculpt_iterate obj, 30, 100

smooth obj, 30, 3



# then program a bond-break/re-form movie

mset 1 x30 1 -30 30 x30 30 -1

mdo 45: unbond 5/c, 6/n, quiet=1

mdo 100: bond 5/c, 6/n, quiet=1

frame 100

as sticks

orient 5-6/n+ca+c

mplay


# NOTE: only tested on PyMOL 1.2.x

Cheers,
warren

 end 

On Mon, Dec 14, 2009 at 1:12 PM, Jason Vertrees jason.vertr...@gmail.comwrote:

 Nick,

 Interesting question.  My best guess at this point is that PyMOL can't
 do what you want.  You can load the XYZ file into multiple distinct
 objects:

load myXYZ.xyz, multiplex=1

 and each object will be shown with proper bonding.  However, the
 moment you try to combine those into one structure they retain the
 bonding topology of the first structure.  If you change any
 intermediate state, then they all change.

 Anyone else?

 -- Jason

 --
 Jason Vertrees, PhD

 PyMOLWiki -- http://www.pymolwiki.org



 On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock nicolasb...@gmail.com
 wrote:
  Hello list,
 
  I have a bunch of xyz files that are along a transition path in a
 molecule.
  When I load all of them into pymol and step through the individual
 frames,
  pymol calculates the bonds only for the initial frame. This leads to
 wrong
  bonding in subsequent frames since some atoms move quite a bit during the
  transition. How can I get dynamic bonding so that bonding is
 recalculated
  for each frame?
 
  nick
 
 
 
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Re: [PyMOL] Pymol access denied at the NIH

2009-12-07 Thread Michael Lerner
Access to pymol.org has been restored.

On Fri, Dec 4, 2009 at 8:25 PM, Michael Lerner 
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 I have no idea why it's been blocked. I filed a ticket with the help desk
 (by clicking on the link in the middle of the Access Denied page) asking
 why the site was blocked.

 I don't see any evidence of hacking on the website. Does anybody else in
 PyMOL-land have any insight into why the site would be blocked?

 Assuming that it's just a clerical error, the help desk would probably
 respond more quickly to a ticket from you than to one from a mere IRTA.

 Thanks,

 -Michael


 On Fri, Dec 4, 2009 at 4:36 PM, Margulies, David (NIH/NIAID) [E] 
 dmargul...@niaid.nih.gov wrote:

 Pymol website access has been denied at the NIH.  How is this happening?


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Re: [PyMOL] Pymol access denied at the NIH

2009-12-04 Thread Michael Lerner
I have no idea why it's been blocked. I filed a ticket with the help desk
(by clicking on the link in the middle of the Access Denied page) asking
why the site was blocked.

I don't see any evidence of hacking on the website. Does anybody else in
PyMOL-land have any insight into why the site would be blocked?

Assuming that it's just a clerical error, the help desk would probably
respond more quickly to a ticket from you than to one from a mere IRTA.

Thanks,

-Michael

On Fri, Dec 4, 2009 at 4:36 PM, Margulies, David (NIH/NIAID) [E] 
dmargul...@niaid.nih.gov wrote:

 Pymol website access has been denied at the NIH.  How is this happening?


 --
 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

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Re: [PyMOL] APBS plugin woes

2009-12-01 Thread Michael Lerner
We solved the problem this afternoon. The version of APBS that comes with
PyMOL does not work on Tiger (10.4). Neither does the universal binary of
apbs-1.2.1b available on sourceforge.

An older version of apbs (0.5) worked. We are in the middle of installing
APBS via MacPorts, as it seems like that should work too.

I've added some troubleshooting instructions to both

http://pymolwiki.org/index.php/APBS
and
http://pymolwiki.org/index.php/User:Mglerner

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote:

 I download and install macpymol-1_2r2.tgz.

 I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
 up.

 Load a pdb file after removing HETATM lines.

 Open APBS Tools and set grid:
 Log:
 Maximum number of grid points exceeded.  Old grid dimensions were
 [129, 97, 129]
 Fine grid points rounded down from [117, 87, 117]
 New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

 Click Run APBS, see hydrogens appear, see residues being selected
 and unselected, then the display says:

 Log:
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


 Help?
 PowerBook, PPC, 10.4.11

 Dave


 --
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Re: [PyMOL] APBS plugin woes

2009-11-30 Thread Michael Lerner
Can you go to the Program Locations tab and find out which version of APBS
you're using? There's a problem with the one in
/Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

I've added instructions for fixing this problem to
http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
top of the page, under APBS Plugin FAQ. Could you try them out and see if
they work for you?

Thanks,

-Michael

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote:

 I download and install macpymol-1_2r2.tgz.

 I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
 up.

 Load a pdb file after removing HETATM lines.

 Open APBS Tools and set grid:
 Log:
 Maximum number of grid points exceeded.  Old grid dimensions were
 [129, 97, 129]
 Fine grid points rounded down from [117, 87, 117]
 New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

 Click Run APBS, see hydrogens appear, see residues being selected
 and unselected, then the display says:

 Log:
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


 Help?
 PowerBook, PPC, 10.4.11

 Dave


 --
 David N. Garboczi, PhD
 Phone: 301-496-4773
 Head, Structural Biology Section (SBS)
 Research Technologies Branch (RTB)
 National Institute of Allergy and Infectious Diseases (NIAID)
 National Institutes of Health (NIH)
 Twinbrook 2/Room 110
 12441 Parklawn Drive
 Rockville, Maryland 20852-1742
 Fax:301-402-0284
 Email: dgarbo...@niaid.nih.gov


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Re: [PyMOL] segmentation fault!

2009-11-23 Thread Michael Lerner
Hi,

I can try to look into this, although I'm not sure what's causing it. Can
you tell me

 - what version of PyMOL you have and how it was installed
 - what version of APBS you have and how it was installed
 - when exactly the segmentation fault happens (are you working with a
particular PDB file, etc.)

Thanks,

-Michael

On Sun, Nov 22, 2009 at 4:00 PM, Mehdi Talebzadeh Farooji 
mahdi...@yahoo.com wrote:

 Dear All,

 I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try
 to call plugin of pymol for APBS, pymol crashes with segmentation fault
 message.  Every suggestion would be welcomed!

 Thanks,

 Mehdi

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

2009-09-04 Thread Michael Lerner
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.uswrote:

 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
 
 
 
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Re: [PyMOL] problems with apbs/pqr

2009-08-05 Thread Michael Lerner
Whoops! I accidentally replied only to James, rather than to the whole list.
PyMOL has some trouble with assigning charges. PDB2PQR handles it, but
manages to generate a bad PQR (missing the space between some columns with
leading minus signs, e.g. -100.2345-100.2345). Fixing the PQR file by hand
fixes the problem.

-michael

On Wed, Aug 5, 2009 at 11:35 AM, Warren DeLano war...@delsci.com wrote:

  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 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


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Re: [PyMOL] is this how i would write a coding sequence?

2009-07-07 Thread Michael Lerner
Aha! I knew there was a better way of doing this, but I was stuck on a
machine that only had an old version of PyMOL. Assuming you're using PyMOL
1.0 or newer, you can just use pseudoatom. To create a sphere of radius 10.0
at the xyz position (50.0,60.0,12.0), just do this:

pseudoatom mysphere, pos=[50.0,60.0,12.0], vdw=[10.0]

it will appear as a kind of cross at first. to show it as a sphere, type

show spheres, mysphere

to make it partially transparent, type

set sphere_transparency, 0.5, mysphere

The sphere that you get will look kind of blocky. You can get a perfect
sphere by raytracing, e.g. typing

ray

If you don't mind the fact that it won't be transparent, you can get a
perfect sphere in the normal viewer by typing

set sphere_mode, 5

To go back to normal spheres after you've done that, type

unset sphere_mode

I think this will be easier than the other way I recommended.

Cheers,

-michael

On Tue, Jul 7, 2009 at 1:55 PM, Benjamin Michael Owen
owe...@marshall.eduwrote:

 I'm trying to use a suggestion another pymol user sent to create a sphere
 of a specific size in a pdb file. Is this the correct coding? I have no
 experience doing any kind of programming so I am not sure if I did this
 right. I put the text I entered in in red if that helps anything.

 ben

 create sphere, resi 24 and resi 864 create a new object from resi 864

 alter sphere, vdw=10.0 # 28.5

 rebuild # necessary if spheres have already been shown

 show spheres, sphere

 alter_state 1, sphere, x,y,z = 50,60,10 # set desired x,y,z coords

 set sphere_transparency, 0.5, sphere # make it transparent

 zoom

 ray


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Re: [PyMOL] pymol question

2009-07-06 Thread Michael Lerner
I'm sure there's a way to actually draw a circle, but for your particular
use it might be better to use a sphere. If you're comfortable with python
scripting, you can use CGO objects. If not, you might do something like
this:

fetch 1hhp
create thing, resi 24 and name ca # create a new object from some single
atom selection
alter thing, vdw=10.0 # set desired radius
rebuild # necessary if spheres have already been shown
show spheres, thing
alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords
set sphere_transparency, 0.5, thing # make it transparent
zoom
ray

you can also use something like select + within to select all residues
within a cutoff, but I got the impression you wanted a nice visualization.


Hope that helps,

-michael

On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen
owe...@marshall.eduwrote:

 Does anyone know how to draw a circle with a given radius in pymol? I have
 a distance that I want to use to see what residues lie on the end of that
 radius, but I have no idea how to write the command to draw the circle.
 Could someone help me please?


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Re: [PyMOL] Missing external GUI and search for the APBS plug-in for PyMOL

2009-03-13 Thread Michael Lerner
I've seen this before when something went wrong with launching X11.

Have you tried launching X11 first, verifying that it works, and then
launching PyMOLX11Hybrid while X11 is already running?

On Fri, Mar 13, 2009 at 1:15 PM, Atreyi Chatterjee chatterj...@mail.nih.gov
 wrote:

 Hi,
 I was trying to find out how to locate and use the APBS plug-in for
 MacPyMOL and when I mailed to the APBS-users list I was advised to
 rename MacPyMOL.app to PyMOLX11Hybrid.app which would make the APBS plug-in
 work in PyMOL.
 I tried following this suggestion and being a complete novice in this field
 I might be missing some simple points here or making some silly mistakes. I
 would be really grateful if you share your thoughts with me.
 My issue is that once i rename MacPyMOL.app to PyMOLX11Hybrid.app I end up
 opening a version of PyMOL that has the the top area or the  External GUI
 missing. Only the bottom window containing the Internal GUI opens up.
 Since the external GUI has all the user friendly menu bars for a layman like
 me it is more familiar and easier to work with. The internal GUI has the
 secondary command line and it would be almost impossible for a person like
 me to work using this only. I am wondering if the PyMOLX11 version works
 only with commands only?
 Or, is it something that I have done that made the external GUI
 disappear!!
 This is what i didwhen i tried opening the PyMOLX11Hybrid on my
 Mac, it asked me to choose an application and asked for the location of
 X11. I specified it from the applications folder and it opened up w/o the
 external GUI.

 W/o the external GUI i cannot access the wizard menu to access the APBS
 tools what am i saying, w/o it I cannot even open a file now!!!

 I do not have multiple monitors connected to my computer and I am not using
 Leopard with spaces enabled. I cannot figure out why the top GUI is missing
 from my screen!
 Is there a way to bring it back?

 Please help.

 Thanks
 Atreyi

 Atreyi Chatterjee, Ph. D.
 Section on Eukaryotic Transposable Elements
 NIH /NICHD/PCRM
 Bldg. 18T, Rm # 106
 Bethesda, MD 20892
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Re: [PyMOL] select by absolute coordinate

2009-03-04 Thread Michael Lerner
Hi,

I have a couple of quick notes about your specific application:

This works well when bilayers are flat. So, it works well for small bilayers
and it works well at the beginning of a simulation. For medium to large
bilayers, undulations throughout the simulation will cause this algorithm to
break.

Here are some other things that don't work:

 - selecting all lipids where atom X is higher than atom Y. In longer
simulations, lipids wiggle around enough that the heads can tilt and the
tails can even be higher than the heads.

 - same as above, but looking at the center of mass of the head vs. the COM
of the tail. This fails for the same reason. It turns out that lipids really
wiggle a lot.

 - etc.

These are easy errors to miss because the algorithms work well at the
beginning of the simulation, so even a quick visual examination won't show
the problems.

In my experience, the easiest thing to do is to use your method on the first
frame of a simulation, inspect the selection visually, and then write it out
explicitly for use in subsequent frames.

You probably know all of this, but I thought I'd mention it in case someone
was tempted to just take your code and apply it individually to each frame
of a simulation without really thinking about it. Unfortunately, I've seen
people make this particular error a few times (in both VMD and C), and
usually you can't tell they're making it just by reading their Methods
section :(.

Cheers,

-michael

On Wed, Mar 4, 2009 at 6:04 AM, Höfling Martin martin.hoefl...@gmx.dewrote:


 Am 04.03.2009 um 06:46 schrieb Warren DeLano:

 Hey Warren,

 It is remarkable that a question like this hasn't come up before, but it
 reveals a rather large whole in PyMOL's selection language:  though we have
 some proximity operators, we are not currently able to select atoms based on
 absolute or relative coordinate vector relationships.

 So the present answer to your question appears to be no.  Sorry about
 that!


 Just to give the application to my question: If you wanna select the upper
 leaflet of a bilayer - an easy method - shown to me in VMD is to select by
 residue all Phosphor atoms with e.g. z  40...

 Well I scripted a bit around it which worked in my case:

 def leafletIndex():
 '''
 Create leaflet indices for upper and lower bilayer, based on Phosphor
 atoms
 '''


 cmd.delete(Phosphor)
 cmd.delete(UpperLeaflet)
 cmd.delete(LowerLeaflet)




 cmd.select(Phosphor,name P*)
 ext=cmd.get_extent(Phosphor)
 lower=ext[0][2]
 upper=ext[1][2]
 middle=upper-lower
 atoms = cmd.get_model(Phosphor)

 cmd.select(UpperLeaflet,None)
 cmd.select(LowerLeaflet,None)

 for at in atoms.atom:
 if at.coord[2]  middle:
 cmd.select(UpperLeaflet,UpperLeaflet or index %d%at.index)
 else:
 cmd.select(LowerLeaflet,LowerLeaflet or index %d%at.index)


 cmd.select(UpperLeaflet,byres UpperLeaflet)
 cmd.select(LowerLeaflet,byres LowerLeaflet)
 cmd.deselect()


 Best
 Martin


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Re: [PyMOL] How to display two or multiple eleectrostatic maps simultaneously with PyMol?

2008-06-27 Thread Michael Lerner
Hi,

The current version of the APBS Plugin (http://www.umich.edu/~mlerner/PyMOL)
has two visualization panes. You can use them to control two separate
molecule/map combinations.

Please let me know if you need more assistance,

-Michael

On Thu, Jun 26, 2008 at 10:28 PM, Youzhong Guo youzhong...@gmail.com
wrote:

 Dear All,

 I have difficulty to display two electrostatic maps with PyMol at the
 same time .

 I can correctly display one map with pdbset1.pqr and pdbset_1.dx as in
 slide No.1.
 I can also correctly display one map with pdbset3.pqr and pdbset_3.dx
 as in slide No.2.
 However, when I tried to load all of those four files with PyMol, what
 I can get is as in slide No. 3 or No.4. As you can see in slide No.3
 or No.4 the map is not correct as expected.

 Please download my files from the following link and see if you can
 simultaneously display two maps as shown in slide  No.1 and No.2 with
 PyMol.

 https://webspace.utexas.edu/yg387/Electron_static_potential.zip

 Thanks in advance,


 Youzhong

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[PyMOL] How to view electron densities from the PDB

2008-06-27 Thread Michael Lerner
Hi,

This is probably a fairly basic question, but I'm stumped. I want to
visualize electron densities along with my PDB file. So, say I'm interested
in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
doesn't seem to read the CIF file (?), so I downloaded and installed the
PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
I tried

sf-convert -i CIF -o Xplor -sf 2djx-sf.cif

but got some errors about the input format.

sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif

seemed to work (it produced a .Xplor file with what looks like data to me).
However, PyMOL gives me errors when I try to load the resulting .xplor file.

This may not be directly related to PyMOL, but I'm hoping it's a common
enough task that someone can point me in the right direction.

Thanks,

-michael

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Re: [PyMOL] drawing axes

2008-06-11 Thread Michael Lerner
@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users




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Re: [PyMOL] how to get version?

2008-06-03 Thread Michael Lerner
pymol.cmd.get_version()

(i kinda expected pymol.__version__ to work, but it doesn't)

On Tue, Jun 3, 2008 at 3:35 PM, Matthew O'Meara mattjome...@gmail.com
wrote:

 Hi All,

 Is there a simple way to test which version of pymol is begin used in a
 script?

 Specifically I would like to know if it is 1.0 or =1.0

 Thanks,

 Matt

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Re: [PyMOL] interior protein-surfaces

2008-05-29 Thread Michael Lerner
I'm not sure it's exactly what you're looking for, but this seems similar:

http://hollow.sourceforge.net/

On Tue, May 27, 2008 at 4:53 PM, Thomas S. Leyh, Ph. D. l...@aecom.yu.edu
wrote:

   From time to time I find it valuable to view the suface of a
 ligand-binding pocket looking out from the surface's interior.   This is
 accomplished in a variety of ways - principally, zooming and clipping.  It
 would be wonderful to be able to represent just the skin of the active
 site wrapping around the ligands, like a sac - this seems quite difficult to
 achieve.  A related problem is that ray-ing a surface that has been clipped
 yields a collection of odd surface regions that represent poorly the
 non-ray-ed version - it is as if the resolution of the ray it too gross to
 capture the clipping edges.

Advice appreciated.

 Thanks,

 Tom Leyh

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Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008?

2008-03-09 Thread Michael Lerner
On Fri, Mar 7, 2008 at 5:04 PM, DeLano Scientific del...@delsci.info wrote:
  So from where I sit, the obvious open-source candidates are:

  APBS (electrostatics -- improve the current plugin)

Please let me know if anyone decides to do this. I have an
(unreleased) improved version, and several ideas for how to improve it
further. I'd be glad to help out.

-michael


  RDKit (cheminformatics, depiction, UFF cleanup, etc.)
  mengine (MMFF small molecule cleanup)
  mpeg_encode (MPEG movie production on Linux, etc.)
  GIMP (image manipulation)
  Blender (general-purpose 3D modeling  animation)
  Jmol (publishing visualizations inside of web pages)
  Firefox (ditto)
  MMTK (molecular mechanics -- Python/flexible)
  GROMACS (molecular mechanics -- C/fast)
  OpenOffice (escape from the microsoft hegemony)

  (NOTE: work is already underway for mpeg_encode and mengine...)

  Are there other key open-source packages we might specifically target for
  integration with PyMOL, either through SOC or beyond?

  Although there are many niche tools, from a prioritization standpoint,
  efforts should focus on integrations that will impact the largest potential
  user base.  So what hypothetical integrations would be useful to virtually
  all medicinal chemists, all structural biologists, all movie-makers, all
  paper-writers, and so on?

  Cheers,
  Warren

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   -Original Message-
   From: Anders Norgaard [mailto:anders.norga...@gmail.com]
   Sent: Wednesday, March 05, 2008 1:10 PM
   To: DeLano Scientific
   Cc: pymol-users@lists.sourceforge.net
   Subject: Re: [PyMOL] Will Pymol participate in Google Summer
   of Code 2008?
  
   On Wed, Mar 5, 2008 at 9:57 PM, DeLano Scientific
   del...@delsci.info wrote:
Anders,
   
 No plans at present, but hey, it is still one whole week before a
week  before the deadline!
  
   :o)
  
Anyone out there with sufficient bandwidth to mentor?
 Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability
would  make a good SOC project?
  
   Well, there is also a whole list of stuff in your PyMOL By
   Popular Demand Survey (Jan 2008) mail, perhaps some of
   these could be bundled into a project?
  
   - An ActiveX Control
   - 2D structure display
   - More documentation, screencasts,  tutorials.
   - Browser plugins
   - Direct MPEG movie export
   - Direct WinAVI movie export
   - Structure cleanup  energy minimization
   - Objects/states split over multiple windows (side by side views)
   - Multi-line text annotations in scenes
   - APBS bundled witih PyMOL
   - Per-object Z clip
   - native Windows user interface in a single window
   - Undo
   - Improved molecular builder
   - Better RigiMOL integration
   - MOPAC integration
   - Sequence alignment editing
   - 3D PDF export
   - Cleaned up matrix  transformation interface
   - Blender integration
   - Nucleic acid building
   - Calculate surface areas and volumes
   - Secondary structure display in sequence viewer
   - Scene buttons / sorter
   - Movie slider ala Cinema4D/Maya/3DSMax
   - Drag  drop programming of object motions
  
   or
  
   Pymol MMTK integration?
  
  
   Best,
   Anders
  
  
  
  
   
 Cheers,
 Warren
   
   
   
  -Original Message-
  From: pymol-users-boun...@lists.sourceforge.net
  [mailto:pymol-users-boun...@lists.sourceforge.net] On
   Behalf   Of
Anders Norgaard   Sent: Wednesday, March 05, 2008 8:53 AM   To:
pymol-users@lists.sourceforge.net   Subject: [PyMOL] Will Pymol
participate in Google Summer of Code 2008?
 
  Hi,
 
 
  I guess that it is one of the great ways to catch young new  
contributors.
 
  http://code.google.com/soc/2008/
 
 
  Best,
  Anders
 
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Re: [PyMOL] Command-line arguments when using PyMOL to launch a script

2008-02-15 Thread Michael Lerner
Hi,

First, the initial error you were seeing was a syntax error:

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

is failing because of the word 3D

Second, that used to fail on Linux systems anyway (it worked on some
other systems). I tend to use optparse, which often requires things to
live in sys.argv. Here's my current workaround:

#argv = sys.argv[sys.argv.index('--') + 1:]
try:
argv = sys.argv
except AttributeError:
argv = pymol_argv
sys.argv = pymol_argv # this is necessary for optparse to
handle the --help option.
try:
argv = argv[argv.index('--') + 1:]
except IndexError:
argv = []

options,args = parser.parse_args(args=argv)

I haven't re-tested Linux recently, though. It might be that the
pymol_argv workaround is not necessary anymore.

-michael

-- 
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Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
http://www.umich.edu/~mlerner



Re: [PyMOL] Distance labels

2008-02-11 Thread Michael Lerner
An object whose name begins with an underscore will not appear in the menu.

On Feb 11, 2008 3:13 PM, Toni Pizà servo...@gmail.com wrote:
 Hi!

 When I create a distance in a pymol session, an object called dist n
 is created, and a label with there name is shown at the right of the
 screen, with the other objects loadeds. Can I create a dist, and
 render the dotted line at the screen, without having the label in the
 right menú?

 Thanks a lot, and sorry for my poor english!

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Re: [PyMOL] apbs plugin for macpymol

2007-12-07 Thread Michael Lerner
 I would like to use apbs from within PyMOL.  I have downloaded and
 installed the latest version of apbs, and apbs_tools.py exists in
 $PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no plugins entry
 in any of the PyMOL menus.

I think that you need to rename the application bundle to
PyMOLX11Hybrid in order to use plugins.

 Am I blind or daft?  But the question I'd
 really like to have answered is how do I get abps to work.

I would suggest

1) register APBS here http://agave.wustl.edu/apbs/download/
2) Install fink ( http://finkproject.org/ ) and then use it to install
apbs (e.g. by typing fink install apbs on the command line).

hope that helps,

-michael


 I'm using educational MacPyMOL, which integrates and extends
 Open-Source PyMOL 1.0r1.

 Thanks.


 Andreas

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[PyMOL] Trouble making pictures in a script

2007-10-25 Thread Michael Lerner
Hi,

I have a Python script that sets a system up and then calls cmd.png()
to render an image. I use it to process several files at a time, and
there's no need to look at it while it's working, so I use

pymol -qcr myscript.py

to launch it. It works fine when I ray trace things, but if I just set
the system up and call cmd.png(), I get this error:

 ScenePNG-WARNING: invalid context or no image.

Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things.
Any ideas? Some of the systems are big enough that cmd.ray() fails, so
I'd like to be able to find a workaround.

Thanks,

-michael

-- 
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Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner



Re: [PyMOL] APBS-electrostatics

2007-10-09 Thread Michael Lerner
It looks like quite a few people are actually still using the
electrostatics wizard, so I updated the code on my website
(http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use
the visualization pane of the APBS plugin these days, but I understand
if the wizard is a little cleaner for some purposes.

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner


On 10/4/07, DeLano Scientific del...@delsci.info wrote:


 Gianluigi,

 The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances
 in a single Python interpreter -- your wizard needs to be updated so that
 the init method takes a _self keyword argument:

 def __init__(, _self=cmd):
...


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 mailto:del...@delsci.info

 Not yet a PyMOL Subscriber, but want to support the project?  Email
 sa...@delsci.com to quote your lab, school, or employer.  Thank you for
 sponsoring this open-source endeavor! -WLD



  
  From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net] On
 Behalf Of Gianluigi Caltabiano
 Sent: Thursday, October 04, 2007 7:55 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] APBS-electrostatics



 Hi everybody,
 I am trying to use the electrostatic wizard to read some .dx file I made.
 It always worked..since I up-graded to pymol 1.0.
 Now it doesn't work ( I have already checked the modification in
 __init__.py file, it's fine).
 The message it give to me is:

 Traceback (most recent call last):
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\parser.py, line 251, in
 parse
 self.result=apply(layer.kw[0],layer.args,layer.kw_args)
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in
 wizard
 r = _wizard(name,arg,kwd,0)
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in
 _wizard
 wiz = apply(getattr(mod_obj,oname),arg,kwd)
 TypeError: __init__() got an unexpected keyword argument '_self'

 Thank you for your help

 Gianluigi Caltabiano


  
  
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Re: [PyMOL] electron density map representation as dot

2007-08-15 Thread Michael Lerner
You can do this with the isodot command.

Are you using the PyMOL-APBS plugin to generate or view electron
density maps? If so, would you like me to add dot representations to
the plugin in the next release?

Thanks,

-michael

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner


On 8/15/07, shivesh kumar shivesh_...@yahoo.com wrote:
 Dear all
 How can the dot representation of electron density map is made as in the
 figure in attachment,I know the mess representation through isomesh
 command.Please suggest.Thanx in advance.
 Shivesh kumar

 shivesh

  
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[PyMOL] Why can't I get to sys.argv on Linux?

2007-08-14 Thread Michael Lerner
Hi,

I'm using PyMOL as a front end to a few scripts. So, I need to get my
hands on sys.argv to process the command-line arguments. On OS X,
everything works just like I'd expect. However, on Linux, I can't get
sys.argv. Here's a very simple Python script:

#!/usr/bin/env python
import sys
print dir(sys)
print sys.argv

When I run pymol -cr ./my_script.py on Linux, I get this:

PyMOLrun ./x.py,main
['__displayhook__', '__doc__', '__excepthook__', '__name__',
'__stderr__', '__stdin__', '__stdout__', '_getframe', 'api_version',
'builtin_module_names', 'byteorder', 'call_tracing', 'callstats',
'copyright', 'displayhook', 'exc_clear', 'exc_info', 'exc_type',
'excepthook', 'exec_prefix', 'executable', 'exit', 'exitfunc',
'getcheckinterval', 'getdefaultencoding', 'getdlopenflags',
'getfilesystemencoding', 'getrecursionlimit', 'getrefcount',
'hexversion', 'maxint', 'maxunicode', 'meta_path', 'modules', 'path',
'path_hooks', 'path_importer_cache', 'platform', 'prefix',
'setcheckinterval', 'setdlopenflags', 'setprofile',
'setrecursionlimit', 'settrace', 'stderr', 'stdin', 'stdout',
'version', 'version_info', 'warnoptions']
Traceback (most recent call last):
  File /users/mlerner/src/pymol/modules/pymol/parser.py, line 287, in parse

parsing.run_file(exp_path(args[nest][0]),__main__.__dict__,__main__.__dict__)
  File /users/mlerner/src/pymol/modules/pymol/parsing.py, line 407,
in run_file
execfile(file,global_ns,local_ns)
  File ./x.py, line 4, in ?
print sys.argv
AttributeError: 'module' object has no attribute 'argv'
 PyMOL: normal program termination.

While pawing around in the PyMOL sources, I found that pymol_argv
shows up. It seems to be what I want, but I don't know how stable it
is. Am I supposed to use it instead of sys.argv?

Thanks,

-michael

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner



[PyMOL] Are there any feature requests for the PyMOL-APBS plugin?

2007-08-09 Thread Michael Lerner
Hi,

I'm working on an update to the PyMOL-APBS plugin. Are there any
features that you would like to see included? As an example, I'm
including the ability to use PDB2PQR to generate PQR files in the next
version. Please request anything you'd like, no matter how
trivial/difficult you think it might be to implement (that's not a
promise that I'll implement it .. just that I'll consider it :) ).

Thanks,

-Michael Lerner

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner



[PyMOL] Command-line arguments when using PyMOL to launch a script

2007-08-01 Thread Michael Lerner
Hi,

I have a script that uses PyMOL to aid with a lot of calculations. So,
I run the script like this:

pymol -c script.py

The script has grown so that it has a lot of options. Right now, I
edit the script every time I want to change them. If it were a normal
Python script, I'd run it like

script.py --do=something --when=now

Is there a standard way to do this via PyMOL? Ideally, I'd like to say

pymol -qcr script.py --do=something --when=now
and have script.py think that sys.argv == ['script.py',
'--do=something', '--when=now'].

I pawed through pymol.invocation.py, and it looks like PyMOL respects
the convention where it won't parse arguments after a '--', so my
current workaround is to launch things like

pymol -qcr script.py -- -do=something --when=now

and then this in my script:

argv = sys.argv[sys.argv.index('--') + 1:]
...
# parse with optparse
options,args = parser.parse_args(args=argv)

So, is there a more standard way of doing this? If not, hopefully
google will find this for me the next time I have this question :).

Thanks,

-Michael
-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner



Re: [PyMOL] APBS

2007-05-24 Thread Michael Lerner

Hi,

Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)?  It fixes some problems and gives better error
messages on others.

Thanks,

-Michael

--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner


On 5/24/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote:





I'll appreciate some help with APBS plugin.



In both Win or Lin the same error appears:



ObjectMapLoadDXFile-Error: Unable to open file!



After googling with this error message I've checked all of the
possibilities:

Map file is loaded OK, folders with apbs.exe and psize.py files do not
contain blanks,

the *.pqr file is created using pdb2pqr server with and without chain
identifier.



At this point I do not know what else to try. Before (about 1 year ago) I've
used it with no problems.

Could someone point me to the problem?

Windows version is 0_99rc6 installed using binaries.

Thanks in advance.



Vaheh Oganesyan


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Re: [PyMOL] Single transparent sphere

2007-04-09 Thread Michael Lerner

The pseudoatom business looks very cool.  I'll have to try it out.

In the meantime, I wanted to mention that you certainly can make
transparent CGOs.  Here's some code that I wrote to visualize dock
output in our lab.  The files it reads in have lines that look like

junk x y z r junk temp junk

Where x,y,z are the coordinates, r is the radius and temp is some
index that we use to look up colors.  If you save this in a file,
you'll have a new command, sds, that will read in such a file and show
the output as spheres.  Transparency defaults to 0.4, but you can
change it.

-michael

#!/usr/bin/env python


Use PyMOL to show DOCK spheres

from pymol import cmd,cgo

colors = {'1':[.66,.66,.66],#'grey'
 '2':[1,0,0],#'red',
 '3':[.55,0,0],#'dark red',
 '4':[0.65,1,1],#'blue2',
 '5':[.25,.88,.82],#'blue7',
 '6':[0.004,.55,.55],#'blue8',
 '7':[0.004,.55,.55],#'blue8',
 '8':[0,1,1],#'blue13',
 '9':[0,1,1],#'blue13',
 '11':[0.60,.98,.60],#'pale green',
 '12':[0.56,.93,.56],#'light green',
 '13':[.20,.80,.20],#'lime green',
 '14':[.23,.70,.44],#'green8',
 '15':[.23,.70,.44],#'sea green',
 '16':[.18,.55,.34],#'sea green',
 '17':[.18,.55,.34],#'green',
 '18':[0,.5,0],#'forest green',
 '19':[0,.5,0],#'forest green',
 '20':[.13,.55,.13],#'dark green',
 '21':[.13,.55,.13],#'dark green',
 }

def graph_temp_via_cgo(name,data,transparency=0):
   
   Data should be [x,y,z,r,temp] where
   x,y,z are the coordinates,
   r is the radius
   temp is something like temperature that we
   use to look up colors.
   
   obj = []
   for x,y,z,r,temp in data:
   #transparency = (y/200.0)
   obj.extend( [ cgo.ALPHA,1-transparency])
   obj.extend( [ cgo.COLOR] + colors[temp])
   obj.extend( [ cgo.SPHERE,x,y,z,r] )
   cmd.load_cgo(obj,name,1)
   return name

def dock_file_to_data(filename):
   data = []
   f = file(filename)
   for line in f:
   if not line.strip():
   continue
   if line.startswith('#'):
   continue
   junk1,x,y,z,r,junk2,temp,junk3 = line.split()
   x,y,z,r = map(float,(x,y,z,r))
   data.append([x,y,z,r,temp])
   f.close()
   return data
def show_dock_spheres(filename,transparency=0.40):
   
   Reads in a DOCK sphere file and graphs the
   results as dock spheres.  You can pass the
   transparency as an additional argument.
   
   transparency = float(transparency)
   data = dock_file_to_data(filename)
   graph_temp_via_cgo('dock_spheres',data,transparency)

cmd.extend('sds',show_dock_spheres)


On 4/6/07, DeLano Scientific del...@delsci.info wrote:



Pre 1.0:

fragment methane, mysph
remove hydro and mysph
alter mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph

Post 1.0:

pseudoatom mysph, vdw=2.0

as spheres, mysph

set sphere_transparency, 0.5, mysph

Cheers,
Warren



 
 From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On
Behalf Of jjv5
Sent: Friday, April 06, 2007 4:55 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Single transparent sphere



Hi,

Does anyone know of a good way to create a single transparent sphere of
varying size? We've tried using a single atom and changing the vdw, but we
are unable to produce a surface of a single atom. CGO objects work but
cannot be made transparent. What we'd really like is a transparent CGO
sphere. Any ideas?

Thanks,
Jim

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Re: [PyMOL] APBS surface

2007-04-02 Thread Michael Lerner

PyMOL doesn't know where the electrostatic potential map comes from.
If you load up a map and a structure, it will show the potential from
that map on that structure.

On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote:


YesI have already done as wrote
My question iswhat if I up load ligand surface with receptor structure?
Will it, as I think, shows me the potential of ligand on the receptor
surface (giving me as sort of negative of ligand surface on receptor's)???

Thank for your answer,

Gianluigi Caltabiano
 Lab of Computational Medicine,
 BioStatistic Dept.
 UAB, Universitat Autonoma de Barcelona
 Spain




- Messaggio originale -
Da: Mike Summers summ...@hhmi.umbc.edu
A: Gianluigi Caltabiano chimic...@yahoo.it
Inviato: Martedì 27 marzo 2007, 20:14:37
Oggetto: Re: [PyMOL] APBS surface


You need to create individual proteins and then create maps for the
individual protein;  e.g, create A,(structure and residues_of_A_only)


Mike


On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote:
 Hi everyone,
 I am working with a protein-protein complex and I have calculated for each
protein, let's say A and B, apbs electrostatic surfaces.
 Everything works fine.
 My question is:
 I have uploaded the structure of protein A and the surface of protein B.
 What it shows to me is a blank surface for most of the protein A but the
part where protein B interact whit it. I think, but I would have
confimations, that I am, in some way, projecting potential values of
protein's  surface B on the surface of protein A, like having a negative
of the B interactions. It seems it works like this since I know both
rotein's interacting residues and now I am facing interacting patch of
residues from protein B on their counnter part on protein A.
 Am I wrong?

 Thank for your answer, in advance,



 Gianluigi Caltabiano
 Lab of Computational Medicine,
 BioStatistic Dept.
 UAB, Universitat Autonoma de Barcelona
 Spain








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*
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  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

Phone: (410)-455-2527
FAX:   (410)-455-1174
Email: summ...@hhmi.umbc.edu
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Re: [PyMOL] Electrostatic surface visualization

2007-03-05 Thread Michael Lerner

On 3/3/07, se...@uniroma2.it se...@uniroma2.it wrote:


Dear all,

I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything seems fine.
Now I would like to visualize this surface AND the secondary structure
of the protein, in order to understand the positive and negative
regions.
How I can do? Some software show the surface in trasparency but it
seems this is not possible in PyMOL.


You can do this with commands like

set transparency, 0.5, myproteinname

or

set transparency, 0.2, iso_pos


A related question: it is possible to color the secondary structure
according to the electrostatic surface properties? I have an NMR titration of
this protein with its partner: I would like to relate the shifts of
the NH backbone with the electrostatic surface.


Not sure about that one.

-Michael



I looked at the archive but I haven't found an answer.

Thanks in advance,
Marco




Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, Tor Vergata
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:se...@uniroma2.it
Tel.:  +39-0672594424
Fax:   +39-0672594328





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Re: [PyMOL] reload modified wizard

2007-02-25 Thread Michael Lerner

I found an old version of my code.  It was just slightly more
complicated than I thought.  Here's a version of the wrapper that I
was using:

import sys

sys.path.append('/home/mlerner/work/src/PyMOL_Plugins/')

import SomethingOrOtherTools
def __init__(self):
   self.menuBar.addmenuitem('Plugin', 'command',
'SomethingOrOther',
label='SomethingOrOther...',
command = lambda s=self:
getSomethingOrOtherTools(s))

def getSomethingOrOtherTools(thing):
   reload(SomethingOrOtherTools)
   return SomethingOrOtherTools.SomethingOrOtherTools(thing)


Let me know if you have any more questions.

-michael

On 2/24/07, Michael Lerner mgler...@gmail.com wrote:

Actually, I did this when I was developing the APBS Plugin.  I put all
of the interesting code in a module called _apbs_tools.  apbs_tools
was just a little wrapper where the init function would import and
reload _apbs_tools and then call through to it.

-Michael

On 2/24/07, DeLano Scientific del...@delsci.info wrote:
 I believe this is a limitation of Python:  once a code module is loaded and
 initialized, it is difficult to reload it...you might be able to hack it
 though.

  -Original Message-
  From: pymol-users-boun...@lists.sourceforge.net
  [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
  Of bgbg bg
  Sent: Saturday, February 24, 2007 5:19 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] reload modified wizard
 
  Hello,
  I develop several custom PyMol wizards. Is there any way to
  reload a modified wizard,  without restarting PyMol?
 
  Thank you.
 
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Re: [PyMOL] reload modified wizard

2007-02-24 Thread Michael Lerner

Actually, I did this when I was developing the APBS Plugin.  I put all
of the interesting code in a module called _apbs_tools.  apbs_tools
was just a little wrapper where the init function would import and
reload _apbs_tools and then call through to it.

-Michael

On 2/24/07, DeLano Scientific del...@delsci.info wrote:

I believe this is a limitation of Python:  once a code module is loaded and
initialized, it is difficult to reload it...you might be able to hack it
though.

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
 Of bgbg bg
 Sent: Saturday, February 24, 2007 5:19 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] reload modified wizard

 Hello,
 I develop several custom PyMol wizards. Is there any way to
 reload a modified wizard,  without restarting PyMol?

 Thank you.

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Re: [PyMOL] Visualizing Molecular Orbitals in PyMol

2007-02-19 Thread Michael Lerner

Hi,

I don't remember the details, but I do remember that I had some
troubles using bricks when I was writing the APBS plugin.  The DX file
format is really simple, though, especially for this sort of thing.

http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format

If I recall correctly, my problems with bricks were mostly that I
wasn't using them correctly, but I didn't figure out how to use them
correctly until after I'd already converted everything to DX.

-Michael Lerner

On 2/19/07, BuzB bmb...@gmail.com wrote:

Hi All,

Thanks to everyone and for the responses to and encouragement about my
query on visualizing molecular orbitals in pymol.

I'm using PyMol 0.99rc6.

I feel like I'm quite close to a solution. I've developed a routine to
compute a 3 dimensional matrix containing the probability amplitudes
of the orbitals, which I can load into a PyMol brick object.

Then, things start to go wrong

When I use the load_brick function in the cmd module;

cmd.load_brick(brik, Brick)

or alternatively,

cmd.load_object(loadable.brick, brik, Brik)

PyMol returns the message;

 ObjectMap: Map Read.  Range = 0.000 to 0.000

but it does display the object Brick in the objects menu. I can then
create an isomesh or surface with the command;

cmd.isosurface(BrikSurf, Brick, 0.1)

But no surface is displayed on screen.

The example file brick01.py that is included in examples/devel does
something almost identical to what I'm trying to do, it displays an
exponentially decaying density, but also with no success in PyMol
0.99rc6. Is there a bug somewhere in the load_brick function that I'm
running into?

Thanks a lot!

bmb197

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Re: [PyMOL] Side by side views

2007-01-25 Thread Michael Lerner

Warren helped me with a similar problem a while ago (I can't find the link
in the mailing list archive), and this might do the job for you:

If you download and run my script at
http://www-personal.umich.edu/~mlerner/Pymol/mg_pymol_utils.py
you can start up two PyMOL sessions.  You then type send_view in one of
them, receive_view in the other one, and the receive_view one will follow
along.

I don't know how to get that all working in one window, but you can always
just paste the images together.

I find this really useful for comparing structures with different ligands
bound, different parts of a dynamics run, etc.

In your case, you might need to align all of the structures to one reference
structure first, so that the views are similar.

Hope this helps,

-Michael Lerner

On 25 Jan 2007 16:32:21 +, David F Burke df...@cam.ac.uk wrote:


Pymol users,

I wish to compare several protein structures and was wondering how or if,
in pymol, one can view two structures
side by side and rotate each structure around their own centre of gravity.
This is a bit like stereo view but with
different structures in the left and right views. Many thanks David
--
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Department of Zoology, University of Cambridge,
Downing Street, Cambridge, CB2 3EJ
Email:df...@cam.ac.uk
Tel: 01223 330933

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Re: [PyMOL] New plugin and Doubt with APBS Tools

2007-01-10 Thread Michael Lerner

We discussed this a bit off-list, and it looks like this was the answer:

The potentials are assigned to points in space.  That's why the
isosurfaces don't change, and also why the surface coloring changes
when you change the shape of the surface.

Hope that helps anyone else who might have this question,

-michael

On 1/9/07, Michael Lerner mgler...@gmail.com wrote:

Raúl,

I don't have time to look at this in detail right now, but .. what
exactly do you mean that the potentials change between frames?  What
happens if you draw isosurfaces?  Do they change?

-michael

On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote:
 Dear all,

 Two things.
 First, I just written a small plugin that uses the
 program reduce to add hydrogens to a molecule or to
 a trajectory loaded in Pymol.(since each frame of the
 trajectory is hydrogenated by reduce, I think that
 protonation states could vary between frames) This
 allow us to have a reliable protonation method in
 PyMOL, without having to save the structure as PDB and
 hydrogenate with another app, and using an open-source
 (as far as I know) and easy to install application.

 Since I don't have any website right now, I will try
 to make it available from the Pymol Wiki. If you want
 the plugin right now, just e-mail me.

 The other thing is a doubt in using the APBS Tools.
 When I use it to calculate electrostatics potentialsof
 a trajectory (but the PQR is made  by PDB2PQR from a
 PDB made with PyMOL, i.e, only from the first
 snapshot)
 I get a .dx map that I think has the potentials only
 for the first frame. When I display the potential
 surface in the trajectory, the potentials seems to
 change between frames, which I wouldn't expect since I
 think that the calculation was performed only for the
 first frame.
 My doubt is: Are these changes alleatory due to a
 change
 of the structure's position changes on the grid, or
 they have some significance?, if the latter, what
 significance? (maybe the changes are produced by the
 motion of polar groups?)

 Thanks in advance,

 Raul

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Re: [PyMOL] New plugin and Doubt with APBS Tools

2007-01-09 Thread Michael Lerner

Raúl,

I don't have time to look at this in detail right now, but .. what
exactly do you mean that the potentials change between frames?  What
happens if you draw isosurfaces?  Do they change?

-michael

On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote:

Dear all,

Two things.
First, I just written a small plugin that uses the
program reduce to add hydrogens to a molecule or to
a trajectory loaded in Pymol.(since each frame of the
trajectory is hydrogenated by reduce, I think that
protonation states could vary between frames) This
allow us to have a reliable protonation method in
PyMOL, without having to save the structure as PDB and
hydrogenate with another app, and using an open-source
(as far as I know) and easy to install application.

Since I don't have any website right now, I will try
to make it available from the Pymol Wiki. If you want
the plugin right now, just e-mail me.

The other thing is a doubt in using the APBS Tools.
When I use it to calculate electrostatics potentialsof
a trajectory (but the PQR is made  by PDB2PQR from a
PDB made with PyMOL, i.e, only from the first
snapshot)
I get a .dx map that I think has the potentials only
for the first frame. When I display the potential
surface in the trajectory, the potentials seems to
change between frames, which I wouldn't expect since I
think that the calculation was performed only for the
first frame.
My doubt is: Are these changes alleatory due to a
change
of the structure's position changes on the grid, or
they have some significance?, if the latter, what
significance? (maybe the changes are produced by the
motion of polar groups?)

Thanks in advance,

Raul

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[PyMOL] Showing the surface

2006-12-18 Thread Michael Lerner

Hi,

I want to show the electrostatic potential surface 10A away from a
protein.  I used to do this by setting all of the vdw radii to 10A,
but I'm wondering if there's a better way these days.  The surface I
got by altering the vdw radii always looked really choppy and not so
smooth.

Thank you,

-Michael Lerner

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Re: [PyMOL] Paths to loaded objects

2006-08-21 Thread Michael Lerner

I think he means for you to have a Load button as part of your
plugin.  That button would first record the path to the file and then
call through to cmd.load().

On 8/19/06, Ron Jacak r...@email.unc.edu wrote:

Peter,

 I'm working on a plugin that reads information appended to the end of
 PDB files to draw CGO objects.  Right now, I have the user specify
 the
 filesystem path to the currently loaded objects through the
 plugin GUI so that I know where to go to find the file.  For one
 object,
 this isn't so bad.  But if users load multiple objects that are in
 different directories, I will have to change the GUI so that the user
 has to specify the path to each object loaded.  This kind of
 situation
 would quickly become tedious.  Does PyMOL store the paths for objects
 that are loaded somewhere?  I know I can get the current working
 directory using getcwd(), so I'm hoping there's a way to get the
 path to
 the loaded objects as well.

 I don't know of a way to get file information from a pymol object,
 but you
 could work around this by using a python dictionary (when the pdb
 file is
 loaded, store the full path to the file in a dictionary using the
 pymol
 object name as the key).

I'm not sure I fully understand your suggestion.  It sounds to me
like what you're saying is that I should add code (e.g. a dictionary)
to the importing.py load() function which saves the file information
of objects as they're loaded.  But then instead of just distributing
my plugin, I would have to get users to change their PyMOL source, as
well (which I'm not willing to do).  Am I understanding correctly?

Any other ways around this problem?

-Ron


Ron Jacak
Graduate Student
University of North Carolina - Chapel Hill

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Re: [PyMOL] rejected atoms during alignment

2006-08-03 Thread Michael Lerner

This is not a great answer, but do you know about the object parameter
for the align command?  I often type something like

align struct1, struct2, object=alignment

and then just look at which things were included/excluded.

-michael

On 8/3/06, Marc Bruning brun...@mpghdb.desy.de wrote:

hello,

is there any way to find out which atoms are discarded during the refinement
cycles of the align command?

regards,
marc

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[PyMOL] How do I show multiple conformations in a single crystal structure?

2006-07-25 Thread Michael Lerner

I have a crystal structure that contains two conformations for a
flexible loop.  They're both in the crystal structure, but have
occupancies less than one.   When I look at the structure in PyMOL, I
see only one conformation.  Is there a command similar to split_states
that will allow me to view both conformations at once?

Thanks,

-michael



Re: [PyMOL] How do I show multiple conformations in a single crystal structure?

2006-07-25 Thread Michael Lerner

Oh, if it helps, the residues are all named things like ACYS and BCYS
for the different conformations.

On 7/25/06, Michael Lerner mgler...@gmail.com wrote:

I have a crystal structure that contains two conformations for a
flexible loop.  They're both in the crystal structure, but have
occupancies less than one.   When I look at the structure in PyMOL, I
see only one conformation.  Is there a command similar to split_states
that will allow me to view both conformations at once?

Thanks,

-michael





[PyMOL] Can PyMOL read amber8 trajectory files?

2006-07-18 Thread Michael Lerner

I have some stuff from an amber8 (sander) MD run that I'd like to
visualize in PyMOL.  When I load it up, PyMOL says something like
assuming amber6 format and dies.  I'm using fink/pymol-py24 on an
intel macbook pro.  I always forget how to load amber files anyway, so
I could easily be screwing something up.  I call my topology file
something.top and here's what happens:

PyMOLload something.top
ObjectMolecule: Assuming this is an Amber6 topology file.
TOPStrToCoordSet-Error: Error reading atom types
/sw/bin/pymol: line23:Bus error

I made that file with amber8.

Thanks,

-michael



Re: [PyMOL] why is PyMOL renaming my residues?

2003-10-02 Thread michael lerner

Hi Warren,


PyMOL's PDB handling is an attempt to navigate a minefield of
incompatible standards which exist in the conventions of various
software packages.

Ugh.  I know more about incompatable PDB files than I ever wanted to.  I 
once wrote something much like Andrew Dalke's UPDB (see 
http://biopython.org/scriptcentral/).  Unfortunately, my version ended 
up being very slow, so I didn't get a chance to give it to the biopython 
folks.  I keep meaning to go back and speed it up, but I think they have 
a good PDB parser now.



Since version 0.90, PyMOL's behavior has changed.  Nowadays,
your input data:


snip


Would be returned as:
 


snip


...which does preserve atom names, but not the order.  Note that
white-space in the atom names is not preserved (an inherent limitation
in PyMOL -- significant white-space within identifier is hell on users
and parsers).  


Conventionally, atom names of length 3 or less are placed in the second
column, not the first -- so your LMN  atom may cause trouble.

That's fine with me.  I just had LMN  and  XYZ in there so that I 
could figure out exactly what PyMOL was changing.



Also note that by some conventions, 2OA2 in a PDB file really means
atom OA22.


I didn't know that.  What conventions are those?


Furthermore, in your example, they [ATOM IDs] are not unique (a mistake?).


yup, a mistake.


However, I am trying to bend PyMOL around to meet your needs a bit
better.

Towards this end, I've created a new setting pdb_retain_ids which
preserves the original PDB serial numbers in the output file.

In future PyMOL versions, so long as

set retain_order, 1
set pdb_retain_ids, 1
set pdb_no_end_record, 1

That's absolutely fantastic.  Right now, I have to use PyMOL, MOE and 
AMBER (sander and carnal are the real problems) on the same systems, and 
anything that makes this less painful is great!  I'll probably set 
retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS 
version within the next couple of days. 


Thanks!

-michael
--
michael lerner




[PyMOL] why is PyMOL renaming my residues?

2003-09-26 Thread michael lerner

Hi,

If I load up a PDB file that looks like this:

HETATM 1313 OA22 NAP   164  28.315  61.969  12.250   
31.54   O 
HETATM 1314 OA23 NAP   164  26.554  62.174  14.275   
21.05   O 
HETATM 1314 ABCD NAP   164  28.554  64.174  16.275   
11.05   O 
HETATM 1314 XYZ  NAP   164  30.554  66.174  18.275
1.05   O 
HETATM 1314  LMN NAP   164  32.554  68.174  20.275   
41.05   O 


and then save it from PyMOL, the resulting PDB file looks like this:

HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00 
31.54   O
HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00 
21.05   O
HETATM3 DABC NAP   164  28.554  64.174  16.275  0.00 
11.05   O
HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00 
41.05   O
HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00  
1.05   O

END

You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to 
3OA2 and ABCD has been renamed to DABC.  It looks to me like residue 
with a four-letter name is getting renamed. 

No .. wait .. it's a little stranger than that .. if I open up the 
second file (the one with DABC) and save *it*, I get this:


HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00 
31.54   O
HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00 
21.05   O
HETATM3 CDAB NAP   164  28.554  64.174  16.275  0.00 
11.05   O
HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00 
41.05   O
HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00  
1.05   O

END

Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 
and stayed there.  LMN and XYZ weren't touched.


Is there a way to supress this behavior?  It causes me a bit of trouble 
when, e.g., my AMBER parameter files expect residues to have certain names.


I'm not sure exactly when PyMOL decides to rename things .. if I 
shift-left-click on one of the residues in the first file (either before 
or after saving), PyMOL says You clicked NAP: /test1///164/OA23 (i.e. 
it gives me the original name).


thanks,

-michael

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[PyMOL] Re: why is PyMOL renaming my residues?

2003-09-26 Thread michael lerner

oops .. two problems with my last message:

1) i said residue a few times when i meant atom .. it should be 
obvious from the context of the message.


2) my email program seems to have messed up some of the formatting in 
the last message .. the original PDB file should look like this 
(assuming i can format it correctly this time):


HETATM 1313 OA22 NAP   164  28.315  61.969  12.250   
31.54   O 
HETATM 1314 OA23 NAP   164  26.554  62.174  14.275   
21.05   O 
HETATM 1314 ABCD NAP   164  28.554  64.174  16.275   
11.05   O 
HETATM 1314 XYZ  NAP   164  30.554  66.174  18.275
1.05   O 
HETATM 1314  LMN NAP   164  32.554  68.174  20.275   
41.05   O 



in case that's still not formatted correctly, each line should begin 
with HETATM, and the point is that the atoms are named OA22, OA23, 
ABCD, XYZ  and  LMN respectively.


also, i noticed that PyMOL is changing the atom ID (OA22 was 1313 in the 
first file, but 1 in the second).  that's not actually causing me any 
trouble, but i'm curious: is there a way to make PyMOL leave the IDs alone?


thanks,

-michael

michael lerner wrote:


Hi,

If I load up a PDB file that looks like this:

HETATM 1313 OA22 NAP   164  28.315  61.969  12.250   
31.54   O HETATM 1314 OA23 NAP   164  26.554  62.174  
14.275   21.05   O HETATM 1314 ABCD NAP   164  28.554  
64.174  16.275   11.05   O HETATM 1314 XYZ  NAP   164  
30.554  66.174  18.2751.05   O HETATM 1314  LMN NAP   
164  32.554  68.174  20.275   41.05   O

and then save it from PyMOL, the resulting PDB file looks like this:

HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00 
31.54   O
HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00 
21.05   O
HETATM3 DABC NAP   164  28.554  64.174  16.275  0.00 
11.05   O
HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00 
41.05   O
HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00  
1.05   O

END

You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed 
to 3OA2 and ABCD has been renamed to DABC.  It looks to me like 
residue with a four-letter name is getting renamed.
No .. wait .. it's a little stranger than that .. if I open up the 
second file (the one with DABC) and save *it*, I get this:


HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00 
31.54   O
HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00 
21.05   O
HETATM3 CDAB NAP   164  28.554  64.174  16.275  0.00 
11.05   O
HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00 
41.05   O
HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00  
1.05   O

END

Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 
and stayed there.  LMN and XYZ weren't touched.


Is there a way to supress this behavior?  It causes me a bit of 
trouble when, e.g., my AMBER parameter files expect residues to have 
certain names.


I'm not sure exactly when PyMOL decides to rename things .. if I 
shift-left-click on one of the residues in the first file (either 
before or after saving), PyMOL says You clicked NAP: 
/test1///164/OA23 (i.e. it gives me the original name).


thanks,

-michael

--
michael lerner