Re: [PyMOL] writing out the surface
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.com
mailto: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
mailto: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
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] writing out the surface
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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
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--
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN 47374-4095
--
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN 47374-4095
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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Re: [PyMOL] writing out the surface
Hi Michael, The answer used to be you can write out the surface as mesh in vrml or povray format, from which you can extract the vertices. I think it's still the proper answer. Cheers, Tsjerk On Jun 11, 2012 5:26 PM, Michael Lerner mgler...@gmail.com wrote: 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 -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] writing out the surface
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] writing out the surface
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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
