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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>
>
>
> --
> 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
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