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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