pymol-users

[PyMOL] writing out the surface

[Michael L. <mgl...@gm...>]

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

Re: [PyMOL] writing out the surface

[Tsjerk W. <ts...@gm...>]

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" <mgl...@gm...> 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


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Re: [PyMOL] writing out the surface

[Hurt, D. (NIH/N. [E] <dar...@ni...>]

And the spacing can be controlled a least a little by using the surface quality setting.


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135

Office  301-402-0095
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From: Tsjerk Wassenaar [mailto:ts...@gm...]
Sent: Monday, June 11, 2012 12:46 PM
To: Michael Lerner <mgl...@gm...>
Cc: pymol mailinglist <pym...@li...>
Subject: 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" <mgl...@gm...<mailto:mgl...@gm...>> 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


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Re: [PyMOL] writing out the surface

[Takanori N. <t.n...@ma...>]

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/pym...@li.../msg10012.html

Best regards,

Takanori Nakane

Re: [PyMOL] writing out the surface

[Michael L. <mgl...@gm...>]

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.n...@ma...> 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/pym...@li.../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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095

Re: [PyMOL] writing out the surface

[Michael L. <mgl...@gm...>]

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 <mgl...@gm...> 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.n...@ma...> 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/pym...@li.../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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> 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

Re: [PyMOL] writing out the surface

[Thomas H. <sp...@us...>]

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 <mgl...@gm... 
> <mailto:mgl...@gm...>> 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.n...@ma...
>     <mailto:t.n...@ma...>> 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/pym...@li.../msg10012.html
> 
>         Best regards,
> 
>         Takanori Nakane

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] writing out the surface

[Michael L. <mgl...@gm...>]

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 <
sp...@us...> 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 <mgl...@gm...<mailto:
>> mgl...@gm...>> 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<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<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.n...@ma....**kyoto-u.ac.jp<t.n...@ma...>
>>     <mailto:t.n...@ma....**med.kyoto-u.ac.jp<t.n...@ma...>>>
>> 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/**pym...@li....**
>> net/msg10012.html<http://www.mail-archive.com/pym...@li.../msg10012.html>
>>
>>         Best regards,
>>
>>         Takanori Nakane
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>



-- 
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095