[Chimera-users] getting surface patches
Diego Amaya
diaamayaram at unal.edu.co
Sun Jun 13 03:56:57 PDT 2021
Hello Tom,
thanks for the info. I'll keep it in mind.
Best regards.
El vie, 11 jun 2021 a las 20:23, Tom Goddard (<goddard at sonic.net>) escribió:
> Hi Diego,
>
> You might want to try our newer program ChimeraX. It does not export
> VTK, but the formats it does export like OBJ and GLTF only include the
> displayed surface patches. Also all our development effort is on ChimeraX,
> so if you need a feature improved it will only happen in ChimeraX, not in
> Chimera.
>
> Tom
>
>
> > On Jun 11, 2021, at 7:51 AM, Elaine Meng via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Diego,
> > If you look at the "export" help link I sent before, there are several
> other formats: STL, OBJ, COLLADA, VRML...
> >
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
> >
> > First use some commands to show patches for a test case, e.g.
> >
> > open 2gbp
> > surface protein & :BGC za<5
> > ~ribbon
> > ~disp
> >
> > And then you can use either the export command or menu: File... Export
> Scene and choose the different formats to try them. I don't know what you
> plan to do with them, so you'd have to try them yourself to decide if any
> will work for you.
> >
> > I tried some of them. Looks like I can get the patches using STL and
> COLLADA. As mentioned in the Limitations in the help link, OBJ has the
> same problem as VTK that it saves the whole surface even when only patches
> are shown at the time of saving.
> >
> > Elaine
> >
> >
> >> On Jun 11, 2021, at 12:42 AM, Diego Amaya via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >>
> >> Hello Elaine,
> >>
> >> Thanks for your explanations. Would it be possible to build the patches
> and export them in another format ?
> >>
> >> Best regards
> >>
> >> El jue, 10 jun 2021 a las 23:56, Elaine Meng (<meng at cgl.ucsf.edu>)
> escribió:
> >> Hi Diego,
> >> Sorry, Chimera VTK export has the limitation that it always exports the
> whole thing (all atoms and the whole surface) even if it is not displayed.
> So you can't get just the patches from some atoms (at least, I can't think
> of a way to do it).
> >>
> >> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
> >>
> >> "VTK export includes only molecule models, molecular surfaces, and
> multiscale surfaces with associated atoms. The molecule export includes all
> atoms and bonds, even if not displayed, and uses dots to represent atoms
> and wires to represent bonds regardless of their display styles in Chimera."
> >>
> >> Secondarily, about displaying atomic patches of molecular surface in
> Chimera (which you could possibly try exporting to some other format):
> >> if you really want patches that go with the atoms, but within the
> context of the full surface, you would not use "surfcat." Normally the
> surface would go around the whole protein, and you could get patches from
> atoms that are in that surface by simply using the "surface" command to
> display those patches. If you use surfcat, you are telling it to instead
> make a surface enclosing only those atoms, ignoring the rest of the protein.
> >>
> >> I usually recommend figuring out exactly what commands you need for
> some example situation (test case) by typing commands directly into the
> command line. Then you can generalize to a script after that. Here is one
> example. Say I want the surface patches of protein atoms that are within
> 5 angstroms of the ligand BGC in structure 2gbp. Commands:
> >>
> >> open 2gbp
> >> surface protein & :BGC za<5
> >>
> >> However, this will not solve the main problem that VTK will still
> export the whole surface including the parts that aren't shown.
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Jun 10, 2021, at 2:04 PM, Diego Amaya via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >>>
> >>> Hello all,
> >>> I'm trying to get surface patches of PDB structures in VTK format. So
> I want to define a patch as the set of atoms within a given radius of a
> specific residue, build the surface corresponding to that patch and export
> the result in VTK format. Additionally, I want to do all this with a python
> script.
> >>>
> >>> Here the code I'm trying but doesn't work :
> >>>
> >>> import pychimera
> >>> pychimera.patch_environ()
> >>> pychimera.enable_chimera()
> >>> import os
> >>> import chimera
> >>> from chimera import runCommand as rc
> >>>
> >>> list_resid = [31, 64]
> >>> radius = 3
> >>> list_pdbs = ['ensayo.pdb']
> >>>
> >>> for resid in list_resid:
> >>> for line in list_pdbs:
> >>> list_atoms = []
> >>> rc('open '+line)
> >>> rc('sel :{} za<{}'.format(resid, radius))
> >>> for a in chimera.selection.currentAtoms():
> >>> list_atoms.append('serialNumber=' + str(a.serialNumber))
> >>> sel_atoms = ' or '.join(list_atoms)
> >>> rc('surfcat patch @*/{}'.format(sel_atoms))
> >>> rc('surface patch')
> >>> rc("export format VTK
> {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius))
> >>>
> >>> rc("close all")
> >>>
> >>> Thanks in advance for your help.
> >>> --
> >>> Diego A. Amaya Ramírez
> >>
> >>
> >>
> >> --
> >> Diego A. Amaya Ramírez
> >>
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>
--
Diego A. Amaya Ramírez
--
*Aviso legal:* El contenido de este mensaje y los archivos adjuntos son
confidenciales y de uso exclusivo de la Universidad Nacional de Colombia.
Se encuentran dirigidos sólo para el uso del destinatario al cual van
enviados. La reproducción, lectura y/o copia se encuentran prohibidas a
cualquier persona diferente a este y puede ser ilegal. Si usted lo ha
recibido por error, infórmenos y elimínelo de su correo. Los Datos
Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra
Política de Datos Personales que podrá consultar en la página web
www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones,
conclusiones y cualquier otro tipo de dato contenido en este correo
electrónico, no relacionados con la actividad de la Universidad Nacional de
Colombia, se entenderá como personales y de ninguna manera son avaladas por
la Universidad.
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