[Chimera-users] getting surface patches
Diego Amaya
diaamayaram at unal.edu.co
Sun Jun 13 03:56:20 PDT 2021
Hello Elaine,
thanks for your help. I'll try it.
Best regards,
El vie, 11 jun 2021 a las 16:51, Elaine Meng (<meng at cgl.ucsf.edu>) escribió:
> 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
> >
> > 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. 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.
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
--
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210613/019d64b3/attachment.html>
More information about the Chimera-users
mailing list