[Chimera-users] getting surface patches

Diego Amaya diaamayaram at unal.edu.co
Fri Jun 11 00:42:23 PDT 2021

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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