surface colouring by selected residues
Dear ChimeraX community, I need to colour the surface by selected side chains to highlight an intermolecular contact. The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true #make a surface. A new surface #10.1 is generated: surface #10/C resolution 7 #color surface yellow at selected residues. color #10 & sel yellow target s The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution. Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04. Thank you and best regards. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun@mrc-lmb.cam.ac.uk
I think what you want is the “color zone” command: color zone #10 near sel distance 3 ... will cause each triangle on the surface to be coloured according to the colour of the nearest atom in the selection within a 3Å cutoff distance.
On 27 Jul 2020, at 14:48, Oleksiy Kovtun <okovtun@mrc-lmb.cam.ac.uk> wrote:
Dear ChimeraX community,
I need to colour the surface by selected side chains to highlight an intermolecular contact.
The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true
#make a surface. A new surface #10.1 is generated: surface #10/C resolution 7
#color surface yellow at selected residues. color #10 & sel yellow target s
The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution.
Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04.
Thank you and best regards. Oleksiy
Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
Tel: + 44 1223 267551 Email: okovtun@mrc-lmb.cam.ac.uk
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
spot on, thank you! I got it, surface polygones are not asssigned to the specific atoms. Best. O
On 27 Jul 2020, at 15:31, Tristan Croll <tic20@cam.ac.uk> wrote:
I think what you want is the “color zone” command:
color zone #10 near sel distance 3
... will cause each triangle on the surface to be coloured according to the colour of the nearest atom in the selection within a 3Å cutoff distance.
On 27 Jul 2020, at 14:48, Oleksiy Kovtun <okovtun@mrc-lmb.cam.ac.uk <mailto:okovtun@mrc-lmb.cam.ac.uk>> wrote:
Dear ChimeraX community,
I need to colour the surface by selected side chains to highlight an intermolecular contact.
The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true
#make a surface. A new surface #10.1 is generated: surface #10/C resolution 7
#color surface yellow at selected residues. color #10 & sel yellow target s
The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution.
Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04.
Thank you and best regards. Oleksiy
Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
Tel: + 44 1223 267551 Email: okovtun@mrc-lmb.cam.ac.uk <mailto:okovtun@mrc-lmb.cam.ac.uk> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun@mrc-lmb.cam.ac.uk
Dear Oleksiy, When you use the "resolution" option to make a Gaussian surface (low resolution) instead of standard molecular surface, the resulting surface is not associated with the underlying atoms, unless you also use "sharpBoundaries true". This is described in the "surface" command documentation, if you want to see more details. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> So technically the coloring command was executed but "sel" did not specify any parts of the surface because the selected atoms were not associate with it. If you use the following it should work as expected: surface #10/C resolution 7 sharpBoundaries true color #10 & sel yellow target s I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 27, 2020, at 6:48 AM, Oleksiy Kovtun <okovtun@mrc-lmb.cam.ac.uk> wrote:
Dear ChimeraX community,
I need to colour the surface by selected side chains to highlight an intermolecular contact.
The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true
#make a surface. A new surface #10.1 is generated: surface #10/C resolution 7
#color surface yellow at selected residues. color #10 & sel yellow target s
The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution.
Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04.
Thank you and best regards. Oleksiy
Dear Elaine, The surface colouring came out clear with your explainer, thank you! Best. O.
On 27 Jul 2020, at 15:37, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun@mrc-lmb.cam.ac.uk
participants (3)
-
Elaine Meng -
Oleksiy Kovtun -
Tristan Croll