Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
Hi Pranav, I’m Cc'ing the chimerax-users@cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine and Co.,
I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera.
Cheers, Pranav
That helped! Thanks a lot! Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab) On Tue, Aug 20, 2019 at 2:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I’m Cc'ing the chimerax-users@cgl.ucsf.edu list (recommended for ChimeraX questions).
I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding.
If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine and Co.,
I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera.
Cheers, Pranav
Hi Elaine, Further to this query, I have a virus.pdb and virus.mrc. I symmetry expanded the virus.pdb using sym #1 assembly 1 and then ran color by zone color zone #2 near #3 distance 5 Where #1 = virus asym unit #2 = virus.mrc #3 = symmetrised #1 however this results in only the surface in the asymmetric unit inheriting the model colors. How do I propagate the colors of all the chains to the entire surface of the capsid? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Tue, Aug 20, 2019 at 7:49 PM Pranav Shah <p.shah.lab@gmail.com> wrote:
That helped! Thanks a lot!
Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)
On Tue, Aug 20, 2019 at 2:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I’m Cc'ing the chimerax-users@cgl.ucsf.edu list (recommended for ChimeraX questions).
I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding.
If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine and Co.,
I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera.
Cheers, Pranav
Hi Pranav, I believe you need to use "copies true" in the sym command to make the full assembly using "real" atomic copies rather than graphical clones. Color zone and other commands only recognize the real atomic copies. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2020, at 10:21 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine,
Further to this query, I have a virus.pdb and virus.mrc. I symmetry expanded the virus.pdb using sym #1 assembly 1 and then ran color by zone color zone #2 near #3 distance 5
Where #1 = virus asym unit #2 = virus.mrc #3 = symmetrised #1
however this results in only the surface in the asymmetric unit inheriting the model colors. How do I propagate the colors of all the chains to the entire surface of the capsid?
Best, Pranav
Amazing! Thank you! May I also know how I can color clipping planes with the same colors? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Fri, Nov 20, 2020 at 6:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I believe you need to use "copies true" in the sym command to make the full assembly using "real" atomic copies rather than graphical clones. Color zone and other commands only recognize the real atomic copies.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2020, at 10:21 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine,
Further to this query, I have a virus.pdb and virus.mrc. I symmetry expanded the virus.pdb using sym #1 assembly 1 and then ran color by zone color zone #2 near #3 distance 5
Where #1 = virus asym unit #2 = virus.mrc #3 = symmetrised #1
however this results in only the surface in the asymmetric unit inheriting the model colors. How do I propagate the colors of all the chains to the entire surface of the capsid?
Best, Pranav
Hi Pranav, You have to use color zone after doing the clipping, as mentioned in this recent post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-November/001642.html> If there wasn't any clipping when you used color zone, the clipping surfaces did not yet exist and did not get colored. Best, Elaine
On Nov 20, 2020, at 10:59 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Amazing! Thank you!
May I also know how I can color clipping planes with the same colors?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Fri, Nov 20, 2020 at 6:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I believe you need to use "copies true" in the sym command to make the full assembly using "real" atomic copies rather than graphical clones. Color zone and other commands only recognize the real atomic copies.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2020, at 10:21 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine,
Further to this query, I have a virus.pdb and virus.mrc. I symmetry expanded the virus.pdb using sym #1 assembly 1 and then ran color by zone color zone #2 near #3 distance 5
Where #1 = virus asym unit #2 = virus.mrc #3 = symmetrised #1
however this results in only the surface in the asymmetric unit inheriting the model colors. How do I propagate the colors of all the chains to the entire surface of the capsid?
Best, Pranav
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine! Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Fri, Nov 20, 2020 at 7:09 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, You have to use color zone after doing the clipping, as mentioned in this recent post:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-November/001642.html>
If there wasn't any clipping when you used color zone, the clipping surfaces did not yet exist and did not get colored.
Best, Elaine
On Nov 20, 2020, at 10:59 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Amazing! Thank you!
May I also know how I can color clipping planes with the same colors?
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Fri, Nov 20, 2020 at 6:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I believe you need to use "copies true" in the sym command to make the full assembly using "real" atomic copies rather than graphical clones. Color zone and other commands only recognize the real atomic copies.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2020, at 10:21 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine,
Further to this query, I have a virus.pdb and virus.mrc. I symmetry expanded the virus.pdb using sym #1 assembly 1 and then ran color by zone color zone #2 near #3 distance 5
Where #1 = virus asym unit #2 = virus.mrc #3 = symmetrised #1
however this results in only the surface in the asymmetric unit inheriting the model colors. How do I propagate the colors of all the chains to the entire surface of the capsid?
Best, Pranav
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Elaine Meng -
Pranav Shah