problem with color by conservation option
Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips.
Best,
Ela Wator
Hi Ela, It is probably not an error, but instead:
It is probably because the conservation is not calculated at positions where there is a high fraction of gaps. I.e. when many sequences have gaps at the position, there are not many "real" residues and the calculation of conservation is less reliable, so conservation is not calculated. You can see this in the sequence window, in the Conservation histogram -- it will be blank in the positions where conservation is not calculated.
However, you can change the parameter to force calculating a value even when there is a high fraction of gaps. To do that, choose Settings from the context menu in the Sequence Viewer window (show the context menu by right-click, or Ctrl-click if on Mac, in the sequence window). https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context
In the Settings, go to the Headers section, and for Conservation, AL2CO parameters, try using a higher value for the allowed "gap fraction" https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings-headers
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 5, 2023, at 4:30 AM, Elzbieta Wator via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator
Thank you for the fast answer. It helped! 🙂 ________________________________ Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: niedziela, 5 listopada 2023 16:00 Do: Elżbieta Wątor elzbieta.wator@doctoral.uj.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] problem with color by conservation option
UWAGA: Wiadomość pochodzi od zewnętrznego nadawcy.
Hi Ela, It is probably not an error, but instead:
It is probably because the conservation is not calculated at positions where there is a high fraction of gaps. I.e. when many sequences have gaps at the position, there are not many "real" residues and the calculation of conservation is less reliable, so conservation is not calculated. You can see this in the sequence window, in the Conservation histogram -- it will be blank in the positions where conservation is not calculated.
However, you can change the parameter to force calculating a value even when there is a high fraction of gaps. To do that, choose Settings from the context menu in the Sequence Viewer window (show the context menu by right-click, or Ctrl-click if on Mac, in the sequence window). https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context
In the Settings, go to the Headers section, and for Conservation, AL2CO parameters, try using a higher value for the allowed "gap fraction" https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings-headers
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 5, 2023, at 4:30 AM, Elzbieta Wator via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator
participants (3)
-
Elaine Meng -
elzbieta.wator＠doctoral.uj.edu.pl -
Elżbieta Wątor