Is there any tool to write some calculated attribute into a header format?
Hi All!
I would like to know: Is there any way or tool to write some calculated attribute into a header format?
I want to see the same color values obtained for some a calculated attribute projected onto a sequence.
I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute.
Thank you in advance.
Hi Sergio, Sorry, there isn’t a way to automatically make residue attributes into a header. We had imagined that people would be calculating properties outside of Chimera, and then using a script or even manually creating a file in the header format to load them as a header. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat
However, you can change the sequence lettering colors to match the ribbon, so if you first colored ribbon by some residue attribute (with Render by Attribute or command “rangecolor”), it could be reflected back into the sequence window in that way. To do that, use sequence window menu Preferences… Appearance, and then for residue letter coloring (near the bottom), choose “coloring scheme: ribbon”. I realize this might not be optimal if some of the coloring makes the letters hard to read.
I attached an example image with my protein colored by residue average bfactor (blue -> red -> yellow) and using “ribbon” coloring of the associated sequence in the alignment.
With a header you could only have one value per column, but with ribbon coloring you could have different values (colors) in the same column if there are multiple structures associated.
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 31, 2018, at 6:05 AM, Sergio Garay sergio.alberto.garay@gmail.com wrote:
Hi All!
I would like to know: Is there any way or tool to write some calculated attribute into a header format?
I want to see the same color values obtained for some a calculated attribute projected onto a sequence.
I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute.
Thank you in advance.
-- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Sergio, If you are comfortable writing Python code, there is a provision for adding custom header types to Multalign Viewer. Look at the MAVHeader module in your Chimera distribution (<your Chimera>/share/MAVHeader), particularly the file ChimeraExtension.py which defines headers for charge variation and CA/backbone/full RMSDs and registers those headers with Multalign Viewer. I imagine you will have questions (LOL!) so I have directed responses to the chimera-dev mailing list, which would seem more appropriate in this case.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 31, 2018, at 11:22 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Sergio, Sorry, there isn’t a way to automatically make residue attributes into a header. We had imagined that people would be calculating properties outside of Chimera, and then using a script or even manually creating a file in the header format to load them as a header. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/de... http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>
However, you can change the sequence lettering colors to match the ribbon, so if you first colored ribbon by some residue attribute (with Render by Attribute or command “rangecolor”), it could be reflected back into the sequence window in that way. To do that, use sequence window menu Preferences… Appearance, and then for residue letter coloring (near the bottom), choose “coloring scheme: ribbon”. I realize this might not be optimal if some of the coloring makes the letters hard to read.
I attached an example image with my protein colored by residue average bfactor (blue -> red -> yellow) and using “ribbon” coloring of the associated sequence in the alignment.
With a header you could only have one value per column, but with ribbon coloring you could have different values (colors) in the same column if there are multiple structures associated.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2018-07-31 at 11.18.18 AM.png>
On Jul 31, 2018, at 6:05 AM, Sergio Garay <sergio.alberto.garay@gmail.com mailto:sergio.alberto.garay@gmail.com> wrote:
Hi All!
I would like to know: Is there any way or tool to write some calculated attribute into a header format?
I want to see the same color values obtained for some a calculated attribute projected onto a sequence.
I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute.
Thank you in advance.
-- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you, Elaine! Very complete answer. I think it will very useful for what I have in mind!
Sergio
On Tue, Jul 31, 2018 at 3:22 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Sergio, Sorry, there isn’t a way to automatically make residue attributes into a header. We had imagined that people would be calculating properties outside of Chimera, and then using a script or even manually creating a file in the header format to load them as a header. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/de...
However, you can change the sequence lettering colors to match the ribbon, so if you first colored ribbon by some residue attribute (with Render by Attribute or command “rangecolor”), it could be reflected back into the sequence window in that way. To do that, use sequence window menu Preferences… Appearance, and then for residue letter coloring (near the bottom), choose “coloring scheme: ribbon”. I realize this might not be optimal if some of the coloring makes the letters hard to read.
I attached an example image with my protein colored by residue average bfactor (blue -> red -> yellow) and using “ribbon” coloring of the associated sequence in the alignment.
With a header you could only have one value per column, but with ribbon coloring you could have different values (colors) in the same column if there are multiple structures associated.
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 31, 2018, at 6:05 AM, Sergio Garay sergio.alberto.garay@gmail.com wrote:
Hi All!
I would like to know: Is there any way or tool to write some calculated attribute into a header format?
I want to see the same color values obtained for some a calculated attribute projected onto a sequence.
I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute.
Thank you in advance.
-- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Sergio Garay