On Jan 15, 2009, at 7:07 AM, Patton, John (NIH/NIAID) wrote:

Hi Elaine, Do you have any information concerning using Protskin in conjunction with Chimera? The only information I have come across applies to PyMol. Thanks, John

Hi John, I haven't tried Protskin, but my understanding is that its purpose is to map conservation in a multiple sequence alignment to protein display. (Protskin page: <http://www.mcgnmr.ca/ProtSkin/intro/> ) Chimera itself can (A) read your multiple sequence alignment (many formats, just use File... Open) (B) calculate any of several measures of conservation (entropy, variability, etc.) - in the sequence window menu, choose Preferences... Analysis, set "Conservation style" to "AL2CO" to access further options for calculating conservation, which is shown as a histogram above the alignment <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mul...

(C) show them on your structure(s) with any color mapping you desire, or with "worm" thickness - any open structure(s) will associate automatically with sequence(s) in the alignment - in the sequence window menu, choose Structure... Render by Conservation, change attribute to "mavConservation" and show with color or worms <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...

Example image, 1bzm colored by conservation in PFAM Carb_anhydrase seed alignment: <http://www.cgl.ucsf.edu/chimera/feature_highlights/1bzm-al2co-highlight.png

This tutorial includes coloring by conservation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> Back to ProtSkin: ----------------- It sounds like ProtSkin emits some file listing the residues and associated values. Certainly you could reformat that into a Chimera "define attribute" file, read it in, and then show the values as in (C) above. Since Chimera already performs the preceding steps quite well and with many powerful options, there hasn't been much impetus to hooking it up to ProtSkin. However, I don't see any barrier other than your needing to convert the output file into the simple "define attribute" format described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...

Getting a sequence alignment: ----------------------------- Perhaps you didn't already have a sequence alignment, and find ProtSkin to be helpful in generating one. There are many alternative approaches. For example, the ConSurf server does a great job of automatically generating an alignment of a diverse set of sequences related to your single uploaded structure. (ConSurf server: <http://consurf.tau.ac.il/> ) There are more ideas in this page I wrote on "sources of sequence alignments" for use in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> I would be happy provide more detailed help on using Chimera to color by conservation as it applies to your system of interest, i.e. feel free to write back. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html