Hi Jim and Dmitri, Since your questions are related, I will attempt a combined answer: (1) structure editing. I would not recommend Chimera for full- fledged homology modeling, but we do have excellent capabilities for mutating a few amino acids here and there and placing reasonable rotamers from backbone-dependent or backbone-independent libraries. This can be done with the Rotamers tool (under Tools... Structure Editing): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/ framerot.html or its command implementation, "swapaa": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html There is also an "addaa" command for extending peptides C-terminally: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html You will see other tools such as Build Structure and Minimize Structure (also implemented as the command "minimize") in the same menu as Rotamers. These tools are not as fully developed as Rotamers, but we continue to improve them. Each tool is documented; one way to see a tool's man page is to start it and click the Help button. Likewise, each command is documented, and one way to see its man page is use the command "help [command]" - for example, "help addaa" (2) interface to true homology modeling software. An interface to Modeller is a future direction, but little has been done so far. Actually, there is Model Loops tool (again, under Tools... Structure Editing) that interfaces with a separately obtained copy of Modeller, but currently it only will model alternative conformations of loops that are already present in your structure. What we do have now is the ability to fetch directly from Modbase from the Chimera command line, as described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/open.html for example, command "open modbase:b2ar_human" today fetches 4 different models of the human beta2-adrenergic receptor as models #0.1-0.4 in Chimera. The modbase structures have the modeller error profile value in the B-factor column, so coloring by B-factor for these structures is really coloring by error profile value. Which brings me to... (3) coloring by attribute value. Actually I believe the flexibility of this feature is a selling point of Chimera, so am somewhat surprised by your comment. Do you mean the coloring itself is limited, or the choice of attributes that can be shown with color? - If the coloring, I should note that you can move the sliders on the histogram, change their colors to whatever you want, and add more color sliders to define the mapping. I guess the main limitation there is that the interpolation between the sliders is linear only, but that still leaves quite an array of possibilities. See the Render by Attribute documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html - If the attributes available, there is a Define Attributes tool with which you can read in your own arbitrary attributes of atoms, residues, or models (using a simple text format), and an Attribute Calculator tool with which you can combine existing numerical attributes with formulae to generate new ones. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html Linked to the Define Attribute page are some example files, including ones that define additional hydrophobicity scales. There is also an Attributes tutorial that uses several attributes-related tools: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html I hope this answers both of your questions, but feel free to write back if I missed something or was unclear - Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 14, 2008, at 11:57 AM, Nicholson, Jim wrote:
Hi:
I still love Chimera (if you remember my last message), but, I need to do some homology modelling. I was using Insight/Homology, but, access to that software has been taken away. I’m wondering if anyone on the Chimera project is using an interface to Modeller or has any recommendations commands that might be usefull, like adding amino acids from a sequence, extending the protein, etc.
Also, the coloring schemes I can see look a little limited. I regularly color by charge or hydrophobicity. I was wondering if there might be something I’m missing in Chimera?
-Jim Nicholson
Program in Neuroscience
University of Maryland
685 W. Baltimore, St., MSTF 5-11
Baltimore, MD 21201
410-706-3418
410-804-5872 (cell)
and Dmitri wrote:
Dear friends and colleagues, I have not really tried the product yet, but was wondering whether it is possible to "edit" a protein's structure by introducing one or two single mutations with the follow-up minimization using Chimera. If so, could you please hint to the algorithm of actions. Thanks a lot in advance! The project is burning :-( Dmitri