Using Chimera to display family shuffling information.
To Whom It May Concern:
I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html
What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself.
Regards,
Matthew Tiffany Postdoctoral Fellow Mark A. Kay Laboratory Stanford University 269 Campus Drive CCSR 2110 Stanford, CA 94305
On Apr 8, 2015, at 5:11 PM, Matthew Tiffany matt.tiffany@icloud.com wrote:
To Whom It May Concern: I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html
What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself.
Regards, Matthew Tiffany Postdoctoral Fellow Mark A. Kay Laboratory Stanford University
Hi Matthew, I’ve CC’d the chimera-users list since my answer doesn’t involve programming...
Chimera itself includes a lot of sequence-structure interactivity and related features. Certainly you could do it semi-manually:
(1) open your 3D structure and sequence alignment in Chimera. You can just the “File… Open” dailog. Chimera understands several sequence alignment formats. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
(2) associate the structure with a sequence in the alignment. I don’t know exactly what your data look like, and so this requires some judgment calls and deciding amongst different strategies. My thought is at least initially, don’t worry about which sequence is associated with the structure, just try to get it associated with any sequence so that the 3D mapping along the alignment as a whole is correct. — approach A: just use sequence window menu Structure… Associations to force association with any one of the sequences, if it didn’t already associate automatically — approach B: add the sequence of the chimeric protein to your sequence alignment, sequence window menu Edit… Add Sequence, use From Structure (if it adds it poorly you may have to go through a few cycles of Edit… Delete Sequences/Gaps to remove it and then adding it back with different alignment parameters) … I’m leaning toward approach B as the better approach, but you can see whether one or the other works better for your situation… http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
(3) then you can select the different parts of the structure for coloring by using the mouse in the sequence window to select the appropriate ranges of residues in the structure-associated sequence http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regions
Another approach to #1-2 above would be to start with a sequence of just your structure (for example, open the structure, use Favorites… Sequence to show its sequence) and Blast against the PDB, then load in the Blast alignment. However, you already have your own alignment so I don’t think it would get you much further. Further, there is a newish “mda” command that performs multiple steps including blasting against PDB, automatically loading in the structures and Blast alignment, and conveniently laying out the structure hits N->C (based on alignment to query) in the 3D display. This also wouldn’t get you much further toward the color mapping of your chimeric structure, but the layout stuff is cool. It might not work if your shuffled cassettes are pretty short though. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 8, 2015, at 5:11 PM, Matthew Tiffany matt.tiffany@icloud.com wrote:
To Whom It May Concern:
I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html
What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself.
Hi Matthew, I'm not aware of any pre-existing plugin that does this. I think that with some effort on your part you would be able to code something in Chimera that does what you want. The most basic thing to know here is that you can read sequence/alignment files via the various parsers (named after the formats they read) found in Chimera's MultAlignViewer.parsers module [corresponding code in <your Chimera installation>/share/MultAlignViewer/parsers]. For instance the parse() function in MultAlignViewer.parsers.readALN takes a Clustal ALN file as its argument and returns a 3-tuple, the first item of which is a list of Sequence objects and the rest of which you can ignore in this context. Is the length of the chimera protein sequence going to be same as the length of the alignment of parents, or are you going to have to insert gaps (including possible beginning/end gaps) to match up the chimera to the parents alignment? The latter is certainly more complicated. Anyway, once they are the same length you would need to identify the "runs" in the chimera that match the various parent domains. I have some ideas but maybe you already know what you're going to do there. Then open the related structure, make a sequence viewer window for it, align the chimeric sequence to it, and assign attributes based on the domain matching to the related structure's residues, and color them however you like either directly in Python or via the Render By Attribute tool. Say you've opened the structure, some vague example code: --- from chimera import openModels, Molecule m = openModels.list(modelTypes=[Molecule])[0] relatedChain = m.sequence('A') # chain A from MultAlignViewer.MAViewer import MAViewer mav = MAViewer([relatedChain]) mav.alignSeq(chimericSequence) matchMap = mav.seqs[0].matchMaps[m] for r in relatedChain.residues: if not r: continue # missing structure index = matchMaps[r] gappedIndex = mav.seqs[0].ungapped2gapped(index) chimericIndex = mav.seqs[1].gapped2ungapped(gappedIndex) if not chimericIndex: continue # falls in gap in chimera parent = chimera2parent[chimericIndex] # computed previously r.parentNum = parent --- After executing the above, the residues of the related structure will have a 'parentNum' attribute. You could use the Render By Attribute tool to color based on that attr, or use it in commands with the atom spec ':/parentNum=X'. Obviously, I've omitted a bunch of detail, but I thought it better to send this and have to ask questions about what you can't figure out yourself rather than try to write out everything in excruciating detail. :-)
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Matthew Tiffany