Hi Sonya, On Jun 24, 2010, at 7:39 AM, Sona Vasudevan wrote:
Hello Eric,
Thanks for all the great features you have added in the last couple of years since I was last in touch with you. This is a fantastic tool!
Thanks! Glad you like it.
I need some help with the alignment editor.
I am trying to import an alignment in fasta format (fasta aligned) (see attached). The alignment as you can see has three structures. I use Load structures from the sequence window and it brings in all the chains corresponding to teh structures.
It does, but there's a subtlety here that I should point out. The first two sequences in the alignment are for 1XVA, chain A and chain B. Chimera opens two copies of 1XVA and associates one copy with each sequence, but it associates chain A in both, since the sequences of the two chains are identical. It doesn't really look at the sequence name to try to figure out which chain to associate, just how well the sequences match and in this case they both match perfectly. By hovering the mouse over the sequence name you can see which structure/ chain it is associated with. To change the association of the second sequence to use chain B, you need to go to the alignment's Structure menu and choose "Associations...". Thus will bring up a panel showing the association of each structure to a sequence. Change the association of "1xva (#1)" from "chain A" to "chain B" and then click OK.
I then use Matchmaker to align them. I have a few questions:
1. Does the match maker use the info from the imported alignment since the structures are already aligned? In other words is the structural alignment I am seeing the saem as that was imported.
No. MatchMaker is its own tool and doesn't use any open alignments. After all, you could have several alignments involving those structures open. If you want to superimpose the structures based on your alignment, use the alignment's own "Structure->Match" menu item. That brings up a dialog offering a variety of options as to how to carry out the match. I like using the "Iterate" option, but it's totally up to you.
2. Is there a way to just output the superposed co-ordinates without the chains that are not being used?
There are probably several ways. One that comes to mind is to click on one of the alignment's "Consensus" letters to select all the residues in that column. Then click into the graphics window and hit the up-arrow key to expand the selection to the entire chain. Then either choose Select->Invert or hit right-arrow to invert the selection -- now the unused chains are selected. Actions->Atoms/Bonds-
delete will delete them. You can then write out what's left.
Keep in mind that if you want to get model 2's coordinates as superimposed with model 0's original coordinates (for instance) then make sure to use the "relative 0" option in the "write" command or check the "Save relative to" option in the Write PDB dialog and choose model 0. Or you could just write out all models current coordinates. They will all differ from their originals, but they will be superimposed.
3. Looks like I can add sequences to the alignement. Can I add a fasta file with many sequences?
No. It is on my to-do list but I haven't gotten to it yet. I'll open a feature-request ticket in our Trac database with you on the recipient list so you'll know when it gets implemented. Sorry!
Thanks so much! I have alignment files for 100 families which are high-qualityas they were manually aligned with Cn3d and I would like to import them into chimera for further analysis.
Thanks so much for your time!
You're welcome! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu