One of the molecules of my crystal structure has density for the two conformations of a loop. I want to build the alternate conformation of the loop using coot. However, haven't figured it out how to do it? I would really appreciate if someone tells me how to do it?
Hi Mohammad,
Did you find the answers your question? I am also interested in this !
Cheers,
Thierry
Hi,
I got answer from CCP4BB and the answers were really helpful . I am adding one answer here it was from Herman-
Probably the easiest way to do it, is to use the “Add Alternate (Alternative) Conformation to a Residue” option in the right panel of coot. Click on it, select “Split All of a Single Residue” (=default) and then click on the first residue of the loop. Repeat this for all residues in the loop. Next move all newly generate alternative residues (conformation “B”) to the alternative density. I would use the “Rotate Translate Zone/Chain/Molecule” option, again in the right panel for this and move the alternative residues one by one to their new positions.
You can use the usual manual rebuilding options to get a good fit to the alternative density. There is (or was, I haven’t tested it recently) one caveat, you cannot use real space refinement including regular and alternative residues, or alternative A and B residues. For real space refinement you HAVE (or HAD) to click only alternative residues of one type (A or B), otherwise the real space refinement will create a big mess. You can also leave it to Refmac of Buster to refine the alternative residues, they are pretty good at it