Hi I am using coot 0.5 pre 1 on linux . I am trying to correct the model after molecular replacement into a 3.3 A map and I have a few questions The map is quite good for all the helical regions but the loops are expectedly hard to build. Thanks to prime-and-witch I have a remarkably bias removed map that I am building into with coot.
1) I am noticing that Regularize-zone seems quite "aggressive" in this version of coot compared to the version I was used to (coot 0.3). In addition , if I understand correctly regularize should not care whether the region being regularized is in or out of density. Is that true? . It seems that sometimes regularize seems to really go out of its way to make it into density..or it may just be my model! 2) It seems that even though some of my model came from "good" geometry for a 2.5 A data derived model, regularize seems to modify it extensively . Is this to be expected. 3) Also I just noticed that I can adjust my weights for the real space refine zone to favor my geometry more than my map. Any idea what are reasonable weights for a 3.3 A map with very few side chains and no carbonyl bumps visible. I find that real space refine does quite often tend to swing my side chains into neighboring mainchain density even though it is obviously wrong. Is there a way to reduce this behavior or avoid it. 4) I had one final question, I used 0.5 pre 1 on Mac osx a few days back and could have sworn that a real space refinement also pulls up an on-the-fly graph of the "goodness" of bond angles, lengths etc every time the command is run . The three bar graphs were color coded from green to red. Is that no longer available in linux 0.5 pre 1 or do I have to turn that option on somewhere. Your help and comments will be greatly appreciated Hari
