hari jayaram wrote:
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?
I believe that that is the case.
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!
You make me slightly worried, but I cannot imagine how that could be
the case.
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.
I rarely use Regularize Zone.
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.
That is what the traffic lights are for.
Refine 3 well fitting residues, the chi squared values should be about 1.0.
If they are not, then adjust the weight until they are.
Now you can refine other regions.
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.
Reduce the weight. Add torsion angle restraints.
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.
Gtk2 vs gtk1 version, I'd guess.
Paul.
