Marie Fraser wrote:
> I'm a new Coot user,
Hello Marie. Welcome.
> having switched to using Molprobity
Good good.
> and coming to Coot primarily because of the validation tools.
> I am now running two versions, 0.3.3 on Linux and version
> 0.4 pre-release on Mac OSX and Linux. I have been having a few
> problems and am wondering if other people have seen these:
> 1) The rotamer analysis works in 0.3.3,
The 0.3.3 uses Dunbrack's library
> but 0.4 gives a different analysis,
That uses Richardson's Library
with many more bad rotamers.
GLNs and ASN and PROs? I worry that I may be mis-using the library.
There may be a +180 degree issue that I am not taking into account.
> 2) Molprobity reduce and probe worked until the update
> to Molprobity3. Now the programs run, but there are no dots
> displayed and the window with the clashes has no information
> visible.
I suspect a difference of opinion on PDB "remediated format" atom names.
Coot has not moved over to PDB remediated atom names yet. Fingers
crossed, it will do. How can I reproduce this problem - are you using
output from the molprobity web server?
> 3) On some projects, the script for Coot from Molprobity
> (older versions of both) gives a window with bad regions as
> expected. On others, the window appears with bad regions but
> the scroll bar is almost the size of the window, not allowing
> scrolling through the bad regions. The projects where this happens
> are large structures with about 4000 residues, so there may be a
> problem with dimensions.
Yes. Please send me the Coot script (no need to send coords).
Paul.
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