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Dear Dialing,
could you first explain why you display hydrogens in coot? Usually
hydrogens are used in refinement in riding (calculated) positions and
not saved to the PDB file, so there should not be any for coot to display.
Maybe solving this questions solves a few of the other ones.
Tim
On 12/05/2011 11:48 AM, Dialing Pretty wrote:
> Dear All,
>
> I am leaning rotamer outlier reduction by Coot.
>
> After select a rotamer and acception, I find some hydrogens in the
> outlier rotamer will be isolated from the rotamer, and the rotamer
> will have new hydrogens at its new position. Is any influence by
> further refine by phenix?
>
> After new rotamer acception, I have did the rotamer auto-fit, I find
> there is a trend on that several oxygens can pack together. How to
> process this problem?
>
> After I save the new PDB file by coot after I selected the new
> rotamers to replace the outlier rotamers, I did a Phenix refine.
> There is an error message at the start says "Number of atoms with
> unknown nonbonded energy typensymbol: 2228". What does it mean and
> how to solve the problem?
>
> Is any simple method by which I can do the rotamer outlier reduction
> by Coot?
>
> I am looking forward to getting your reply.
>
> Dialing
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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