Re: [ccp4bb]: Geometry problems in Refmac

["Ben Sandler" <sandler@msg.ucsf.edu>]

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I'm not sure what information is relevant- I was hoping 
there might be some sort of characteristic error that 
generally produced this sort of problem.  

The geometry distortions look pretty general- the ligand 
just seems to turn mushy and get bent out of shape.  For 
example, there are aromatic rings which look visibly 
scrunched, with the bond lengths and angles distorted by 
maybe 10% or so.  There's also a hydroxyl coming off one 
of the aromatic rings, and it's tilted to one side, in 
defiance of the 120 degree bond angles specified in the 
geometry file.

I read through the tutorial and as best I can tell, I've 
done everything by the book as described there:

http://www.ccp4.ac.uk/dist/examples/tutorial2000/html/refine-tutorial.html

I also checked the library file myself, and the ideal bond 
lengths and angles are all there.  It seems as if the 
program is just ignoring them, or is using abnormally 
loose geometric restraints.

-Ben
On Tue, 22 Apr 2003 13:40:42 -0700
  "Frank von Delft" <loretta@scripps.edu> wrote:
>Hi Ben 
>
>Not really, since telephathy is still in its infancy. 
> That sort of problem is usually subtle, but you give 
>very little information so it's rather hard to 
>troubleshoot.  I recommend posting more details, such as 
>cif files, what geometry gets distorted, etc.  
>
>Cheers
>phx.
>