Re: [COOT] real space refine with insertion codes

2019-11-09 Thread Paul Emsley 

On 08/11/2019 19:51, Seth Harris wrote:


I'm sure this has been asked, but after some searching I can't find hints. Apologies if redundant, but can 
someone refresh me on how to get Coot to be graceful about residues with insertion codes...particularly 
during real space refinement. I have a protease structure with very good resolution/density but some odd 
numbering conventions with insertion code (e.g. 124A, 124B, 124C between residues 124 and 125 numbering) in 
other areas continuous residues have non-contiguous numbering. When doing real space refinement both 
situations tend to blow apart, each individual insertion code-numbered residue becoming its own disconnected 
amino acid and well out of the density,


Hi Seth,

The refinement module of 0.8.x dates back to 2004 when I didn't know much about 
anything.

The refinement module of 0.9.x has undergone a significant overhaul. 0.9-pre works with insertion codes (in 
my testing) and I am reluctant (to the point of it not happening) to try to tease out correct peptide 
linking in the crufty 0.8.x version.


So, try 0.9-pre. My plan is to ramp up the build system on the VMs next week. 
Or you can get it from CCPEM.

Regards,

Paul.



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Re: [COOT] real space refine with insertion codes

2019-11-08 Thread Eleanor Dodson 
I am afraid I always renumber - I hate insertion codes because they seem to
generate so many obscure problems..
Eleanor

On Fri, 8 Nov 2019 at 19:51, Seth Harris  wrote:

> Hi all,
>
> I'm sure this has been asked, but after some searching I can't find hints.
> Apologies if redundant, but can someone refresh me on how to get Coot to be
> graceful about residues with insertion codes...particularly during real
> space refinement. I have a protease structure with very good
> resolution/density but some odd numbering conventions with insertion code
> (e.g. 124A, 124B, 124C between residues 124 and 125 numbering) in other
> areas continuous residues have non-contiguous numbering. When doing real
> space refinement both situations tend to blow apart, each individual
> insertion code-numbered residue becoming its own disconnected amino acid
> and well out of the density, I assume due to sterics and it not
> interpreting these as being connected. Also common in Fab structures.
>
> I know there are painful workarounds to number it contiguously without
> insertions and then add back when done refining (but then you find one more
> thing...), but I am aspiring to greater elegance these days. Also hoping I
> don't have to define with LINK records or such for each case?
>
> Thanks,
> Seth
>
> --
>
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