Re: [ccp4bb]: modified amino acids in refmac5

[Garib Murshudov <garib@ysbl.york.ac.uk>]

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>

Hi
There are two ways for dealing with modified amino acid residues
1) Using link record. You create dictionary for added group. Then use link
between this
group and amino acid it is attached to. You can just run refmac5 with
MAKE LINK yes
and it will create link for you if groups are close to each other. Then you
can modify or your description of
link. Description of link can have info about bond angle bond length,
deletion of atoms addition of atoms etc.
I like this option more as youy keep your original residue name.

2) Create dictionary entry for the modified amino acid and declare it as
L-peptide. This option works
with refmac 5.1 (which is available from york's ftp
ftp://ftp.ysbl.york.ac.uk/pub/garib/).


regards
Garib

>
>
> Hi,
>
> The problem is as follows...I am refining structures with refmac5 which
> contain modified (acylated) cysteine residues. Needless to say that no
> corresponding library entries exist in the standard set. I can "easily"
> make the library entries for the residues so that the correct geometry is
> retained, but refmac does not seem to handle these residues as being part
> of the chain, i.e. the C-N distances on both side of such a residue
> increase during refinement. Apparently, the program breaks my protein
> chain on both sides of the modified amino acid to start with.
>
> It also gives this error for each "broken" peptide bond in the beginning:
>
>   INFO:     connection is found (not be used) dist=   1.416 ideal_dist=
> 1.329
>             ch:AA res:  88  LEU      at:C    --> ch:Aa res:  89  ACC
> at:N
>
> And, of course, complains about the VDW outliers later on...
>
> I tried reading the fantastic manual, but was not able to extract the
> relevant info. I started from the cysteine residue entry, adding the
> atoms of the acyl group at the SG and so on but did not touch any of the
> main chain atoms there.
>
> All the best,
>
> Pete
>
>



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Garib N. Murshudov, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 62 87, work:  +44 (1904) 43 25 65
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