[ccp4bb]: modified amino acids in refmac5

[Petri Kursula <pkursula@sun3.oulu.fi>]

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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

                    ---------------------------------------
                              Petri Kursula, Ph.D.
             Petri.Kursula@oulu.fi     http://cc.oulu.fi/~pkursula
                 Department of Biochemistry and Biocenter Oulu
                       University of Oulu, Oulu, Finland
                    =======================================