[ccp4bb] Removing a ter line present in the middle of the chain

[Rashi Aggarwal]

Dear all,

I have an unnatural amino acid in my structure which I could successfully
add in coot. The amino acid is taking the right bonds when viewed with
coot. However, the pdb file has a ter line just above the residue.

If I remove this line and submit the pdb to refmac it again adds the ter
line, I can still remove it and go ahead with validation but is it the
right thing to do?

Thanks

Best,
Rashi

[ccp4bb] Adding unnatural amino acid

[Rashi Aggarwal]

Dear all,

I am trying to add an unnatural amino acid to a structure in coot. I was
able to successfully place the residue in the electron density. Also, I
could establish links between the residue and the polypeptide chain using
the 'make links' option in coot.

However, I was wondering how to establish covalent bonds between the
unnatural amino acid and other residues in the peptide chain. Any advice
will be appreciated

Thanks

Best,
Rashi

[ccp4bb] R free flag

[Rashi Aggarwal]

Hello,

I am trying to refine a structure that is deposited in PDB. I have
downloaded the _sigmaa.mtz file from the electron density server.

Trying to run refmac using this mtz file gives me the popup free R label
has not been set.

How can I set free R label in an existing mtz file so that after refinement
I can get the R and Rfree?

-Rashi