On 16/12/2019 22:32, Karim Rafie wrote:
I am currently working on structure of a protein complex and am trying to identify the sequence of a protein
chain (24mer) that hasn't been seen/described before. Thankfully, the map is good enough allowing me to
identify two positions along this chain to which I can model in larger residues with a high degree of
confidence, allowing me to identify a potential sequence. However, to use a more unbiased approach I decided
to check all possible sequences that match the pattern of this 24mer, i.e. the number of residues between
the two positions as well as allowing for a randomisation of these two positions with other large residues
that could potentially fit.
I have all the potential sequences that match this patter and now I would like to write a script in coot
that allows me to loop over all possible sequences and:
(1) read the coordinates of a polyAla mock chain with the correct coordinates
(2) simple mutate the chain to one of the identified possible sequences
(3) save the new coordinates as a pdb file
(repeat)
see attached.
I'm usually quite happy to read up and figure things out by myself, however I've never scripted in coot
before and am a bit under a time pressure, which is why I'm reaching out to the community.
Any advice and/or info would be appreciated.
How about using Buccaneer side-chain building mode?
Paul.
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(let ((seq "DVSGTVCLSALPPEATDTLNLIASDGPFPYSQD")) ;; or whatever
(let ((imol (read-pdb "poly-ala-frag.pdb")) ;; or whatever
(ch-id "A")) ;; presumably
(let* ((residues (residues-in-chain imol ch-id))
(n-residues (length residues))
(n-trials (- (string-length seq) n-residues)))
(for-each (lambda (i-trial)
(let ((file-name (string-append "trial" (number->string
i-trial) ".pdb"))
(mol-name (string-append "trial" (number->string
i-trial)))
(imol-copy (copy-molecule imol))
(frag-seq (substring seq i-trial (+ i-trial
n-residues))))
(mutate-chain imol-copy ch-id frag-seq)
(set-molecule imol mol-name)
(write-pdb-file imol-copy file-name)))
(range n-trials)))))
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