On 02/12/11 14:45, Simon Kolstoe wrote:
I've got a text file with multiple conformations of a ligand that has been
docked to a protein using autodock, which I am trying to split into separate
pdb files in order to visualise in pymol/coot etc.
Previously I've used the script pasted below, but it is now falling over just
after it creates the pdb file with the error:
expr: syntax error
csplit: }: bad repetition count
./split_results.com: line 11: syntax error near unexpected token `('
./split_results.com: line 11: `foreach f ($outputname.[0-9][0-9][0-9])'
This doesn't answer your question.
But I'd just do it in Coot:
(define (split-multi-alt-confs)
(using-active-atom
(let ((alt-confs (residue-alt-confs aa-imol aa-chain-id aa-res-no
aa-ins-code)))
(for-each (lambda (alt-conf)
(let* ((ss (string-append "//*/*/*: ," alt-conf ""))
(imol-new (new-molecule-by-atom-selection aa-imol ss))
(new-name (string-append (strip-extension (molecule-name
aa-imol))
"-alt-conf-" alt-conf)))
(set-molecule-name imol-new new-name)))
(residue-alt-confs aa-imol aa-chain-id aa-res-no aa-ins-code)))))
Centre on your interesting ligand with multiple alt-confs and then use
scripting -> scheme
(split-multi-alt-confs)
If you want to write out the various pdb files, you can add in a
(write-pdb-file imol-new (string-append (molecule-name imol-new) ".pdb"))
before the set-molecule-name... line.
Paul.
