Dear Oliver, merely as a coment: the program mrtailor (http://shelx.uni-ac.gwdg.de/~tg/research/programs/mrtailor) achieves something very similar: it requires an alignment between the sequence inside the PDB file and the target sequence and operates on all matching chains. The result is very similar to chainsaw but intended for the use of mulit-chain PDB files, i.e. the non-matching chains are left untouched in the output PDB rather than removed.
Surely there is no python exercise involved ;-) Best, Tim On 01/04/2014 03:54 PM, Oliver Clarke wrote: > Hi all, > > I’m just going to post this in case it’s useful to anyone else - and if not, > at least I’ll be able to google it for later reference. > > It was more of a python learning exercise for me than anything else - I’m > sure there is probably a better and easier way to do this - but perhaps it > will be useful to someone. > > This is a script that is useful in a fairly specific situation - when you > have a molecular replacement solution of a large, multi protein complex and > you want to mutate each chain in the search model to match the target > sequence. > > It reads a file (seq_name) containing the target sequences in fasta format > (with an additional “>” line after the last sequence, order of the sequences > is not important), matches them each to the best aligning chain in the > molecule (mol_id), and aligns and mutates the chain before finally > associating each target sequence with the appropriate chain. At the moment it > only looks for one chain matching each target sequence, but it would be easy > enough to modify it to take account of multiple identical copies. > Unfortunately at the moment it spawns one info-dialog per align_and_mutate > job, because I don’t know how to automatically dismiss them from within the > script. > > It uses a couple of modules from Biopython, so Biopython will need to be > installed and accessible to coot for this script to work (place Bio and > BioSQL directories inside the site-packages subdir of Coot’s python > installation and modify the PYTHONPATH variable in /usr/local/bin/coot > accordingly). It will also only work with coot nightlies r4872 or later. > > Incidentally, biopython seems to play pretty happily with coot, no negative > effects that I’ve noted so far, and it has a few useful tools, particularly > for dealing with sequences (e.g. being able to directly blast the sequence of > a PDB and return the sequence of the top hit). > > Any comments/criticisms much appreciated - am trying to teach myself python > but am starting from scratch pretty much, so if there is any obviously stupid > code in this script I’d love to know how to make it better! > > Cheers, > Oliver. > > > > > > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
signature.asc
Description: OpenPGP digital signature
