Hi Paul,
that's fantastic, thanks for the quick response. Haven't heard of the Buccaneer side-chain building mode yet. I'll have a look asap. Best, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden ________________________________ From: Paul Emsley <[email protected]> Sent: 16 December 2019 16:28:33 To: Karim Rafie; [email protected] Subject: Re: Simple mutate and save coordinates 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. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
