Dear all,
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) 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. Best wishes, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
