Load your pdb file with Pymol. Then use the following command:
save somename.fasta
Or for a just one chain:
save somename.fasta, chain A
The file is saved in the same folder as your pdb file. Now you can do an alignment (or whatever you need to do with the sequence).
Note: if you have residues which have alternative conformations it's best to remove these alternate conformation. If not, Pymol will add two residues to the sequence file instead of one. To remove alternate confomations in Pymol:
remove not (alt ''+A)
alter all, alt=''
alter all, alt=''
For more info see here.
Thanks for the post! Handy!
ReplyDeleteThank you!
ReplyDeleteYou saved my life...REALLY THANK YOU !!!
ReplyDeleteNever knew that this could be done in Pymol. Thanks for the post!
ReplyDelete