Hi Kelvin,
that "fasta" command right now only dumps the sequence to the log window, it
doesn't return or save the sequence to a file. This is probably because for my
use case it was always sufficient to copy and paste the sequence from the log
window. However, it's not too difficult to improve
Hi Kelvin,
the "psico" module provides a "fasta" command which maintains the gaps.
However, psico will not work with PyMOL 0.99 which is quite old and uses an
ancient Python version (psico requires Python 2.6 and and the PyMOL 1.2 API).
Psico installations instructions and download link:
http:/
Due to the possibility of insertion codes and non-sequential residue numbering,
I believe there is no way to avoid aligning the residues in the ATOM records
with the sequence in SEQRES in order to find gaps. I don't know of a program
to do this.
The structure validation server at RCSB ADIT2 makes t
Hello,
I am using PyMOL 0.99rc6. I am wondering if there is a means to obtain
a FASTA sequence from a loaded pdb file that maintains the gaps due to
missing portions of the structure? I found one program that will strip
the sequence from pdb files, but it simply reads out the amino acids
tha
