Hi there,
I am trying to plot a series of clipping slabs through a protein
structure, but would like to show an additional figure to indicate where
the 'slices' are from (similar to what you would do with a MRI or
CT-scan in medicine - something akin to '
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
Dear all,
I would like to show a transparent surface of a ligand, with the ligand
'inside' as sticks.
I created a new object of the ligand, then tried to show the surface, which
fails.
With this information here:
http://sourceforge.net/p/pymol/mailman/message/27299068/
# do not ignore
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
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:
Hi Tobias -
It seems to me that you may not have hidden the lines/sticks from the object
where you’ve shown the surface. For overlapping objects, the normal
non-ray-traced view appears to give precedence to the object that was present
in the viewer first. Try disabling and re-enabling your
