Dear PyMOL experts,
in GPCR crystal structures it is quite common to have fusions with
lysozyme or BRIL in the third intracellular loop. The residue numbers of
the inserted domains are often incremented by 1000. As a result, the two
residues at the fusion point jump from for example 223 to 1002. As a
result, gaps exist in the cartoon representation at the fusion points.
Increasing cartoon_gap_cutoff does not help as PyMOL rather connects the
C- and N-termini of the GPCR fold. In stick representation, the peptide
bonds at the fusion points are represented fine. I could not find any
options like "cartoon_use_peptide_bonds" or "bond_cartoon selection,
selection". A workaround would probably be to renumber the residues of
the fusion protein and use insertion codes, I did not try this yet. An
example is pdb id 4eiy.
Is there a better solution, have I overlooked an option?
Best regards,
Norbert
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
