Hi,
I may have found a bug in the way pymol interprets connectivity of
atoms. I noticed this in one pdb structure that I am working with 1RV1.
Steps to reproduce:
fetch 1RV1
#extract one of the ligands to it's own object
extract 'lig', /1RV1//A/110
#add hydrogens
h_add lig
Now look at atom C2
Just adding that N1, C2, and N3 in that ring are all sp2 hybridized. So the
H on the adjacent N is also in the wrong place.
Q: How is PyMOL determining ligand atom hybridization, by the way? Not
using the ligand CIF file at PDB, I guess?
Bob Hanson
On Fri, Jun 7, 2013 at 10:51 AM, Matthew Baum
I must say, 'cartoon skip' does not do what I thought it would do.
fetch 1RV1
cartoon skip, i. 55
# now a helix section is turned into a loop
cartoon skip, i. 56
# now there is a break, but two non-helix ends
cartoon skip, i. 57
# now there is a break, with two non-helix ends
I guess I understan
Subject: RE: [PyMOL] Possible hydrogen addition bug
Hi all,
I believe this would be as a result of the "pdb" file not containing the
hybridisation information. When you manually change that bond to be double
(using the builder module) and then add hydrogens it is correct. This is not an
uncom
Please see the following URLs for reference. Basically you are duplicating an
object and then setting one (say Model A) with some level of transparency and
one (say Model B) without transparency. And then 'hiding' portions of Model B
(using 'cartoon skip') would reveal the transparency in Model
