On 03/04/12 11:18, Antony Oliver wrote:
I am really enjoying the functionality of LIDIA in the recent versions of Coot
— thank you Paul.
Glad you like it :-)
Just a couple of questions / ideas / feature requests though...
A) LIDIA doesn't always seem to show all hydrogen bonds, i.e. particularly from
the ligand to the protein
How are you generating hydrogens? Hydrogenate region?
Do you mean that they are shown in 3d graphics but missing in the 2d
view? Or that Coot's H-bond determination algorithm (which,
incidentally, is an implementation of McDonald & Thornton (1994)) fails
to detect your H-bonds?
— it may be coincidental, but for many of my ligands the pi-pi stacking "indicator" may
well get "in the way" and prevent the H-bonds from displayed properly?
You mean they are co-migrating under refinement.. Hmm could be. I've
reworked the residue placement recently, r4072.
B) Is is possible to define "anchor" residues, such that the LIDIA
representation is always shown in the same orientation? This was one thing that always
bugged me about LIGPLOT.
No, you can't do that yet - it would be nice to have. It's on the list :-)
Cheers,
Paul.
