>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 :-)
I really do, I've been looking for something like this for quite a while
now!
>> 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?
Mea culpa ‹ adding hydrogens via the very obvious "hydrogenate region"
button (once I had probe correctly defined in my PATH) - sorts everything
out - Doh!
So scrub my A) issues.
>> ‹ 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.
I think this is probably ok, now that I've sorted out my H's.
>> 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
>:-)
Great, looking forward to it reaching the top of the list. Being able
to
'simply' compare a series of inhibitors bound to the same protein will be
an invaluable tool.
>Cheers,
>
>Paul.
Many thanks,
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
email: [email protected]
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
