Dear Ansuman,
The PDB_REDO server has extensive ligand validation, but it won't tell you
explicitly whether the ligand is there or not. You have to figure that out from
the validation scores.
High real-space R values or low real-space correlation coefficients are a hint
that your ligand isn't t
Dear all
Please tell me the names of good servers / tools which calculate the
size and surface area of the active site pocket of a protein..
--
Regards
Faisal
School of Life Sciences
JNU
hmm - crystallographically difficult. The usual way is to make a dictionary
file from the chemical information about the ligand. try to build something
obeying the chemical restraints into the density - refine those coordinates
and validate them.
Eleanor
On 19 September 2014 22:06, ansuman biswas
Dear All,
I have collected a diffraction dataset from a crystal soaked in a solution
containing the ligand of interest.
After refining a few cycles, I can see some density in the active site pocket,
but not so clear to model the ligand unambiguously.
Is any tool available to validate whether th
Dear All,
Sorry for off topic e-mail.
I have two structures of the same protein one in apo form and other in
substrate bound form.
The substrate bound structure shows 20 degree movement with respect to one
domain. I want to screen the inhibitor for that. Can anyone tell me if any
company makes a
Dear Veerendra,
Based on the very limited information you give, it is hard to figure out what
really is the problem. However, here are some comments:
-Molecules in the asymmetric unit: If e.g. there are two molecules in the asu
and you searched only for one, you might get good phaser statistics
Dear CCP4 members,
Recently I have collected native data at 3.3 A resolution. The structure of the
protein should have two domains. The structure of c terminal domain from
homologous (30 seq similarity) is known. I took n terminal domain from another
homologous protein. I ran the phaser using t
Dear All,
I would like to draw your attention to two job vacancies at Diamond Light
Source to develop the XFEL Hub
(http://www.diamond.ac.uk/Science/Integrated-facilities/UK-XFEL-Hub.html) based
at Diamond.
Software Scientist /Senior Software Scientist for diffraction methods
http://www.diamo
Hi Charles,
This message usually means that refinement of cell parameters and distance
blows up, e.g. huge cell dimensions and a huge distance. That is probably the
reason behind the suggested method to fix the distance in IDXREF. However, I
suspect that your error occurred in the INTEGRATE st
