Thanks James for your reply. I my naive way, I thought that when doing paired
refinement, it would be sufficient to run several cycles of refinement with
simulated annealing followed by a thorough real space rebuilding. What is your
thought about using the "jiggling" of additional cartesian ann
Beside the good propositions of fixing the environment, flip the peptide, or
using PDB_REDO, I would suggest the following additional attempts:
Try
1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate
directly to Ala. See which ones remain visible in a diff map and bring them
If you dont use Phenix, print the figures of
https://doi.org/10.1016/S0969-2126(02)00743-8
and use them beside your screen. Helps a lot if you wanna have a quick look at
Rfact distributions..
>>> Paul Emsley 14.06.17 15.25 Uhr >>>
On 14/06/2017 14:09, Khoa Pham wrote:
> Dear CCP4 members,
>
Hi Abhishek
Im by far not as experienced as others in the bulletin board, but I made the
experience that automated water update with Phenix leads to an aggressive
placement of solvent molecules, which can be damped a bit by restricting H-bond
distances of newly placed waters. As Robbie and Elean
Dear Rohit
Additionally to the very good suggestions, I'd feed the structure into
the PDB_REDO server. Its a fast and easy way to detect if the refinement
strategy is correct. The server gives you a good feeling how tight the
x-ray weights need to be.
If however PDB_REDO does not manage to decreas
el
> > for which bits are wiggly, but they'll never think to color it by
> > occupancy.
>
> Let them fly ... at least for protein atoms ...
>
> Carlos
>
> > --------
> > *From:* CCP4
Picking up the mail of Pavel, Phenix refines occupancies..
If you expect the loops to be disordered, did you try to lower the
occupancy of these residues, following Ethan Merritt statement that
"general uncertainty [...] is represented better by occupancy <1
rather than an arbitrary large B fact
Hi,
I just checked the PIC sever tim suggested. very nice indeed. If
you only want to map different interfaces and the amino acids involved
in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I
used it extensively to find out whether a certain set of crystal contacs lead
Dear All
I've been reading several mails that adress the problem of acetylated N-termini
when refining peptide ligands with refmac. I managed to include LINKR records
after running refmacs "review restraints" as suggested by Eleanor Dodson in one
of the mails I found:
LINKRC ACE I 0
