This is more-or-less exactly the task I'm building ISODE for. It's early
days, still quite rough around the edges and by no means complete, but
if you have a machine with a decent GPU running a modern Linux distro,
then it's easily available as a plugin to ChimeraX after installing the
latest daily build from
https://www.rbvi.ucsf.edu/chimerax/download.html. Think of it as an
interactive real-space refinement environment, and you won't be far off.
This video is getting a little dated now, but should give you some idea
of what it can do:
https://drive.google.com/open?id=0B6uMjfjuw4k8aUdyTEJWeEJ1UnM. I'm
currently working on a longer, narrated demo/tutorial video showing all
the latest features (interactive position/rotamer/secondary structure
assignment, a very fun tool for shifting stretches in register, ...).
There are some caveats:
- It doesn't yet do any building (adding or removing of atoms/residues)
- It requires all residues to be complete including hydrogens
- Currently only protein, nucleic acid and metal ions are supported
(although the metal ions need more work to be properly useful)
Let me know if it's of interest, and we can talk more offline.
Cheers,
Tristan
On 2017-07-13 00:17, Rhys Grinter wrote:
Dear All,
I'm currently in the process of refining a low(ish) resolution
structure at 3.2 Ang, with a fair level of anisotropy. I processed the
data through the anisotropy server
(https://services.mbi.ucla.edu/anisoscale/ [1]), which elliptically
truncated the data to 4.0, 3.8 and 3.2 Ang. This really improved the
maps and allowed me to trace the majority of the chain and build most
side chains.
The R-factors are reasonable (0.29 work and 0.35 free respectively).
but I'm having trouble with over fitting in refinement as I continue
to refine. What parameters/restraints would the community generally
use when refining this kind of structure? Additionally Refmac doesn't
seem to read the structure factors from the anisotropy server output
file properly, giving vastly inflated R values and strange looking
maps.
Cheers,
Rhys
--
Dr Rhys Grinter
Sir Henry Wellcome Fellow
Monash University
+61 (0)3 9902 9213
+61 (0)403 896 767
Links:
------
[1] https://services.mbi.ucla.edu/anisoscale/
