Hello Charles,
Thanks so much for your answer. I will try that
you propose in the last paragraph and I will write later with the news =)
Best
Diego
Le 06/09/2016 16:38, Charles Schwieters a écrit :
Hello Diego--
I am working with XPLOR-NIH adding CrioEM density map
potentials during the calculation. Due to my system is a symmetric
oligomer, I am working
also with NCS condition (turning on the flags PVDW and PELE).
I would like to ask you if is also possible to turn on the Density Map
Energy term for the NCS images of my molecule (v.g. as the flag PDVW
and PELE but for the density map energy term)?
The short answer is "no," but please see the last
paragraph. Presumably your map corresponds to the complete oligomer,
so that the density map for the entire construct must be used. It is
possible that the density map might be more quickly generated by using
the symmetry operators, but this is not yet implemented.
Do note: PVDW and PELE work with strict symmetry facility in the old
XPLOR interface. It is not clear to me that using electrostatics is a
good idea- so please be careful with that.
To be completely clear, when using strict symmetry the coordinates of
a single subunit are explicitly represented, and the coordinates of
the other oligomer subunits are generated using symmetry
operations. The advantage of this approach is that there are fewer
coordinates positions to determine, and one doesn't have to worry
about symmetry restraints or their associated energies.
You can use strict symmetry within Xplor-NIH's Python interface using
the symSimulation facility. This supports all of the native Python
energy terms including the density map term, and the RepelPot term for
purely repulsive interactions. There is an example of its use in
python/tests/symSimulation.py in the Xplor-NIH distribution. It seems
I haven't gotten around to writing documentation, though, so please
bug me if you'd like to use this, and I'll pull things together.
best regards--
Charles
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
