This is the latest release - AmberTools22
I've tried both .mrc and .ccp4 - I should probably check .dx too. I'm
using default boundary conditions (I assume open) with a small-ish buffer -
here are the relevant command-line options:
--buffer 7.0 --grdspc 0.35,0.35,0.35 --volfmt mrc --tolerance 1e-05
It might be worth mentioning that I'm _only_ interested in the water
density around a ligand binding site.
Brian
On Tue, Jun 28, 2022, 7:37 PM tluchko <tluchko.protonmail.com> wrote:
> Hi Brian,
>
> What version of AmberTools are you using? Are you using open or periodic
> boundaries? Is the output MRC or CCP4 format?
>
> Tyler
>
>
> Sent with Proton Mail secure email.
>
> ------- Original Message -------
> On Tuesday, June 28th, 2022 at 11:04 AM, Brian Radak via AMBER <
> amber.ambermd.org> wrote:
>
>
> > Hopefully Tyler sees this.
> >
> > I'm having a bit of a hard time visualizing grid output from
> > rism3d.snglpnt. Everything seems to be translated relative to the input
> > protein, which I realized is exactly what the manual says the default
> > behavior should be. I tried the (discouraged) --centering 0 option, but
> > this seemed to cause the densities to wrap around the grid in weird ways,
> > so that's probably not what I'm looking for. I don't recall having this
> > issue with the old OpenDx file format, but I'm more than happy with the
> > upgrade to .mrc otherwise.
> >
> > What's the recommended way to visualize densities around a protein? Is
> > there a way to output the translated solute coordinates? Do I just need
> to
> > turn off centering and prepare my inputs more carefully? Something else?
> >
> > Regards,
> > Brian
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:48 PDT
