[phenixbb] phenix auto sharpen local sharpening masking artifacts?

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Thu Feb 1 09:17:22 PST 2018

Hi Oli,

I have not investigated masking artifacts in auto_sharpen, so I would be
very happy to have a look at your map if you can share it.   I am a
particularly interested because (see below) I would have expected that any
part of your map that is far from any atoms in your model would be flat as
the masking procedure should select only parts of the map that are near
your model.  If this is not happening I may need to fix something.

When you use auto_sharpen with a model, by default the map will be masked
around the model (mask_atoms=True).  This means that there is the
possibility of some model bias, as masking removes density that is outside
the model.  Auto-sharpen uses phenix.map_box to do this masking, with a
default of 3 A around all atoms in the model for this mask
(mask_atoms_atom_radius=3) , plus a "soft" boundary of an additional 3 A
beyond that (soft_mask=True).

If you want to minimize model bias, you can set mask_atoms=False instead,
or increase the radius for masking.  You can also use sharpening without
the model (I recommend trying this as it is almost as good as sharpening
with a model).

In model-based local sharpening, auto-sharpen carries out sharpening in one
box of density at a time within the map. The boxes are chosen only in
regions that contain atoms in your model, and the density for a point in
the final map is the weighted average of densities for all boxes that
overlap that point.  For regions where there are no atoms in your model,
the density from overall (global) sharpening is used.

So to answer your key question, there should normally be minimal model
bias, but it can certainly be present.  The way to determine if there is
model bias is a very simple experiment:  Take your model, remove something
from that model that is a small part of the model but that is very clear in
the density (for a high-res map, remove a few side chains with good density
for example, for a low-res map remove a helix).  Run the procedure again
with this slightly modified model.  If the density changes substantially in
the region where you manipulated the model...you have model bias.

All the best,
Tom T

On Thu, Feb 1, 2018 at 9:46 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi,
> I’m trying to run phenix.auto_sharpen with local sharpening, because I
> have an EM map that has a reasonably substantial variation in local
> resolution. This is the command I used:
> phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26
> local_sharpening=true local_aniso_in_local_sharpening=true model.pdb
> nproc=4 seq_file=seq.fasta >& log &
> The resulting map looks beautiful (maybe a little too beautiful??) around
> the model, but shows some funky looking squared-off masking artifacts in
> the density further away from the model (in the micelle region). I tried to
> add a screenshot but the list wouldn’t let me. Am I doing something wrong?
> And can I trust that the density is completely free of model bias?
> Cheers
> Oli
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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