[phenixbb] Resolve NCS masks

Thomas C. Terwilliger terwilliger at lanl.gov
Sat Sep 18 12:07:37 PDT 2010

Hi Florian,

>> Is it possible to output the NCS and/or solvent masks Resolve is using
>> during the Autosol run (similar as the options from the stand alone
>> Resolve version) such as:
>> mask_as_mtz
>> ncs_mask_file mask.mtz
>> protein_mask_file

I think you have to make a separate run of resolve to write out a mask.
You would have to choose a particular resolve run from the AutoSol job and
re-run it with one of your commands above.

I would be interested to hear how useful these mask maps are to you. If
this is an important feature then I could put it into AutoSol as well.

>> What are the best criteria (other than the final maps of course)
>> within the output from Phenix.resolve to judge if the NCS (and/or
>> solvent) mask was chosen adequately? (NCS_overlap?) I am mostly
>> concerned if the masks chosen do include some of the more peripheral
>> parts of my protein molecule and do not flatten these regions.

I look at the NCS correlation, which normally should end up very high
(i.e., 0.9) except sometimes at low resolution. Then I look at the
fraction of the asymmetric unit that is accounted for within the masked
region (should be pretty similar to the non-solvent fraction).

The NCS averaging should not flatten your peripheral regions...but the
solvent flattening part of density modification indeed can do this.  One
way to reduce that effect is to set a smaller "solvent fraction" than
actually exists.

>> Secondly, it is possible within Phenix Autosol wizard to supply a pdb
>> file (with dummy atoms) for the mask for Resolve to construct the NCS
>> mask?
>> i.e. similar to
>> set mask_pdb file= dummyatom.pdb

Yes, you can do this, and it is another way to get around the problem of
excessive flattening of peripheral parts of your molecule. Here is some
documentation on it (see doing this is a bit ad hoc and risky as you are
adding a command to ALL resolve jobs within your AutoSol run):

How can I specify a mask for density modification in AutoSol/AutoBuild?

If you want to specify a mask, add this command:

resolve_command_list=" 'model ../../coords.pdb'  'use_model_mask' "

where there are " and ' quotes and coords.pdb is the model to use for a
mask. Note the "../../" because coords.pdb is in your working directory
but when resolve runs the run directory is 2 directories lower, so
relative to that directory your coords.pdb is at "../../coords.pdb". You
will know it is working if your resolve_xx.log says:

Using model mask calculated from coordinates

Note: this command is most appropriate for use with the keyword
"maps_only=True" because phenix.autobuild also uses "model=..." so that
iterative model-building may not work entirely correctly in this case. Two
parts that may not function correctly are "build_outside_model" (which
will use your model as a mask and not the current one), and evaluate_model
(which will evaluate your starting model, not the current model).

I hope that helps!
-Tom T

More information about the phenixbb mailing list