[phenixbb] exclude clashes for non-symmetry contacts

Oleg Sobolev osobolev at lbl.gov
Fri Nov 2 11:10:33 PDT 2018

Hi Edwin,

Looks like something is wrong with inputs, most likely parameter file. Can
you please share the inputs (model, ligands - if any, additional parameter
files) off-list so we can reproduce and fix the issue. Do you use GUI or
command-line? Do you use GUI atom selection editor to define NCS groups?

Everything will be kept confidential.

Best regards,
Oleg Sobolev.

On Fri, Nov 2, 2018 at 9:56 AM, Edwin Pozharski <pozharskibb at gmail.com>

> Thanks - we could have an argument about what is "natural" here, but
> that's philosophical.
> The only option that works for me so far is to move the other model to the
> neighboring unit cell and disable symmetry clashes.  As I said, it's an
> ugly hack, but it seems to work.  I do run into further issues because omit
> map calculation fails complaining about clashes, but that's a problem for
> another day.
> Problem with alternate conformer based approach is that it's pain to merge
> the two models - by hand it would take too long, but I do have reasonable
> coding abilities so I wrote a little tool that merges two pdb files into
> one and marks models with altlocs.  However, phenix.refine fails when
> trying to read my NCS definitions even though it appears to have validated
> them just fine (see log file excerpt below).  Any suggestions - am I maybe
> defining NCS groups wrong?
> Validating user-supplied NCS groups...
>   Validating:
> ncs_group {
>   reference = "altloc A"
>   selection = "altloc B"
> }
>   OK. All atoms were included in validated selection.
>  ...
> ==================== Process input NCS or/and find new NCS
> ====================
> Number of NCS groups: 1
> Traceback (most recent call last):
>   File "/ibbr/phenix-1.14-3228/build/../modules/phenix/phenix/command_line/refine.py",
> line 11, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/command_line.py",
> line 106, in run
>     log=log)
>   File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/driver.py",
> line 450, in __init__
>     ncs_groups_as_phil = iotbx.phil.parse(ncs_groups_str)
>   File "/ibbr/phenix-1.14-3228/modules/cctbx_project/iotbx/phil.py", line
> 81, in parse
>     process_includes=process_includes)
>   File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/phil/__init__.py",
> line 2178, in parse
>     primary_parent_scope=result)
>   File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/phil/parser.py",
> line 120, in collect_objects
>     scope_extract_call_proxy_cache=scope_extract_call_proxy_cache)
>   File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/phil/parser.py",
> line 134, in collect_objects
>     words=collect_assigned_words(word_iterator, lead_word),
>   File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/phil/parser.py",
> line 31, in collect_assigned_words
>     str(lead_word), lead_word.where_str()))
> RuntimeError: Missing value for selection (input line 3)
> On Thu, Nov 1, 2018 at 7:50 PM Oleg Sobolev <osobolev at lbl.gov> wrote:
>> Dear Edwin,
>>> The alternative is probably to define the second orientation as an
>>> alternative conformation.  Aside from aesthetic objections, I don't want to
>>> lose the ability to restrain NCS - I need two orientations to be identical
>>> structures, and I am not sure yet whether I can use NCS groups defined via
>>> alternative conformers.
>> I think this would be the easiest way forward and it looks like a very
>> natural use of alternative conformations. You can definitely define NCS
>> groups and even automatic search works. I'm attaching a small dummy example
>> I experimented on. Two overlapping helices: chain A with altloc A and
>> occupancy 0.5, chain B with altloc B and occupancy 0.5. Nothing prevents
>> you from defining NCS groups using "altloc A" and it should work, but I
>> imagine there should always be equivalent selection in terms of "chain A".
>> Best regards,
>> Oleg Sobolev.
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