Tim Stevens wrote:
>>>Did you use the formatConverter? If you use the Pdb format, then the
>>>input has to be an official PDB file. Otherwise use pseudoPdb, and
>>>select the naming system. It should handle multiple models without
>>>problem (though there might be problems if it does not recognize the
>>>end-of-model string).
>>>
>>>
>> Many thanks I have got import of multiple pdbs to work as you
>>suggested by using pseudopdb. However, now the structures don't seem to
>>be being put into a single structure generation and my restraint
>>violation analysis seems to be only against a single structure ....
>>help again!
>>
>>
>
>Incidentally, for those of you using Analysis to do the violation
>analysis, then at the moment it only uses one structure model at a time.
>However, from the next version Analysis has the ability to use ensembles
>throughout. Here the data model object to define the ensemble is
>StructureGroup where isEnsemble=True.
>
>
Hi Tim
Thanks for the info, for those who want this but can't wait till the
next release here is a macro I hacked to do basic constraint analysis
caveats
1. its very raw and under tested but seem to work
2. It creates a new restraint violation list each time you run it...
(and i don't know how to delete these other than by writing another macro)
3. it grabs a StructureGeneration rather than a StructureGroup and I am
not quite sure how these interrelate (or if they are at all related)
def structure_set_violations(argServer):
project = getArgServerProject(argServer)
structure_generation = argServer.getStructureGeneration()
nmrProject = project.nmrProjects[0]
contraint_store =
argServer.chooseObject(nmrProject.nmrConstraintStores)
if contraint_store == None:
return
constraint_list =
argServer.chooseObject(contraint_store.constraintLists)
if constraint_list == None:
return
print structure_generation.molStructures
if structure_generation.molStructures == None:
return
if len(structure_generation.molStructures) == 0:
return
print constraint_list
#argServer.getConstraintList()
#print structure_generation
violationList =
getStructureViolations(constraint_list,structure_generation.molStructures)
print 'violList',violationList
regards
gary
--
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Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-2331407
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