Dear Charles,
Thanks for your reply.
The number of the residues had been corrected and the ambiguous
restraints obtained from chemical shift perturbation analysis had been
added for the docking. Now the script worked well and outputted
reasonable structures.
There are another two questions:
1)
dock_pre.py(84): rampedParams.append( MultRamp(0.05,1.0, "pre.setScale(
VALUE )") )
dock_pre.py(88): from residueAffPotTools import create_ResidueAffPot
dock_pre.py(89): ra = create_ResidueAffPot('hydphob',
interdomainContacts=True,
dock_pre.py(90): potentialName="Miyazawa")
create_residueAffPot: residue GUA not known
create_residueAffPot: residue CYT not known
.....
I've checked the manual the "Miyazawa" is used for protein, just
disregarded the messages,right?
2)In the .viols files, the difference between obs and cal PRE values is
very large for the PRE restraints. Are there any parameters in prePot I
need to adjust?
Many thanks.
Best
Changdong
>
> Hello Changdong--
>
>>
>> As I only have PRE data for the protein/dna complex without any
>> intermolecular NOE constraints, the results from "newRefine.py" are not
>> good in which the input complex structure was modeled manually.
>> After searching the mailing list, Charles suggested in a message that
>> the calculation should be better started based on the
>> /eginput/diffTens/dock.py.
>>
>> I modified the dock.py and replaced the diffPot with prePot (the
>> chemical shift perturbation was not included).
>>
>> The script worked, but there two problems:
>> 1) the protein structures were disrupted in all the output
>> structures.
>
> I suspect your ivm setup is incorrect. Please think carefully about
> the lines
>
> dyn_fix.group( 'resid 301:334' )
> dyn_fix.fix( 'resid 94:207' )
>
> dyn_free_sch.group( 'resid 301:334' )
> dyn_free_sch.fix( 'resid 301:385 and (name CA or name C or name N or name
> O or name HN)' )
>
> perhaps you intended to specify residues 94:207 in the final line?
>
>
>> 2) there is a relative orientation between protein and dna in the
>> output, but they do not have direct contact.
>>
>> I'm not sure the problem is coming from the experimental data or
>> something wrong in my modified script.
>>
>
> It would be best to use highly ambiguous restraints obtained from
> chemical shift perturbation analysis. Failing that, you might be able
> to use a Rgyr restraint to pull the subunits together.
>
> Charles
>
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