Thanks for the suggestion. I am using Rosetta but did not find a flag to turn this switch of protonation-states off, yet.
I will go with the deletion of atoms in the pdbs until the next release comes out.
Best regards,
Marcel
Marcel Jurk
Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
Solution NMR (AG Schmieder)
Robert-Roessle-Str. 10
13125 Berlin
Germany
eMail: [log in to unmask]
Phone: +49-30-94793223
Fax: +49-30-94793169
>>> Rasmus Fogh 05.08.11 17.55 Uhr >>>
Dear All,
From the next unreleased version it will be possible to have different
atoms, provided that all atoms are present in the first model of an
ensemble. Missing atoms will simply get an occupancy of 0.0. Whether that
is a smart thing to is TBD.
Which program are you using? Yasara had this capability, but it could be
turned off (which would likely be a good idea in this case).
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 5 Aug 2011, Wayne Boucher wrote:
> Hello,
>
> Tim says:
>
> As long as the His variant with the most atoms is entered into Analysis you
> can probably load both types of structure (some coords will be missing for
> the lost H+), but making an ensemble is another matter (atoms must be the
> same - a PDB rule not just us).
>
> You could have a different ensemble for each state, and yes deleting the
> extra atoms would probably work.
>
> Wayne
>
> On Fri, 5 Aug 2011, Marcel Jurk wrote:
>
>> Hello,
>>
>> The lowest energy structures I am getting have different protonation states
>> for a single histidine side-chain. How would one deal with this, since I
>> can't merge all structures into one ensemble. Deleting manually all HD2 or
>> HE2 protons in the pdb files?
>>
>> Best regards,
>> Marcel
>>
>>
>> Marcel Jurk
>> Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
>> Solution NMR (AG Schmieder)
>> Robert-Roessle-Str. 10
>> 13125 Berlin
>> Germany
>>
>> eMail: [log in to unmask]
>> Phone: +49-30-94793223
>> Fax: +49-30-94793169
>>
>
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