[phenixbb] Phenix building residues not found in input sequence file

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Oct 18 08:43:30 PDT 2011

Hi Allan,

I assume that there is density showing protein in the region where
autobuild is building these extra residues...is that right?  If so...then
is the remainder of the model matched very well to sequence (i.e., is more
or less what you expected to see found, plus there is extra density?)

It could be that there is really something in the crystal that you didn't

It could also be that part of the structure is not (or not correctly)
assigned to sequence, so that this part of the structure really does go
with part of your sequence.

Does that help?

It would be interesting to hear more details of this.

All the best,
Tom T

>> Hi everyone,
>> Apparently my Phenix (1.6.3-473) is building in extra residues in the
>> C-terminal region, which is not found in my input sequence file.
>> It's trying to build a model which is longer than I expected. Phenix
>> building 87 extra amino acids. Any clue what's wrong?
>> I made sure that these amino acids are not residues found in the
>> N-terminal region or anywhere else in the protein.
>> Allan
>> --
>> Allan Pang
>> PhD Student
>> G35 Joseph Priestley Building
>> Queen Mary University of London
>> London
>> E1 4NS
>> Phone number: 02078828480

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