[phenixbb] [ccp4bb] Autobuild in specific area

Zhang Foggy foggyccp4 at gmail.com
Sat Sep 13 21:51:33 PDT 2014

Hi, Tom,

Thanks for your great suggestions.
Here is my awkward situation: protein-A has 900 amino acids, while
protein-B only 70. When I tired your first suggestion, I found that the
program only built up the protein-A part. No extra model was built up at
Additionally, there is no published model for protein-B. Sequence alignment
and homolog modeling indicate that there are about 40 aa forming two
alpha-helix with the rest unknown. I can only see clear density on one
alpha-helix at the moment, and the R/Rfree values are 0.37/0.43 (2.5 A,
P1). Regarding to your second suggestion, I do not find this option though
GUI yet, will try tomorrow. Do you have any other suggestions on my
situation? Thank you in advance.



2014-09-13 21:03 GMT-05:00 Terwilliger, Thomas Charles <terwilliger at lanl.gov

>   Hi Foggy,
>  This is a situation that autobuild does not address very well yet.  Yes,
> you want rebuild_in_place=False.  And yes, if you do that it will remove
> your model and rebuild it. It will also try to build into the remainder of
> the map.
>  In practice, you already have pretty much the best that autobuild is
> going to produce.  Delete the protein A chains that autobuild built, and
> put in your original protein A. Now you have your original model plus
> whatever autobuild was able to build.
>  An alternative is:  select "consider_main_chain_list=True" .  This will
> take your input model A and at each step it will check to see if parts of
> that model are better than any other model that it has built. This can help
> for keeping the input model that you put in.
>  All the best,
> Tom T
>   ------------------------------
> *From:* CCP4 bulletin board [CCP4BB at JISCMAIL.AC.UK] on behalf of Zhang
> Foggy [foggyccp4 at GMAIL.COM]
> *Sent:* Saturday, September 13, 2014 10:40 AM
> *Subject:* [ccp4bb] Autobuild in specific area
>   Hi, All,
>  I am trying to use Autobuild to build a protein-protein complex model. I
> obtained partial phase solution (protein-A) through MR, and can see some
> density of protein-B near protein-A. I would like to use Autobuild to build
> protein-B model into this area. I load data file, initial density map file,
> sequence file (both of protein A and B), and protein A model, and run
> Autobuild. However, The "rebuild-in-place" function confused me a lot, no
> matter I set it to True or False. When I set to True, it only rebuilt
> protein A model without adding any additional residues; while I set it to
> False, it deleted the input protein-A model, and rebuilt a new one... Could
> somebody tell me how to build the protein B model with keeping the input
> protein A model in Autobuild? Thanks.
>  Foggy
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