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
all.
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.
Best,
Foggy
2014-09-13 21:03 GMT-05:00 Terwilliger, Thomas Charles : 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 [[email protected]] on behalf of Zhang
Foggy [[email protected]]
*Sent:* Saturday, September 13, 2014 10:40 AM
*To:* [email protected]
*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