[phenixbb] [ccp4bb] Autobuild in specific area

Sun Sep 14 06:34:30 PDT 2014

Hi Foggy,

Here is another thing you can try:

Ignore the chain B completely for now, just you would a ligand.  Run autobuild with rebuild_in_place=False, and then afterwards with rebuild_in_place=True to get the best model you can. Even without 10% of the model I'd expect you might get a bit better model than you have now that way.

Then focus on chain B. If you cannot see something fairly clearly in your map then autobuild won't be able to either.  So if there is clear density for chain B, autobuild should build it using the methods Kostya and I suggested before.  You can also use phenix.cut_out_density to just cut out the density for chain B and then you can build into that density with phenix.find_helices_strands or phenix.build_one_model, then put it back in the unit cell.

All the best,
Tom T

________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Konstantin Kogan [konstantin.kogan at helsinki.fi]
Sent: Sunday, September 14, 2014 12:18 AM
To: Zhang Foggy
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] [ccp4bb] Autobuild in specific area

Hi Foggy,

I had similar situation recently. I would suggest to build manually or in coot (place a helix) at least one helix that you see clearly. Then check that protein a and protein b (helix) are different chains in model pdb. Then provide the sequences of both chains. In this situation autobuild will certainly rebuild this helix with real sequence and will try to build more (don't forget to select 'build outside model' option). I would also increase the number of rebuilding cycles to something 20-30. In my case it took around 7 cycles until it started to put any new amino acid.

Kostya

On Sep 14, 2014, at 7:51 AM, Zhang Foggy wrote:

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 <terwilliger at lanl.gov<mailto: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<mailto:CCP4BB at JISCMAIL.AC.UK>] on behalf of Zhang Foggy [foggyccp4 at GMAIL.COM<mailto:foggyccp4 at GMAIL.COM>]
Sent: Saturday, September 13, 2014 10:40 AM
To: CCP4BB at JISCMAIL.AC.UK<mailto:CCP4BB at JISCMAIL.AC.UK>
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.
[https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif]
Foggy

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