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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Foggy,
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<div>Here is another thing you can try: </div>
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<div>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.</div>
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<div>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.</div>
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<div>All the best,</div>
<div>Tom T</div>
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<div id="divRpF287292" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Konstantin Kogan [konstantin.kogan@helsinki.fi]<br>
<b>Sent:</b> Sunday, September 14, 2014 12:18 AM<br>
<b>To:</b> Zhang Foggy<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] [ccp4bb] Autobuild in specific area<br>
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<div>Hi Foggy,
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<div>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.</div>
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<div>Kostya</div>
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<div>On Sep 14, 2014, at 7:51 AM, Zhang Foggy wrote:</div>
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<div dir="ltr">Hi, Tom,
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<div>Thanks for your great suggestions. </div>
<div>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.</div>
<div>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.</div>
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<div>Best,</div>
<div><br>
</div>
<div>Foggy</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2014-09-13 21:03 GMT-05:00 Terwilliger, Thomas Charles <span dir="ltr">
<<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<div style="direction:ltr"><font>Hi Foggy,</font></div>
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<div style="direction:ltr"><font>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.</font></div>
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</font></div>
<div style="direction:ltr"><font>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.</font></div>
<div style="direction:ltr"><font><br>
</font></div>
<div style="direction:ltr"><font>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.</font></div>
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<div style="direction:ltr"><font>All the best,</font></div>
<div style="direction:ltr"><font>Tom T</font></div>
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> CCP4 bulletin board [<a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a>] on behalf of Zhang Foggy [<a href="mailto:foggyccp4@GMAIL.COM" target="_blank">foggyccp4@GMAIL.COM</a>]<br>
<b>Sent:</b> Saturday, September 13, 2014 10:40 AM<br>
<b>To:</b> <a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a><br>
<b>Subject:</b> [ccp4bb] Autobuild in specific area<br>
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<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:14px">Hi, All,</span>
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<div style="font-family:arial,sans-serif; font-size:14px">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.</div>
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<div><img src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif"></div>
<div>Foggy</div>
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