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<div style="direction: ltr;"><font size="2">Hi Foggy,</font></div>
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<div style="direction: ltr;"><font size="2">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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<div style="direction: ltr;"><font size="2">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>
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<div style="direction: ltr;"><font size="2">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 size="2">All the best,</font></div>
<div style="direction: ltr;"><font size="2">Tom T</font></div>
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<div id="divRpF149043" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zhang Foggy [foggyccp4@GMAIL.COM]<br>
<b>Sent:</b> Saturday, September 13, 2014 10:40 AM<br>
<b>To:</b> CCP4BB@JISCMAIL.AC.UK<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 id=":4jx" class="" tabindex="0"><img class="" src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif"></div>
<div id=":4jx" class="" tabindex="0">Foggy</div>
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