[phenixbb] Wishful thinking with AutoBuild?

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Aug 4 11:07:00 PDT 2008


Thanks for all the replies folks.

Tom

When using helices_strands_only=True, would that in Autobuild be  
different than the automatic helix finding at the end of autosol (with  
no sequence file) ?

Thanks

FR

On Aug 4, 2008, at 12:03 PM, Thomas C. Terwilliger wrote:

> Hi Francis,
>
> I would say that a standard run of autobuild needs a decent map (after
> density modification) where you can see where a model would be built.
>
> If you have a worse map than that, or low resolution (>3.5 A), then  
> try
> this keyword:
>
> helices_strands_only=True
>
> in which case autobuild will run a lot faster and just try to build
> secondary structure in, skipping all the loops and skipping chain
> extension.  It can build helices where you can hardly see them. If  
> you are
> lucky then the map will get better after this..then you can try  
> feeding
> the resulting overall_best_denmod_map_coeffs.mtz and  
> overall_best.pdb in
> to a regular run of autobuild.
>
> Best of luck,
> -Tom T
>
>
>>
>> Hello all
>>
>> Given a mediocre to bad experimental density map, what hopes does
>> AutoBuild have of building a model? i.e. Should I be able to tell
>> clear helicies and side chain density in the experimental density map
>> before even attempting an autobuild?
>>
>> Thanks
>>
>> FR
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>
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>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D




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