[phenixbb] homology models in sculptor

[Gabor Bunkoczi]

Dear Oliver,

apologies for the late reply, I have just come back from holiday.

As far as homology models are concerned, I am not convinced that the 
common model preparation methods are applicable, and this is because the 
structure is optimized, i.e. the original geometry is not preserved. As 
for the side-chain pruning step, you ran into a technicality, and it is 
possible to mimic the Schwarzenbacher algorithm by choosing appropriate 
parameters for the "similarity" algorithm; let me know if this is what 
you need, but on reading your email my understanding is that you just 
want to explore your options, and as I have made clear in the previous 
sentence, I do not think this is the right way to go.

For homology models, we have good experience with mapping the estimated 
error to the structure. If you get these values from your modelling 
program, I can help you to convert these into B-factors. If you don't, 
you can still use the accessible structure area  of your structure and 
the sequence similarity values from your alignment. Switch off 
main-chain deletion and side-chain pruning, and switch the B-factor 
modification to either "asa" or "similarity", or "asa+similarity". If 
you go down this route, please let us know how you are getting on. We 
have not done an extensive study with homology models, and it would be 
interesting to know how these simple options perform.

BW, Gabor

On 2014-04-06 10:57, Weiergräber, Oliver H. wrote:
> Hello,
> 
> I am using phenix.sculptor for modification of a homology model in a
> challenging case of molecular replacement.
> The input model is complete (except at the termini), i.e. it exactly
> matches the target sequence as defined in the alignment file.
> In this scenario, are there any caveats to consider with individual
> options in sculptor?
> Specifically, a quick test seems to indicate that the Schwarzenbacher
> algorithm for side chain pruning does not work, i.e. not a single atom
> is removed from the model, whereas the alternative "similarity" option
> leads to deletion of a few hundred atoms.
> I'm using sculptor from the command line, and the log file indicates
> my input is interpreted correctly.
> 
> Best regards
> Oliver
> 
> 
> ================================================
>   PD Dr. Oliver H. Weiergräber
>   Institute of Complex Systems
>   ICS-6: Structural Biochemistry
>   Tel.: +49 2461 61-2028
>   Fax: +49 2461 61-9540
> ================================================
> 
> 
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