[phenixbb] modelling of a novel protein

Pavel Afonine pafonine at lbl.gov
Tue Dec 7 21:17:43 PST 2010


explore and use more tools in phenix.refine that are not used by 
default, such as:
- automated water picking and refinement (ordered_solvent=true);
- TLS;
- fix_rotamers;
- if you get the latest development version then it will use the 
advanced real-space refinement (lockit) running by default as part of 
refinement run;
- iterate this with manual building/rebuilding,
... etc.


On 12/7/10 6:10 AM, intekhab alam wrote:
> Hi
> I am trying to solve the structure of RNA polymerase in complex with 
> its protein primer. The size of protein primer is 70 amino acids which 
> i complexed with the polymerase and collected a data of the complex 
> crysta at 2.3A. The space group is C2  and after Molecular replacemnet 
> with full length polymerase in auto MR i got 3 subunits in ASU.
> The parameters of MR solution  RFZ=71.5 TFZ=41.2 PAK=0 LLG=8812 
> suggests that the solution is correct. I used autobuild for model 
> building which gave me the model of the polymerase as well as some 
> extra density that i am considering as the other protein. After 
> several round of refinemnt i have R and R free of 27and 32 respectively.
> My queries:
>  1. I want to know ,how can i improve my R as well as R free.
>  2. How can i model  other protein as the density is weak and not 
> complete, how can i improve the map of the other protein so that i can 
> b ebale to trace the c-alpha backbone, i was able to model only 10 
> amino acids so far.

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