...I forgot to mention that the protein has C2 symmetry.
Joel
On 2014-01-08 08:29, Sjors Scheres wrote:
> Hi Joel,
> We have had good results doing exactly what you suggest: make a soft
> mask
> around the region that you want to improve (it may be any shape, but
> values should be in [0,1], 1 being what you want to keep, 0 being what
> you
> want to mask away). You can provide this 3D mask on the auto-refine (or
> Class3D) GUI.
> If the masked out region is small compared to the entire molecule then
> it
> may be better to perform only local angular searches around angles
> assigned without any mask.
> HTH, S
>
>
>
>> Hi Sjors,
>> I'm working with a membrane protein and the structure shows
>> better-resolved features in the extracellular portion, compared to the
>> transmembrane portion. I believe that the resolution of the
>> transmembrane region is compromised because of a combination of two
>> factors. First, most of the protein mass is extracellular and that
>> region thereby dominates the alignment. Second, there might be some
>> degree of flexibility where the extracellular portion of the protein
>> meets the transmembrane portion.
>>
>> Can you suggest a strategy to improve the resolution in the
>> transmembrane region? Perhaps using a soft-spherical mask around this
>> region during 3D refinement? It's important to note that the protein
>> essentially looks like a rod protruding from the membrane, and I have
>> good angular coverage of the side views.
>>
>> Thanks,
>> Joel
>>
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