[Chimera-users] Blast protein

Bobo Dang bbdang at uchicago.edu
Tue Feb 5 09:43:20 PST 2013


Thank you.

bobo

On Tue, Feb 5, 2013 at 11:06 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Bobo,
> Chimera itself is not judging the match.  It is simply the Blast program, using the cutoff E-value (and database and matrix) that you had specified in the "Blast Parameters" dialog before running the search.  Assuming you used "pdb" database and didn't make some huge change in the cutoff E-value from the default, yes, it means there are no structures in the PDB with similar sequences to your query.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Feb 4, 2013, at 9:16 PM, Bobo Dang wrote:
>
>> Hi guys,
>> I was trying to build homology model using chimera.
>>
>> The uniprot ID of the molecule I want to build is Q9X2V8, when I was
>> trying to blast to find the homologs which have structures.
>>
>> It returns "no BLAST matches found".
>>
>> Does this mean there is no Q9X2V8 homolog from PDB? how does Chimera
>> judge one molecule could match (could be the homolog)?
>> thanks
>> bobo
>



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