[Chimera-users] How to predict/model the structure of two known structure proteins

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 22 09:28:30 PST 2015


Dear Hoang,
Blast should find the matching PDB structures with those default settings.  Just now I tried using a fasta file with only the last line of sequence shown in your image, and it correctly found PDB 2LW9.

The results dialog first appears empty, but later when the search is done the results appear.  So maybe you just needed to wait a few minutes for the results.

However, if you wait  a long time and still don't get results, you could skip the Blast part and instead:

(A) create (outside of Chimera) a 3-sequence alignment containing your target fusion protein and the sequences of each of the template PDB structures, in any of the formats Chimera can read:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>

(B) open that sequence alignment and the two template PDB structures in Chimera, then proceed starting with step #4 in my previous message.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010645.html>

Another possibility that I forgot to mention before is to use the new "mda" multidomain assembler command (in Chimera 1.10.1 or newer daily build) with your fusion-protein fasta file as input.  This automates several of the steps in my previous  message, including running Blast, up to the point of opening the Modeller dialog.  Of course, Blast will have to be working correctly, but my tests suggest that it is.  The "mda" command has several options, and I don't know whether you would need to use any of those options for it to find the desired template structures.  However, it might still be worth a try because then you don't have to do steps #2-5 yourself.  See the syntax and option information here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html>

I hope this helps,
Elaine

On Jan 22, 2015, at 6:05 AM, Phan Trong Hoang <hoang at ipk-gatersleben.de> wrote:

> Dear Meng,
> Thank you very much for your reply.
> I have tried as you wrote (please see figure 1), but I face the problem. There is a Blast:query appearance but there is no information about PDB....please have a look at the attached picture (figure 2). I tried with the sequence of one protein in PDB. The same table appeared with no more information. Could you show me how to fix it or there are other steps to avoid this step.
> Thank you
> Best regards
> Hoang




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