[chimerax-users] Using ChimeraX Modeller interface

[Elaine Meng]

Hi Tiglath,
This is mostly a question about Blast, since you didn't even get to the Modeller part yet.

(1) Using Blast. To specify a sequence as Blast query you have to first open the sequence, and then use the blastprotein command (not the Blast dialog) to specify the sequence.  We would like to improve the Blast dialog so that you can input a sequence (ticket #3014) but it is not yet possible, so you have to use the command instead.

User Guide for blastprotein command:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/blastprotein.html>

... in that page, if you click "sequence-spec" link in the usage line, it goes to another page explaining how to specify the sequence:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/seqspec.html>

To open the sequence, you could open a fasta file, OR you could fetch it automatically using Uniprot ID.   You could even open a multiple sequence alignment and specify an individual sequence from it as explained in the link above.

The following example commands fetch a sequence from Uniprot and then run blast on it:

open uniprot:p00812

.... then there is a sequence window with title bar "Seqview [ID: p00812]"  so that you know that the sequence ID to use in the "blastprotein" command is p00812 

blastprotein p00812

(2) Looking at Blast results.  You must choose a dimer structure as the template if you want to model your sequence as a dimer.  Unfortunately that is not obvious from the Blast results.   You may want to also go to the RCSB PDB website and look at the information for those specific structures there to see if they are dimers.  I probably wouldn't open the structure from the Blast dialog, but instead if RCSB PDB website shows that the biological unit for that structure is a dimer, I would then open the biological unit directly with the "open" command, for example:

open pdbe_bio:1wva maxAssemblies 1

(in my example it is a trimer)
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

Even if you don't use the Blast dialog to get the structure, you should use it to get the sequence alignment between the template and the query, by using the checkbox on the left of the specific hit and the "Show in sequence viewer" button near the top of the dialog.

(3) When you finally have a dimer template structure open, then you get to the Modeller part (menu: Tools... Sequence... Modeller Comparative).  It has an option "Make multichain model from multichain template" that is already turned on by default, to make your dimer model from the dimer template.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 24, 2020, at 4:34 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> 
> Hi
> My name is Tiglath and I'm trying to use ChimerX Modeller interface to build a dimer model of a protein I'm currently studying. I first tried to run a BLASP search to find templates but it seems that in ChimeraX, this works differently than in Chimera. In the user guide it says that if the query is a sequence whose structure hasn't been determined, then it's not necessary to specify particular chains. However, when I try running the BLAST search it doesn't do anything. It seems that it is necessary to specify a chain number. But how is this possible if I don't know the template for the target sequence? Am I missing something? Also, I'm a little bit unsure how the Modeller interface works for building dimers.
> 
> I would be very glad for your help.
> Thank you
> Tiglath