[chimera-dev] Drawing crystal structures

[Elaine Meng]

Hi WC Chai,
How to find a crystal structure for your protein is not really a Chimera question, but I'll try to give you some ideas.  Maybe there just aren't any crystal structures for your protein (the structure has not been solved experimentally), and in that case you might be able to predict the structure, but it would only be a prediction.

One way to check if there is an experimental 3D structure is to find your protein in UniProt.  For example, if I go to the uniprot page for human LDL receptor,
<https://www.uniprot.org/uniprot/P01130>
... then go down to the "structure" section of that page,
<https://www.uniprot.org/uniprot/P01130#structure>
... it lists several "PDB Entry" codes.

An example without any experimental structures is human amyloid protein-binding protein 2.  In its Uniprot page, you can see there is no structure section, and the "structure" quick link on the left is grayed out.  
<https://www.uniprot.org/uniprot/Q92624>

If there is a known structure of a protein similar to yours, you may be able to predict your protein's structure using comparative (homology) modeling. Chimera has a tool for running Modeller comparative modeling on a web service, but you would have to find the known structure and then also create a sequence alignment of your sequence with the sequence of the structure.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
Here is a discussion of different ways to get those required inputs in Chimera:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>

You should be aware, however, that there are hundreds of different programs and several web servers for predicting protein structure, so you may want to do more reading/searching to learn more about this area so you can make an informed decision on what to use.  Some of these may be easier than the Chimera approach mentioned above.

Another idea is to look in ModBase, a database of already-predicted structures from Modeller.  You can search by UniProt ID.  For example, if I search ModBase for human amyloid PBP2 mentioned above (database accession Q92624)
<https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi>
... I find this model
<http://modbase.compbio.ucsf.edu/modbase-cgi/model_details.cgi?queryfile=1586192341_9717&searchmode=default&displaymode=moddetail&seq_id=9ee7b074d06741f119fcd8489c54f749MAAVGPSC>

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

P.S. chimera-dev is for questions about programming related to Chimera.  Questions about how to use Chimera should be sent to chimera-users at cgl.ucsf.edu
<http://www.rbvi.ucsf.edu/chimera/docs/feedback.html>

> On Apr 5, 2020, at 11:45 PM, Chai, Wern Chern - chawy134 <wern_chern.chai at mymail.unisa.edu.au> wrote:
> 
> Hi there,
> Hope you are well.
> I'm struggling to draw my protein structure (no known PDB). I've searched online for manuals, guides etc. but can't seem to find any help.
> It will be much appreciated if you could guide me on how to do this, or point me in the right direction.
> In the meantime, stay safe!
> 
> Thank you.
> 
> Regards,
> WC Chai @ Brian Chia
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