Using some crazy methods I've found a couple hundred regions of interest on sequence segments of multiple proteins and I'm looking to annotate them on 3D structures where available. However, since I'm dealing with mostly viral proteins many of the crystal structures are incomplete. Also, the sequences may differ slightly (with possible insertions or deletions) between my reference sequences and the crystal structure.
Also, most of the 3D structures have numerous side-chains. So in some instances a ROI which appears only once should actually be labeled multiple times in the crystal structure.
Does anyone know of a tool which can handle all of these instances in an automated fashion? I have plenty of programming knowledge so something that's scriptable would be fine. I just don't deal with crystal structures that often so I'm not familiar with the idiosyncrasies and the common toolsets out there.
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written
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Will
1 answer
If you have residue level information of your region, you could accomplish this using command-line program MolScript. I have used this as a part of several structural bioinformatics work-flow/webserver to map/high light residues of interest (See Figure 2 of this manuscript that describe a webserver for structure quality assessment using propensity/substitution scores) .
It is highly customizable, the program is driven by a steering file (see example here) that takes all necessary parameters and a PDB file from the command-line, you may automate it for developing a pipe-line or to generate figures from several structure using a script. .
Please see a sample output here: 
Manuscript describing MolScript is available here. You can also render high-quality images by combining Molscript with Raster3D (See example 3 below).
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What do you mean by "annotate them", e.g. having them in a structure viewer with a different colour?
Yes, that's exactly what I'm looking for. I know how to do it by hand but doing it for thousands of structures automatically would be really helpful!