How to "merge" monomeric structures in COOT (WinCoot) - pdb files
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6.7 years ago
HTH • 0

Hi,

I am relatively new to modeling programs. I have a structural file from the PDB database, which is a monomer. I would like to show the entire structure (which is trimeric), but I don't understand how to do so.

I have access to COOT (WinCoot) and know that it should be possible to show the entire structure there by somehow "merging" or "combining" three of the monomers to its proper trimeric structure. I have tried to find good tutorials, but usually they just describe how to use the basic functions of coot - or how to do refinement based on density maps (which is different than my aim).

Could anyone recommend a good webpage or tutorial for my problem, or tips on how to get on the right track for this?

All help appreciated!

pdb coot • 4.1k views
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6.7 years ago
Collin ▴ 1000

Have you looked into whether there is a PDB biological assembly for your PDB file? Sometimes the crystal asymmetric unit is a monomer, but additional information is provided that shows the protein in its biologically relevant context (perhaps a dimer or trimer). I usually check RCSB to look at the alternative bioassemblies by clicking on the image carousel (e.g. http://www.rcsb.org/pdb/explore/explore.do?structureId=1DD1 ). If so, you can download that PDB file containing atom coordinates of that biological assembly. I would imagine any protein structure viewer would work then. As an example, downloading the second biological assembly for 1DD1 (a dimer) could be done by formatting the url as ftp://ftp.wwpdb.org/pub/pdb/data/biounit/PDB/all/1dd1.pdb2.gz.

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Yes, thank you I found the biological view/assembly of the molecules in its "trimeric" state. This was really useful to know, however, it would be nice to know how to do it on my own for future reference.

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