Hot answers tagged pdb
The "chain identifier" does exactly what it says: it identifies the polypeptide or other molecular chain. For some structures, there is only one, so you'll only see an identifier A. However, many structures show two or more proteins bound together, or an enzyme complexed to a substrate, or a small molecule inhibitor in a binding pocket - there are many ...
There are no MTRIX cards for that molecule. This seems like the easiest path: http://www.rcsb.org/pdb/explore.do?structureId=4G3Y Download Files -> Biological Assembly 1 i.e.: http://www.rcsb.org/pdb/files/4G3Y.pdb1.gz And read that file into Coot (should you wish)
The residue numbering convention in the PDB is more-or-less entirely up to the depositor of the structure. While generally speaking sequential numbers are next to each other, there is no guarantee of that fact. For example, the PDB allows for what are called "insertion codes", which are extra residues which interrupt the regular sequence progression. For ...
This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need some experimental data on the structure of your proteins. If your proteins have not been structure ...
The PDB-file only contains the asymmetric unit, and no information on a potential biological relevant multimer. So you will need to get information about the state in solution experimentally. That being said, one can often deduce from the size of the contact surface whether you have a potential quarternary structure. You can do this by hand, but the ...
In babel: babel my.mol2 my.pdbqt -xh -x states options for writing .pdbqt files -h says keep hydrogens
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