DynDom Run Help

Input Fields

Filename or PDB code

The PDB file can be taken from the standard PDB database or be your own file. To select your own PDB file use the BROWSE button adjacent to the input field or type in the full filename including the path. You may select a file from the PDB database by simply entering the 4 letter PDB code, though all these names : 4ake, pdb4ake, pdb4ake.ent, 4ake.pdb, will select the same PDB file.

Chain Identifier

In this field you should enter the chain identifier code letter used within the PDB file to select the chain you want. If the PDB file contains a single chain there may be no chain identifier, in which case you should leave this field blank. You will receive error messages (see below) if you select an invalid chain or use a chain identifier when one is not required. The error message will also contain a list of valid chain identifiers so that you may select the correct chain.

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Errors

Must specify chain identifier for .... Valid chain identifiers for .... are : ., .

All the chains in the PDB file use a chain identifier, and therefore you must enter the required chain identifier. The valid chain identifiers for this PDB file are listed at the end of the error message.

. is not a valid chain identifier for .... Valid chain identifiers for .... are : ., .

There is no chain with the chain identifier you entered in this PDB file. You may only use one of the chain identifiers listed at the end of the error message with this PDB file.

Only one chain in conformer .. (....), which has no chain identifier. Leave chain identifier field empty to select this chain.

As stated in the error message you entered a chain identifier when one is not required, as there is only a single chain in the PDB file that has no chain identifier. Leave the chain identifier field empty.

Sequence identity is less than 40%

Equivalent residues are determined by a sequence alignment program. If the sequence identity is less than 40% the structures of the two chains may be incompatable and the analysis is halted.

Conformer .... solved by NMR not x-ray diffraction

We are currently excluding PDB files from the database solved by NMR.

All backbone atoms are required in .....

For DynDom to run each residue within the PDB chain must contain at least the N, CA and C backbone atoms. If any of these atoms are missing the program will fail to run.

Conformer .... file not found

This means that either the file is not contained within the PDB database or you may have forgotten to enter the full path to access your own file.

Must specify conformers 1 and 2

You have not entered any names in the Filename or PDB code field.

Conformers are identical. ....(.) and ....(.)

You have entered exactly the same conformer names and chain identifiers for conformer 1 and 2. Did you mean to use two different chain identifiers?