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The
missing residues/atoms in the PDB file can be found out and fixed in Schrödinger
program's Prime module refinement.It will
automatically detect the missing atoms in a residue and will fix it.
After fixing it can energy minimize it.For missing portions of residue
it can build
the missing portions using homology model.The other option for fixing
missing
atoms is to use the following server:
http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php
Dear All,I have a PDB file which does not have the REMARKS cards 465 (for missing residues) and 470 (for missing atoms). This is not a deposited PDB file. Is there any program to figure out the missing residues and atoms (some programs complain about missing atoms) ? Or do I have to check in any particular file generated during the processing of the diffraction data? The S2C program from Prof. Dunbrack's Lab does not show any option of uploading pdb files (this solution was mentioned to a previous query on the BB).Thanks in advance,sreetama