I have some questions about 'groups' in .pdb files
To date I have called these things 'residues', but I understand that
'group' is a more generic and inclusive term. So I will switch.
I have learned more about these things in the past few weeks. Please
correct me if any of these things are wrong:
- The groups which happen to be amino acid residues define protein
chains. The 3d position of the alpha-carbon is key for generating various
graphical representations of secondary structure (trace, backbone,
- Protein chains *can* contain groups which are not predefined amino
acids, as in 1hiv. [currently a problem for Jmol; how to recognize that
these HETATMs with this strange group name form a legitimate part of the
- The groups which happen to be nucleotides define dna/rna. For purposes
of generating graphical representations, the 3d position of the
phosphorous is comparable to that of the alpha-carbon in proteins.
- group numbers are not always consecutive integers. They can be deleted
(as in ?) or inserted (as in 1hag). The insertion codes can also run in
reverse (as in the beginning of 1hag). [currently a problem for Jmol; it
currently assumes they are consecutive integers]
- I am still struggling because I don't know what to do with HOH.
According to the .pdb format, every HOH is part of a unique HOH group.
But I don't want to allocate all those data structures if they are not
going to be used.
Q: Would it be OK to throw all HOH into one consolidated HOH group?
Q: Should all these HOH molecules be part of a virtual 'chain'?
These questions apply to other HETATMs as well.
Q: Should all the HETATMs in a group be collected into a group data
Q: What 'chain' do they form a part of?
I think these same questions apply to smaller, simpler .pdb files that
are not macromolecules.
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