From: Chris Neale (
Date: Wed Jun 09 2021 - 18:34:22 CDT

Dear users:

does anybody know if it's possible to load many different PDB files into
the same molecule and have those PDB files have different system
compositions? An example would be to be able to run "vmd -f *.pdb" on a
large collection of PDB files of the same protein family, etc. I realize
that some selection tools would then break (e.g., a selection of "resid 19"
might not always play nice), but sensible selections, like "protein"
"water", etc might be OK. I know that there are some good ideas with
putting particles far away for things like constant pH simulations, but
that's not as generalizable as loading in all SH2 domains in the PDB, for

I realize that I could script image generation, or load hundreds of
separate molecules with a "vmd -m *pdb" command, but none of those is as
intuitive for browsing structural data where some models may have missing
residues, insertions, different sequences, different numbers of water, etc.

If such a capability does not exist, can anyone guess how hard it would be
to implement right in the GUI? I'm not asking for anyone to actually do
this, just trying to get a sense of how hard it would be.

PS: I've got 10+ years experience with VMD, and I'm fairly confident that
this is not possible at the present time. However, I'm asking since (a)
somebody might have a great alternative solution and (b) in any event I'm
interested in learning how hard this would be to implement.

Thank you for your advice,