From: Peter Freddolino (
Date: Thu Dec 17 2020 - 22:50:15 CST

Dear Kelly,
While I can't speak to this particular problem, the pdb files that VMD
writes are standards-compliant as far as I can tell. Are you able to
identify what aspect of the files written by VMD is causing a problem for
Phenix? An example would help, but even better would be if you were to
actually track down what formatting difference is causing the issue, eg, by
taking a Phenix-readable PDB, reading into VMD and writing the VMD-written
form (which presumably won't work with Phenix), and gradually morphing one
into the other until you find where the issue actually is. (This may be
moot if Phenix actually gives you an informative error message.) If you can
identify the problem, then one can first tell which programs fault it is,
in a sense (that is, is VMD writing non-standards compliant PDBs, in which
case we should fix it, or is Phenix making an invalid assumption about what
the files should look like, in which case the Phenix developers should fix
their PDB reader), and also you could probably write a quick intermediate
script to convert the vmd-written PDBs to something that Phenix likes.


On Thu, Dec 17, 2020 at 8:59 PM McGuire, Kelly <> wrote:

> After running a long simulation and saving each frame of the trajectory as
> a PDB, we are trying to open those PDB files in Phenix and save them as MTZ
> files. However, Phenix does not like the PDB format that VMD creates.
> Phenix requires the same PDB format as that found from downloading a file
> from the protein data bank. An example of the required format we need can
> be given if requested. Does anyone have experience with Phenix and getting
> your PDB trajectory outputs into that program? Maybe another format that
> VMD does write may work?
> *Dr. Kelly L. McGuire*
> *PhD **Biophysics*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*