need instructions on how to fake out GenResAtoms.py if we need to manually add a residue to seed

[Jmller56]

for P450/OleT, the cysteine coordinated to the heme will be excluded in the seed1 (substrate only) To fix this, we needed to add the appropriate parts of the residue to res_atoms.dat The v1 script probe_freq_2pdb.py script will place fragments into a pdb as long as they are flagged as seed on the command line GenResAtoms.py will crash because it needs the manually placed residues to also be in freq_per_res.dat.

So, the flexibility of probe_freq_2pdb.py needs to be added to GenResAtoms.py, or we need to improve the documentation to show this unusual case.

[natedey]

Is this still an issue with existing scripts?

[natedey]

We don't use GenResAtoms.py anymore - I think we assimilated it with rinrus_trim2_pdb.py Still, instructions on how a user can manipulate res_atoms.dat to manually construct a set of models is important.

[tsantaloci]

The manual way to trick rinrus_trim2_pdb.py is to manually type in the CYS residue at the appropriate line in the res atom file. If you want the CYS in every model generate place the CYS in the second line of res_atoms.dat.

[tsantaloci]

Also, the manual program driver can be used too create models based off of customized res_atoms.dat files

[natedey]

there needs to be an automated way to do this. Currently, this task requires a lot of user knowledge/intervention and breaks the driver program flow. Also, the issue was more to have clear documentation about what specific things need to be added to the res_atoms file to get known possible outcomes