[phenixbb] CryoFit run failure

Kim, Doo Nam doonam at lanl.gov
Thu Apr 11 08:54:18 PDT 2019

Hello Joseph,

Sorry for late reply, your email was not in my inbox.

I just changed my setting so that email to phenixbb at phenix-online.org will come to my inbox directly.

Thank you for sharing your input file. I just ran your input pdb file, it appears that "SO4, "CD" are not in amber03 forcefield.

I just added my comments like this

Solution if these residue/atoms are important: Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be removed/fixed

If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add parameters.

It is rather a sad fact that most MD simulation force fields do not support all kinds of rare residue/atoms.

cryo_fit2 is under development to address this issue using phenix.eLBOW

Solution if these residue/atoms are not important:

Remove these \"wrong\" atoms/residues from user's input pdb file. Run cryo_fit again

Solution if your user's pdb file is big:
Probably cryo_fit will change conformation just minimally, I would extract out these \"wrong\" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file

If you do
git pull
at your <phenix>/modules/cryo_fit
and run again, you will see results at least to the final stage (that I can't run because of lack of map).

best regards,

From: Finney, Joseph (NIH/NCI) [C] <joseph.finney at nih.gov>
Sent: Monday, April 8, 2019 9:09:23 AM
To: Kim, Doo Nam
Cc: bugs-from-web at phenix-online.org; phenixbb at phenix-online.org; Esser, Lothar (NCI)
Subject: CryoFit run failure

Hey Doonam,

As I said before I figured I would have some additional questions. The new version of phenix (1.15-3459-000) fixed my issues last week with the tutorial dataset. However, I am having trouble with our own testing dataset. As before we are testing in GUI version first. I am using the same run conditions for both the tutorial set and out testing set.

I am attaching the log of the tutorial set as well as the log of our testing set and the test PDB. The density map is too large for email.

The major error I see is “Step 1 didn't run successfully” from the ferrtest run. Looking at the tutorial PDB, it seems as though the header, the terminations, and the nonstandard atoms have been removed prior to use. I tried this and got a different error: “pdb file cleaning is not done, exit now”

Do you have any recommendations on how to succeed?

Thanks in advance!
Joseph Finney [Contractor]
Software Developer
National Cryo-EM Facility
Cancer Research Technology Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research Inc.
PO Box B Frederick, MD 21702
Tel: (301) 228-4313
Cell: (615) 512-2053
Joseph.finney at nih.gov<mailto:Joseph.finney at nih.gov>

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