# Extracting PDBs from a Silent file: "Can't find residue type for ARG"

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Extracting PDBs from a Silent file: "Can't find residue type for ARG"
#1

Hello everyone,

I am refining protein structures into Cryo-EM maps, and my output is a silent file. Currently, I am attempting to extract the pdbs from the silent file so that I can analyze and score the structures. The protein has a missing loop, and it is failing on the C-terminus right before the missing loop. Specifically, my error for each structure is "ERROR:  can't find residue type for ARG:CtermTruncation at pos 114 in sequence G".

I have tried to cluster it with cluster_decoys.sh, use score_jd2, and add ARG.params to my file to no avail. My current script is "extractsilent.sh" and it is outputting "extractsilent.log". I have attached the cluster_decoys and extractsilent scripts below as .txt files along with my error log.

Do you have any suggestions or experience in this area that could help me overcome this?

Thank you all for your time.

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Sat, 2020-10-17 16:20
avsrivatsa

Hello,

I cannot be sure what your problem is without knowing how your silent file was generated, but you might want to try adding the flag: and then trying to extract again. (also I usually use the extract_pdbs app for this, but I'm not sure it matters!)

-crystal_refine true

or:

-missing_density_to_jump true

Sun, 2020-10-18 22:53
danpf

Your suggestion worked & I was successfully able to pull out the pdbs. Thank you for your time.

Mon, 2020-10-19 18:16
avsrivatsa