# How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?

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How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?
#1

Hi, I am doing the design of a batch of decoys.

I want to block the designs of residues 1-9 and residues 80-91 for all the pdbs.

However, some of the pdbs do not have certain residue numbers (e.g. pdb1 has missing residue number 1, pdb2 has missing residue number 82).

May I know how to specify residue numbers so I can still use a single resfile for the whole batch of pdbs?

Since the pdbs were renumbered by a specific numbering scheme (where the numbering of some loops were standardized), I want to avoid additional renumbering of the pdbs.

Any good idea how to do this?

Another option, is it possible to by-pass any error due to the missing residues not found in pdbs?

Thanks a lot!

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Wed, 2019-05-08 02:30
johnnytam100

This is not a use case resfiles were designed for - I'm not aware of a clean way to do this.  It's an interesting problem.

If you know C++ you can open the code up and put in an exception catch that just ignores resfile lines that refer to nonexistent residues?  I can point you to approximately where it would go.

Wed, 2019-05-08 08:29
smlewis

smlewis, thank you for the suggestion!

Sadly, I know nothing on C++..

I have already done it in the hard way: generated individual resfiles for all pdbs.

It will be nice if the next releases of rosetta include features of omitting errors from resfile, just a suggestion.

Thanks!

Wed, 2019-05-15 18:45
johnnytam100