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

[Anonymous]

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!

[Anonymous]

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.  

[Anonymous]

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!

[Author]

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