# Using Rmsd RosettaScripts filter with alignment files

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Using Rmsd RosettaScripts filter with alignment files
#1

I have a homology model that contains a residue insertion and thus a 1:1 residue RMSD calculation cannot be performed. I would like to try the Rmsd RosettaScripts Filter with an alignment file to get the correct C-alpha RMSD calculation. However, I'm not sure how to create this alignment file. I've tried the alignment Grishin file I used for Homology modelling but receive this error:

File: src/protocols/protein_interface_design/filters/RmsdFilter.cc:217

[ ERROR ] UtilityExitException

ERROR: Assertion template_segm.size() > 10 failed. MSG:there must be more that 10 residues to calculate RMSD over

My first guess is that I'm not using the correct alignment format. The output file is also attached in case I'm overlooking anything.

This is new territory for me so any advice on performing these RMSD calculations is appreciated!

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Sun, 2020-11-08 15:51
bjharris

You're correct that the Rmsd filter doesn't take Grishin formatted alignment files. It takes FASTA-formatted ones.

Sun, 2020-11-08 18:56
rmoretti