Can SCWRL process more than one amino acid chain at the same time?

Question

[flame233]

Hello,

I’ve been learning to make mutations to a single beta chain of an HLA molecule with SCWRL and had success so far. However, I was wondering if it is possible to make mutations in the Alfa, Beta, and peptide chains all at the same time, in one run by processing the entire pdb file, without deleting anything. The setup of the -s file I tried is something similar to the following:

mikeehviiqaefyln

AgdtQprflwqGk

pvskmrmatpllmqalp

Each line for A, B and peptide chains respectively. The problem is that the program reads all of them as a single line, resulting in a: ‘Warning! Length of the provided sequence exceeds the number of residues! Sequence will be truncated!’. Also tried separating them with commas and using separate files with no luck. Is this possible to achieve? Could you also include water atoms in the -s file as a lowercase 'w'?

Thank you.

Answer 1

[flame233]

Already found the answer. The program reads the chain sequences in a linear sense, like: A->B->C. Then you just have to add the “-s” file sequence in the same order, without any interruptions. E.g

PDB file:

chain A: LEQVKHECHFFNGTERV chain B: RFLDRYFYHQEEYVRFD chain C: SDVGEYRAVT -s file: leqvkhEchffnGtervrfldryfyhqEeyvrfdsdvgeyravt

Just be careful when using PDB editor, as it has the tendency to change dots with commas, making the files sort of unreadable to the software. (Also extracts the wrong number of amino-acids, with SCWRL corrects when parsing individual chains).

Haven´t found the answer about how to use waters though.

Cheers