[Chimera-users] Programmatic trimming of PDB files based on alignment with reference structure

Zachariah Schuurs zachariah.schuurs at hdr.qut.edu.au
Wed Nov 13 19:56:57 PST 2019

Dear Chimera Team,

I have a reference protein domain and then a series of PDB files which all contain the same domain. I have programmatically been able to script an alignment of the reference to the same domain in the other files whereby he domain in the proteins of interest are isolated using the zone select method. This however leaves me with fragments and often misses some of the domain features of the interest proteins that occur outside of the specified zone.

I am wondering if it is possible to write a python script that selects the area on the protein of interest by selecting the residues in the sequence alignment after MatchMaker is conducted. For instance - protein #0 is my reference protein, which is 150 residues long. My protein of interest contains the same domain as the reference, but is 500 residues long. Upon conducting MatchMaker and getting an output sequence alignment, the 150 residues of #0 (the reference) are selected, along with the aligned residues in the protein of interest. It is possible to select the residues in the sequence alignment window (as in the picture) but I wish to be able to script it. The selected 150 residues (or so) in the protein of interest are then saved as their own trimmed file. I have been able to write a python script for completing the MatchMaker etc, but I am not sure how to achieve the selection of residues in #1 based of the alignment with #0, or if it is even possible.


Zachariah Schuurs  | PhD Candidate
CARP - Cancer & Ageing Research Program
Institute of Health and Biomedical Innovation | Queensland University of Technology
Level 6 | Translational Research Institute | 37 Kent St | Woolloongabba QLD 4102
T: +61 7 3443 7296   | E: zachariah.schuurs at hdr.qut.edu.au | Web: www.carp.org.au<http://www.carp.org.au/>

I acknowledge the Turrbal and Yugara, as the First Nations owners of the lands where QUT now stands. I pay respect to their Elders, lores, customs and creation spirits. I recognise that these lands have always been places of teaching, research and learning.

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