Hello I am trying, for teaching purposes, to morph deoxy hemoglobin 1HBA and oxy hemoglobin 1BBB to show the O2-linked quaternary change. I get an obviously wrong morph, attached. Chimera is probably pairing different subunits? Do you think this morph can be done? Thank you Stay safe and well Francesco
Francesco Malatesta Professor of Chemistry and Biochemistry FEBS Education Ambassador Department of Biochemical Sciences Sapienza University of Rome Tel: +39 06 49910944 Fax: +39 06 4440062 Cell: 338 6961519
Excellence in Learning and Teaching Biochemistry A FEBS Education Meeting Rome, September 16-17, 2019 www.sites.google.com/uniroma1.it/eltbiochemistry2019
Hi Francesco, You just need to get the correct chains paired up for morphing. Chain pairing is described here: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing
In this case, with both structures having chains A-D, the automatic pairing for morphing is A with A, B with B, etc. However, that is not the same pairing that you have spatially. Spatially you have A on top of C (and vice versa), B on top of D (and vice versa). So before doing the morphing, you need to change the chain IDs of one of the structures so that A is on top of A, B is on top of B, etc.
There is a Change Chain IDs tool in menu under Tools... Structure Editing. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html
However, in this e-mail message I can describe it more concisely with a command. I believe this will do the necessary renaming in your case:
changechains A,B,C,D C,D,A,B #1
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html
Then you can make the morph correctly.
Happy teaching, and you stay safe and well too!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 29, 2020, at 3:28 AM, Francesco Malatesta francesco.malatesta@uniroma1.it wrote:
Hello I am trying, for teaching purposes, to morph deoxy hemoglobin 1HBA and oxy hemoglobin 1BBB to show the O2-linked quaternary change. I get an obviously wrong morph, attached. Chimera is probably pairing different subunits? Do you think this morph can be done? Thank you Stay safe and well Francesco
participants (2)
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Elaine Meng
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Francesco Malatesta