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 -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. -- * Emergenza Coronavirus: facciamoci contagiare dalla solidarietà aiutando i nostri ospedali universitari Le donazioni possono essere inviate alla Fondazione Roma Sapienza che devolverà il ricavato al Policlinico Umberto I e Ospedale Sant'Andrea. È possibile donare: – con bonifico bancario (iban: IT72P 01030 03213 000063 259373, bic: PASCITM1R13, beneficiario "Fondazione Roma Sapienza", causale "emergenza coronavirus") – con carta di credito, attraverso il PayPal della Fondazione Sapienza <https://www.fondazionesapienza.uniroma1.it/node/776>
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 -
Francesco Malatesta