does chimara allow changing of the primary sequence of the protein?
Dear Sir/Madam, I am a PhD student working for the University of East Anglia. I have just downloaded the Chimera software and I really like the look of it. So far I have found it very user friendly. I was wondering if the software allows incorporating changes into the protein structure? I am working on the mutant of my protein of interest. I have found, through experimental procedures, that when I mutate one residue it changes the properties of the protein. I was wondering if the effects I am seeing are due to changes in the protein structure. I would like to visualise it. I am not interested in generating crystal structure of the mutated protein or anything like that. I really would like to insert a different amino acid into the structure that already exist. I understand it might be incorrect but all I want to achieve is a "prediction". Would chimera software do that for me? Kind regards, Marta Mikolajczak
Dear Marta, Yes, you can do a simple virtual mutation changing the sidechain from one amino acid type to another, with command "swapaa" or the "Rotamers" tool (in menu under Tools… Structure Editing). See this previous post for more details, and links to manual pages and a tutorial: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008185.html> This is only a simple first-order prediction. It will not change the rest of the structure or estimate the change in stability or binding energy. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 14, 2014, at 9:34 AM, "Marta Mikolajczak (BIO)" <M.Mikolajczak@uea.ac.uk> wrote:
Dear Sir/Madam,
I am a PhD student working for the University of East Anglia. I have just downloaded the Chimera software and I really like the look of it. So far I have found it very user friendly. I was wondering if the software allows incorporating changes into the protein structure? I am working on the mutant of my protein of interest. I have found, through experimental procedures, that when I mutate one residue it changes the properties of the protein. I was wondering if the effects I am seeing are due to changes in the protein structure. I would like to visualise it. I am not interested in generating crystal structure of the mutated protein or anything like that. I really would like to insert a different amino acid into the structure that already exist. I understand it might be incorrect but all I want to achieve is a "prediction". Would chimera software do that for me?
Kind regards,
Marta Mikolajczak
This has been very helpful, exactly what I was looking for, thank you very much! Kind regards, Marta ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: 14 August 2014 18:27 To: Marta Mikolajczak (BIO) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] does chimara allow changing of the primary sequence of the protein? Dear Marta, Yes, you can do a simple virtual mutation changing the sidechain from one amino acid type to another, with command "swapaa" or the "Rotamers" tool (in menu under Tools… Structure Editing). See this previous post for more details, and links to manual pages and a tutorial: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008185.html> This is only a simple first-order prediction. It will not change the rest of the structure or estimate the change in stability or binding energy. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 14, 2014, at 9:34 AM, "Marta Mikolajczak (BIO)" <M.Mikolajczak@uea.ac.uk> wrote:
Dear Sir/Madam,
I am a PhD student working for the University of East Anglia. I have just downloaded the Chimera software and I really like the look of it. So far I have found it very user friendly. I was wondering if the software allows incorporating changes into the protein structure? I am working on the mutant of my protein of interest. I have found, through experimental procedures, that when I mutate one residue it changes the properties of the protein. I was wondering if the effects I am seeing are due to changes in the protein structure. I would like to visualise it. I am not interested in generating crystal structure of the mutated protein or anything like that. I really would like to insert a different amino acid into the structure that already exist. I understand it might be incorrect but all I want to achieve is a "prediction". Would chimera software do that for me?
Kind regards,
Marta Mikolajczak
participants (2)
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Elaine Meng -
Marta Mikolajczak (BIO)