Fusing or bonding two protein chains?!
Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain. Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani SPMS-CBC-04-37, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371
Hi Maziar, Yes -- it sounds like you already have the structures in the desired relative position. In that case, you would next combine the two models into one model (which could change residue numbering or chain ID so that there will not be conflicts) and then add a bond. The structures you open in Chimera should be separate PDB files, not one PDB file, because you want Chimera to do the combining and renumbering. If you start with one PDB file there will already be conflicts. You would open the two separate PDB files and then do the following: Combining models. Can be done with the "copy/combine" function in the right side of the Model Panel (open from Favorites menu), or with the command "combine" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> Adding the bond. Can be done with the "Adjust Bonds" section of Build Structure (in menu under Tools... Structure Editing) or the command "bond" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> However, if you did NOT already have the structures in the desired relative position, you could use the "Join Models" section of Build Structure to do all of the above: move one structure to form a bond of the specified geometry, combine the two into one model, and form the bond. You might want to try that anyway... just make sure you have saved your previous positions, for example as a session, beforehand. 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 Oct 15, 2010, at 11:49 AM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain.
Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani
Hi Elaine, Thanks for the reply. I'm using Chimera 1.5 (build 30106) and can't find the "Join Models" feature anywhere in Chimera's tools. I looked it up online and apparently there is a small documentation about that which does not correspond to the current Chimer interface: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm... Does it still exist? Cheers, Maziar -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Saturday, 16 October, 2010 5:10 AM To: #MAZIAR SOLEYMANI ARDEJANI# Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Fusing or bonding two protein chains?! Hi Maziar, Yes -- it sounds like you already have the structures in the desired relative position. In that case, you would next combine the two models into one model (which could change residue numbering or chain ID so that there will not be conflicts) and then add a bond. The structures you open in Chimera should be separate PDB files, not one PDB file, because you want Chimera to do the combining and renumbering. If you start with one PDB file there will already be conflicts. You would open the two separate PDB files and then do the following: Combining models. Can be done with the "copy/combine" function in the right side of the Model Panel (open from Favorites menu), or with the command "combine" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> Adding the bond. Can be done with the "Adjust Bonds" section of Build Structure (in menu under Tools... Structure Editing) or the command "bond" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> However, if you did NOT already have the structures in the desired relative position, you could use the "Join Models" section of Build Structure to do all of the above: move one structure to form a bond of the specified geometry, combine the two into one model, and form the bond. You might want to try that anyway... just make sure you have saved your previous positions, for example as a session, beforehand. 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 Oct 15, 2010, at 11:49 AM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain.
Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani
Dear Elaine, I installed the latest daily build and the "join model" is included there. Thanks, Maziar -----Original Message----- From: #MAZIAR SOLEYMANI ARDEJANI# Sent: Wednesday, 20 October, 2010 12:24 PM To: 'chimera-users@cgl.ucsf.edu BB' Subject: RE: [Chimera-users] Fusing or bonding two protein chains?! Hi Elaine, Thanks for the reply. I'm using Chimera 1.5 (build 30106) and can't find the "Join Models" feature anywhere in Chimera's tools. I looked it up online and apparently there is a small documentation about that which does not correspond to the current Chimer interface: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm... Does it still exist? Cheers, Maziar -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Saturday, 16 October, 2010 5:10 AM To: #MAZIAR SOLEYMANI ARDEJANI# Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Fusing or bonding two protein chains?! Hi Maziar, Yes -- it sounds like you already have the structures in the desired relative position. In that case, you would next combine the two models into one model (which could change residue numbering or chain ID so that there will not be conflicts) and then add a bond. The structures you open in Chimera should be separate PDB files, not one PDB file, because you want Chimera to do the combining and renumbering. If you start with one PDB file there will already be conflicts. You would open the two separate PDB files and then do the following: Combining models. Can be done with the "copy/combine" function in the right side of the Model Panel (open from Favorites menu), or with the command "combine" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> Adding the bond. Can be done with the "Adjust Bonds" section of Build Structure (in menu under Tools... Structure Editing) or the command "bond" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> However, if you did NOT already have the structures in the desired relative position, you could use the "Join Models" section of Build Structure to do all of the above: move one structure to form a bond of the specified geometry, combine the two into one model, and form the bond. You might want to try that anyway... just make sure you have saved your previous positions, for example as a session, beforehand. 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 Oct 15, 2010, at 11:49 AM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain.
Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani
If you want the documentation to match the features of the Chimera you downloaded, use the Chimera Help menu. If you are looking on the web, and the URL does not have a version number in it, that is the "development" documentation -- it will usually be newer than what you have downloaded. Best, 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 Oct 20, 2010, at 12:29 AM, #MAZIAR SOLEYMANI ARDEJANI# wrote:
Dear Elaine, I installed the latest daily build and the "join model" is included there. Thanks, Maziar
-----Original Message----- From: #MAZIAR SOLEYMANI ARDEJANI# Sent: Wednesday, 20 October, 2010 12:24 PM To: 'chimera-users@cgl.ucsf.edu BB' Subject: RE: [Chimera-users] Fusing or bonding two protein chains?!
Hi Elaine, Thanks for the reply. I'm using Chimera 1.5 (build 30106) and can't find the "Join Models" feature anywhere in Chimera's tools. I looked it up online and apparently there is a small documentation about that which does not correspond to the current Chimer interface: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm... Does it still exist? Cheers, Maziar
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#MAZIAR SOLEYMANI ARDEJANI# -
Elaine Meng