Addition of phosphates to PDB structures
Hi all, I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this. Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site. I would very much appreciate any responses, Thanks, Carlos Donado The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Carlos, How to add a phosphate group is discussed in this earlier post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html> Chimera does not "dock" ligands into binding sites automatically. If you are using only Chimera and not docking programs, probably the most reasonable way is to superimpose the protein with a related protein structure that does contain the ATP, then remove or hide (depending on what you want to do next) the related protein structure except for the ATP part. It's easy to superimpose proteins using the MatchMaker tool (or mmaker command). For details see the documentation, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> General discussion of methods for superimposing structures: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Of course you could also open your protein and an ATP molecule as separate models and then try moving the ATP into the site by hand, possibly rotating some bonds of protein sidechains or in the ATP, but that is usually quite difficult. How to "freeze" (deactivate) one structure so that only the other one moves: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> How to rotate bonds: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust> 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 May 9, 2012, at 4:34 PM, Donado, Carlos wrote:
Hi all, I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this. Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site. I would very much appreciate any responses, Thanks, Carlos Donado
Hi Elaine, Thank you for your prompt reply; I will try your suggestions. Also, since you mentioned docking programs, which one would you suggest using in conjunction with Chimera specifically for the purpose of docking ATP into a known ATP binding site? Thanks, Carlos ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Wednesday, May 09, 2012 8:32 PM To: Donado, Carlos Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Addition of phosphates to PDB structures Hi Carlos, How to add a phosphate group is discussed in this earlier post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html> Chimera does not "dock" ligands into binding sites automatically. If you are using only Chimera and not docking programs, probably the most reasonable way is to superimpose the protein with a related protein structure that does contain the ATP, then remove or hide (depending on what you want to do next) the related protein structure except for the ATP part. It's easy to superimpose proteins using the MatchMaker tool (or mmaker command). For details see the documentation, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> General discussion of methods for superimposing structures: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Of course you could also open your protein and an ATP molecule as separate models and then try moving the ATP into the site by hand, possibly rotating some bonds of protein sidechains or in the ATP, but that is usually quite difficult. How to "freeze" (deactivate) one structure so that only the other one moves: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> How to rotate bonds: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust> 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 May 9, 2012, at 4:34 PM, Donado, Carlos wrote:
Hi all, I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this. Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site. I would very much appreciate any responses, Thanks, Carlos Donado
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Carlos, The only docking program I have ever used is DOCK: <http://dock.compbio.ucsf.edu/> ...but I should admit that was many years ago. The superposition approach should be much simpler, and so I personally would not resort to using a docking program unless the superposition approach proves inadequate for some reason. If you do want to ask for opinions on which docking program to use for this purpose, CCL.net may be a suitable forum, or to ask about DOCK in particular, you could post to dock-fans@docking.org Best, Elaine On May 10, 2012, at 12:07 PM, Donado, Carlos wrote:
Hi Elaine,
Thank you for your prompt reply; I will try your suggestions. Also, since you mentioned docking programs, which one would you suggest using in conjunction with Chimera specifically for the purpose of docking ATP into a known ATP binding site?
Thanks, Carlos
Hi Elaine, One last question. I tried using the Matchmaker option in Chimera and read the documentation but was unable to find a way to superimpose two molecules (chains) within the same PDB files. I am sure you are aware that a lot of PDB files have more than one structure for the same protein present in the file, whether it be inactive, active, with an inhibitor bound to it or what not... I found that Chimera will only let me match objects in two different PDB files. Is there a straight forward way to do this? Thanks! Carlos ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 10, 2012 8:02 PM To: Donado, Carlos Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Addition of phosphates to PDB structures Hi Carlos, The only docking program I have ever used is DOCK: <http://dock.compbio.ucsf.edu/> ...but I should admit that was many years ago. The superposition approach should be much simpler, and so I personally would not resort to using a docking program unless the superposition approach proves inadequate for some reason. If you do want to ask for opinions on which docking program to use for this purpose, CCL.net may be a suitable forum, or to ask about DOCK in particular, you could post to dock-fans@docking.org Best, Elaine On May 10, 2012, at 12:07 PM, Donado, Carlos wrote:
Hi Elaine,
Thank you for your prompt reply; I will try your suggestions. Also, since you mentioned docking programs, which one would you suggest using in conjunction with Chimera specifically for the purpose of docking ATP into a known ATP binding site?
Thanks, Carlos
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Carlos, You could use the "split" command to make each chain a separate model, probably more convenient than the alternatives of editing PDB files by hand before opening them in Chimera or opening multiple copies of the same PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> 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 May 11, 2012, at 1:29 PM, Donado, Carlos wrote:
Hi Elaine, One last question. I tried using the Matchmaker option in Chimera and read the documentation but was unable to find a way to superimpose two molecules (chains) within the same PDB files. I am sure you are aware that a lot of PDB files have more than one structure for the same protein present in the file, whether it be inactive, active, with an inhibitor bound to it or what not... I found that Chimera will only let me match objects in two different PDB files. Is there a straight forward way to do this? Thanks! Carlos
Hi I would like to ask if anyone knows how to create the redox potential surface by chimera. thanks a lot Francesca Cantini
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Hi Francesca, That sounds like something that requires a quantum-chemical calculation, which Chimera does not do, sorry. However, if you instead meant electrostatic potential (ESP), please see this previous post about methods for ESP map calculation: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-May/007551.html> ... and this related tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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 May 14, 2012, at 5:12 AM, Francesca Cantini wrote:
Hi
I would like to ask if anyone knows how to create the redox potential surface by chimera.
thanks a lot
Francesca Cantini
Hi Carlos, If you have exactly the same sequence you can use the "match" command to align chains, for example to move chain B to align it with chain A using C-alpha atoms: match #1:.B@CA #1:.A@CA move chains A new feature request to align chains with MatchMaker was made 7 months ago but hasn't been implemented. http://plato.cgl.ucsf.edu/trac/chimera/ticket/10134 Tom
Hi Elaine,
One last question. I tried using the Matchmaker option in Chimera and read the documentation but was unable to find a way to superimpose two molecules (chains) within the same PDB files. I am sure you are aware that a lot of PDB files have more than one structure for the same protein present in the file, whether it be inactive, active, with an inhibitor bound to it or what not... I found that Chimera will only let me match objects in two different PDB files. Is there a straight forward way to do this?
Thanks! Carlos ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 10, 2012 8:02 PM To: Donado, Carlos Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Addition of phosphates to PDB structures
Hi Carlos, The only docking program I have ever used is DOCK: <http://dock.compbio.ucsf.edu/> ...but I should admit that was many years ago.
The superposition approach should be much simpler, and so I personally would not resort to using a docking program unless the superposition approach proves inadequate for some reason. If you do want to ask for opinions on which docking program to use for this purpose, CCL.net may be a suitable forum, or to ask about DOCK in particular, you could post to dock-fans@docking.org
Best, Elaine
On May 10, 2012, at 12:07 PM, Donado, Carlos wrote:
Hi Elaine,
Thank you for your prompt reply; I will try your suggestions. Also, since you mentioned docking programs, which one would you suggest using in conjunction with Chimera specifically for the purpose of docking ATP into a known ATP binding site?
Thanks, Carlos
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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participants (4)
-
Donado, Carlos -
Elaine Meng -
Francesca Cantini -
Tom Goddard