[Chimera-users] Addition of phosphates to PDB structures

Tom Goddard goddard at sonic.net
Fri May 11 14:59:35 PDT 2012

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 at CA #1:.A at CA move chains

A new feature request to align chains with MatchMaker was made 7 months 
ago but hasn't been implemented.



> 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 at cgl.ucsf.edu]
> Sent: Thursday, May 10, 2012 8:02 PM
> To: Donado, Carlos
> Cc: chimera-users at 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 at 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.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list