[Chimera-users] Fitting multiple atomic structures in a density map

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 16 09:05:59 PDT 2013


Hi Andy,
I'm not sure what you mean by didn't help.  Sequential fitting should not allow multiple atomic structures to go in the same place.  There is more than one video linked to that page, doublecheck if you looked at the one for "sequential fitting":

<http://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/>

You would first put both structures in starting locations approximately where you think they should be, and then fit both structures using the same command. For example, if map were #0 and structures #1,2, something like:

fitmap #1,2 #0 sequence 10 resolution 10

Sequential fitting is my only idea because this option was created specifically to fit multiple structures without overlaps.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>

Best,
Elaine

On Jul 16, 2013, at 2:56 AM, Anindito Sen <emailanindito at yahoo.co.in> wrote:

> Hi Elaine,
> I followed the protocol shown in the video tutorial (the link you provided), unfortunately it did'nt help. Is there any other way I can tackle the problem?
> Thanks
> Andy
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: "<chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu> 
> Cc: Anindito Sen <emailanindito at yahoo.co.in> 
> Sent: Saturday, 13 July 2013, 1:53
> Subject: Re: [Chimera-users] Fitting multiple atomic structures in a density map
> 
> Whoops, second link was supposed to be:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
> 
> On Jul 12, 2013, at 9:51 AM, Elaine Meng wrote:
> 
> > Hi Andy,
> > You might try the sequential fitting option of the "fitmap" command.  After it fits one structure, it removes the density from that part of the map before fitting the next.  Details here including link to an example video:
> > 
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
> > 
> > I hope this helps,
> > Elaine
> 
> > On Jul 12, 2013, at 12:43 AM, Anindito Sen wrote:
> > 
> >> Dear All,
> >> I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting  the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position. 
> >> 
> >> How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å  at FSC cutoff of 0.5
> >> Thanks
> >> Andy
> > 
> >



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