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

Anindito Sen emailanindito at yahoo.co.in
Tue Jul 16 02:56:44 PDT 2013

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?


Dr. Anindito Sen (Ph.D)
>Department of Cell Biology & Anatomy
>Graduate School of Medicine
>University of Tokyo
>Tel & fax: +81-3-5841-3339

 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:

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
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 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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