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

Tom Goddard goddard at sonic.net
Tue Jul 16 10:26:41 PDT 2013


Hi Andy,

  If the sequential fitting option doesn't help you I'd suggest subtracting the density for your first fit molecule from the map, then fitting the second molecule in the remaining map.  This is essentially what the sequential fitting does, but you'll have better control and insight into what is going on if you do it by hand.  To subtract a fit of molecule #1 from map #0 at 8.5 Angstroms resolution use the molmap and "vop subtract" commands, for example

	molmap #1 8.5 model #5
	vop subtract #0 #5 minRMS true

The first command creates a simulated map from the molecule, and the second command subtracts it from the experimental map.  The minRMS option handles the fact that the experimental map and the simulated map have different normalization.  It says to subtract a multiple of the simulated map that minimizes the residual of the difference map.  Using the difference map you should be able to fit your second molecule in without it migrating into the location where the first molecule was fit.

	Tom



On Jul 16, 2013, at 9:05 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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