[Chimera-users] fitmap search within specified radius

Tom Goddard goddard at sonic.net
Tue Jun 5 17:26:49 PDT 2012

Hi Hernando,

   Good idea.  I've added a "radius" option to the fitmap command that 
limits the global search to translations less than or equal to the 
radius value.  For example,

     fitmap #1 #0 search 15 radius 50

does 15 fits using random translations of molecule #1 into map #0 in 
random directions by distances ranging from 0 to 50 (uniform random 
distribution) from the current molecule placement.  It also does a 
random rotation.  The "radius" option only works when the "search" 
option is specified.  The local optimization can move the molecule 
further away than the radius.  The radius value only controls the 
initial random placement that starts each fit optimization.  If you 
don't specify radius then you get the usual behavior where it searches 
over the entire map.


> Thanks Elaine,  I use both methods (subregion&  symmetry)  and both worked well.
> I would still add limiting radius of search option to my "desired list of features" as it  would make the fitting process in certain cases easier. In any case I found chimera-fitmap to be a great tool.
> Best
> Hernando
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Thursday, May 31, 2012 6:53 PM
> To: Hernando J Sosa
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] fitmap
> Hi Hernando,
> Not exactly that, but one possibility is to crop the map to the area of interest.  See Volume Viewer menu: Features... Subregion selection, use the mouse to draw a box around that area, and crop to hide the rest of the map.  By default the global search keeps the geometric center of the structure within the bounding box of the displayed part of the map, as described in the global search "placement" option:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#global>
> Also, if the map is symmetrical and you want to only place the structure in one symmetric location, see the description of the "asymmetricUnit" option (i.e. if the map is symmetric but doesn't have symmetry information attached to it in Chimera, you might be able add that information with the "measure symmetry" command).
> 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 31, 2012, at 3:25 PM, Hernando J Sosa wrote:
>> Thanks Elaine. That certainly help.
>> Now I have another question I see that the global search can be restricted in shift or rotation but can it also be restricted to a certain radius from the current position ?
>> Thanks
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