[Chimera-users] fitmap

Hernando J Sosa hernando.sosa at einstein.yu.edu
Thu May 31 15:25:35 PDT 2012

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 ?  


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, May 31, 2012 5:29 PM
To: Hernando J Sosa
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] fitmap

Hi Hernando,
Commands use "specifications" which for whole models are the model numbers (also shown in the Model Panel), for example:

fitmap #0 #1

...if the pdb structure is model 0 and the density map is model 1.   There are also lots of options you could include after the model numbers, see

I hope this helps,
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 2:17 PM, Hernando J Sosa wrote:

> HI,
> What is the correct syntax to run the fitmap command?. I have a pdb 
> structure named  C1 and a density map (spider format) named MV (names as appear in the Model panel).  If I try in the command line:
> fitmap C1 MV
> I get the error:
> fitmap invalid volume argument "MV"
> What  am I doing wrong?
> Thanks

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