[Chimera-users] Generating a map from atomic molecule

[Tom Goddard]

Hi Zhihai,

  The reason your map surface shows the triangulation is because the grid spacing is large.  You made the map with molmap with 30A resolution.  By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case.  Apparently this is too coarse for your needs.  So spedify a finer grid spacing in the molmap command.  For instance

	molmap #0 30 gridSpacing 3

to produce 30 A resolution with 3 A grid spacing.  Here is the molmap documentation

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html>

  Tom


> On Apr 16, 2015, at 8:45 PM, 李智海 wrote:
> 
> Hi Tom,
> It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and  I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction.
> Please tell me how can I get rid of this. Thank you!
> 
> Best wishes!
> 
> 
> Zhihai Li
> 
> <molmap_30A.png><FFT.png>
> 
> Zhihai Li
> 
> Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics.
> School of Life Sciences, Xiamen University.
> Xiang'an Road(South), Xiang'an District, Xiamen City,
> Fujian Province, China.
> 
>> On Apr 15, 2015, at 1:28 AM, Tom Goddard  wrote:
>> 
>> Hi Zhihai,
>> 
>>   If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid.  If #0 is the atomic model and #1 the reference map.
>> 
>> 	molmap #0 8 edgePadding 50
>> 	vop resample #0 onGrid #1
>> 
>> Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map.
>> 
>> 	Tom
>> 
>> 
>> 
>>> On Apr 13, 2015, at 9:00 PM, 李智海  wrote:
>>> 
>>> hi,
>>> here I want to generate a density map from a atomic model in Chimera,  then convert the generating map into .pif file to do as the initial map performing in Auto3dem.
>>> I have met some questions to successfully finish these work.
>>> 
>>> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size.
>>> 
>>> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. 
>>> 
>>>  
>>> Thanks in advanced!
>>> 
>>> Best wishes!
>>> 
>>> Zhihai Li
>>> 
>>> 
>>> 
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>> 
> 

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