[Chimera-users] Using vop to cover a whole molecule

Tom Goddard goddard at sonic.net
Mon May 22 10:24:46 PDT 2017


The problem was the map file had symmetry operators using lowercase x,y,z in the symmetry operators in the CCP4 file header and Chimera only parses uppercase X,Y,Z.  When I open your map I see in the Chimera reply log the following warning

Unable to parse symmetry operators of dnaxraydata.map
x, y, z                                                                         x+1/2, -y+1/2, -z                                                               -x, y+1/2, -z+1/2                                                               -x+1/2, -y, z+1/2                                                               

Since it can’t read the 4 symmetry operators the vop cover command only uses unit cell translational symmetry.    I see using “volume #0 dumpHeader true” a comment in the map header saying “From clipper Xmap”.  So I guess that software writes lowercase x, y, z.  I’ve changed Chimera to accept upper or lower case symmetry operators.  This will be in tonight’s Chimera daily build.  Thanks for reporting the problem.

	Tom

> On May 19, 2017, at 4:48 PM, Tom Goddard  wrote:
> 
> Hi Pradeep,
> 
>  Maybe your xray density map is not a full asymmetric unit so the whole unit cell cannot be reconstructed from it.  Or maybe the symmetry operators aren’t in the map file so it is only using unit cell translations.  Can’t be sure what the problem is without access to the specific data files.
> 
> 	Tom
> 
>> On May 19, 2017, at 11:37 AM, Pradeep Pallan wrote:
>> 
>> Hi All,
>> 
>> I would like to know how to extend an e-density map
>> in y or z direction. Here is my case:
>> 
>> The DNA structure that was refined in shelx. 
>> Model #0 is DNA and the e-density map is model #1.
>> When I used vop cover #1 atom #0, the electron density
>> covers the molecule along two axes, and for the third axis
>> it covers partly. How to extend the e-density map in a particular 
>> axis? 
>> 
>> Thank you!
>> -- 
>> 
>> -------------------------------------------------------------------
>> Pradeep Pallan
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> 
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