[Chimera-users] Computing xray density from structure factors

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 4 13:55:46 PDT 2009

Hi Mike,

  If it is just a matter of computing a Fourier transform that is easy.  
Chimera already has libraries that does that.  The trouble will be 
parsing the CIF file.  Chimera reads molecular structure CIF and mmCIF 
files using a third party library called mmLib.  I don't know if mmLib 
will read the structure factors.  If you send me an example CIF file 
with structure factors I'll give it a try.


-------- Original Message --------
Subject: Re: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: Tom Goddard
Date: 9/4/09 12:41 PM
> Hi Tom,
> ...
> If I had to lobby for any particular ticket on your list it would be 
> #201. What I would add in way of description on that ticket is that 
> I'm not talking about using SHELX in Chimera. What I meant to say is 
> for Chimera to read a standard format CIF file containing the 
> reciprocal space transform of the real space electron density. The fft 
> routines to transform back to real space have been around forever and 
> are in most all modern languages. 
> All crystallography packages can write this type of file containing 
> h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in 
> degrees). This the preferred format for sending data to the PDB.
> I'm not looking to add a bunch of "stuff" to your already huge pile 
> but I thought most of this was already in the public domain. After 
> all, nothing is impossible for the guy that doesn't have to do it. 
> It's all easy and straightforward, right? ;0)
> As for the issue of reading the CIF, P21/n is a very common alternate 
> setting of P21/c and the PDB symmetry list does not contain it.
> Thanks again!!
> Cheers,
> Mike
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
> <<< 
> ------------------------------------------------------------------------>>>

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