[Chimera-users] Computing xray density from structure factors

[Michael Day]

Hi Tom,

Attached is the structure factor file corresponding to iat03.

Cheers,
Mike

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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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Beckman Institute, Room 116
Phone: (626) 395-2734
Fax: (626) 449-4159
e-mail: mikeday at caltech.edu
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On Sep 4, 2009, at 1:55 PM, Tom Goddard wrote:

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.

     Tom

-------- 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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