[CP2K:4964] Outputting cell information and fractional coordinates

Efrem Braun efrem... at gmail.com
Wed Aug 2 11:43:35 UTC 2017

Similar question applies when using pwtools. io.write_cif is happy to write 
a cif file in fractional coordinates given a CP2K output pdb, but is it 
assuming that CP2K was writing the pdb using a convention that CP2K isn't 

On Wednesday, August 2, 2017 at 10:39:51 AM UTC+2, Efrem Braun wrote:
> Would someone be willing to explain this problem in some more detail? I'd 
> like to convert the last snapshot of my pdb trajectory into a cif file 
> containing fractional coordinates. I was planning to do this using obabel 
> to get the cif file containing Cartesian coordinates, and then using obabel 
> again to get a fractional coordinate file. However, I believe that obabel 
> does the second conversion assuming that crytallographic conventions 
> regarding the unit cell (
> https://en.wikipedia.org/wiki/Fractional_coordinates#In_Crystallography) 
> are followed, and per this thread, I'm not sure whether this is the case.
> Efrem Braun
> On Friday, January 31, 2014 at 4:34:37 PM UTC+1, FX Coudert wrote:
>> > There is now an alternative dump format called DCD_ALIGNED_CELL which 
>> dumps the coordinates based on a cell alignment as described which should 
>> allow a reconstruction of the scaled coordinates only from the DCD dump 
>> data (to single precision accuracy). 
>> Thanks! 
>> FX
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