<div dir="ltr">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 using?<br><br>On Wednesday, August 2, 2017 at 10:39:51 AM UTC+2, Efrem Braun wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div>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 (<a href="https://en.wikipedia.org/wiki/Fractional_coordinates#In_Crystallography" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fen.wikipedia.org%2Fwiki%2FFractional_coordinates%23In_Crystallography\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHbzwm4_LN3oKNURVRvGegE_pgeg';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fen.wikipedia.org%2Fwiki%2FFractional_coordinates%23In_Crystallography\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHbzwm4_LN3oKNURVRvGegE_pgeg';return true;">https://en.wikipedia.org/<wbr>wiki/Fractional_coordinates#<wbr>In_Crystallography</a>) are followed, and per this thread, I'm not sure whether this is the case.</div><div><br></div><div>Efrem Braun</div><div><br>On Friday, January 31, 2014 at 4:34:37 PM UTC+1, FX Coudert wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">> 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).
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<br>Thanks!
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<br>FX</blockquote></div></div></blockquote></div>