Frederick J. Hollander wrote:
> Hello to all --
> Heard about and saw this marvelous program at the ACA meeting last summer
> and finally got a round tuit.
> I downloaded coot, 0.3.3 version because I couldn't seem to get a
> more modern version to work on my Centos5 Linux. (I may try again later
> with an ubuntu 0.4.x version now that I know that the 0.3.3. works.)
>
Yes, I recently saw the problem with CentOS too. CentOS does something
strange with the dependency libraries.
I had to make links to libxxx.so, IIRC. But other than that it was fine.
> It starts up fine, I can read in a .res file and it shows the cell and
> the symmetry and all is good until I attempt to read in the .fcf file
> created with the "acta" command in shelxl. I have attached as a text file
> (err.txt) the messages that appear in the mother window. Nothing appears in
> the visualization window and no map is calculated.
> I inspected the fcf file and it _looks_ OK. I have attached a file with
> the first lines in it as header.fcf.
> Given that I just got started, the probability of user error is high, so
> I call on you for assistance and correction.
>
There is not much room for user error. My analysis is that the cif
parser chokes on the _refln_observed_status part of the record (I don't
know why).
I'd imagined that fcf files would have
_refln.F_meas
_refln.F_meas_sigma
_refln.F_calc
_refln.phase_calc
You do not have _refln.phase_calc. (I'd also imagine that shelxl is
better at calculating phases than Coot is.) I'd guess that this is
addressed by the FMAP 2 command to which Dale refered (I don't know really).
clipper (which handles the symmetry in coot) does indeed grok your
symmetry symbols:
got cell from cif: Cell (14.277,53.0023,16.7955, 90,108.616, 90)
Found symmetry equivalents.....
INFO:: Found cif symmetry operator x, y, z
INFO:: Found cif symmetry operator x+1/2, -y+1/2, z+1/2
INFO:: Found cif symmetry operator -x, -y, -z
INFO:: Found cif symmetry operator -x-1/2, y-1/2, -z-1/2
INFO:: space_group from symm ops in cif: P 1 21/n 1
Resolution limit set to 0.96643
import_hkl_info read 14 hkls
Hope this is of some help.
Paul.
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