Hi,
Most of the errors in your listing are normal for Coot. It decides
the file format by trying to read the file in a bunch of different
formats and if there is a failure it simply tries another. Eventually
it figures out, correctly, that you have a .fcf file and starts
to process it. Coot does not read .fcf files itself so first it
converts the file to a .fcf.cif format and reads that. This step
too seems to be working.
Your problem is in reading the .fcf.cif file. Coot can't read
the cell and symmetry information from that file. You should
take a look at that file's headers to see if there is anything
strange in there.
I see that your space group is P21/n. Since Coot is aimed at
macromolecules it may not work properly with that space group.
One of the more knowledgeable people in the list could perhaps
let us know for sure.
There are two issues with P21/n. Coot may not know how to
calculate an FFT for that space group, and your .fcf file does
not include any phases. Of course, with your space group all
the phases will be zero (assuming the amplitude can be negative)
so you don't need phases, but I expect that Coot is not ready
for such space saving tricks.
I have always used FMAP 2 to calculate my .fcf's. Is that
how you are doing it? If so then Shelxl, with your space group,
is writing a very different .fcf file than Coot is used to. It
might be simplest for you to expand your molecule to P21 and
let Coot work in familiar territory.
Dale Tronrud
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.)
> 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.
>
> Frederick Hollander
> X-ray Crystallographic Laboratory, College of Chemistry, University of
> California at Berkeley, Berkeley, CA 94720, USA.
> [log in to unmask]
> http://xray.cchem.berkeley.edu
>
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