The executable "coot" is really a wrapper shell script for "coot-real", which is the coot binary.
The shell script in essence sets up the environment in which coot runs.
The relevant variable for finding the coot refmac dictionary (library) directory is called $COOT_REFMAC_LIB_DIR
Where these point to will be different for different installations.
For my OS X pre-built coot, it looks like this:
cat /usr/local/bin/coot
#!/bin/sh -f
source /Library/Coot/bin/init.sh
export COOT_REFMAC_LIB_DIR=/Library/Coot/share/coot/lib
export COOT_PYTHON_DIR=/Library/Coot/share/coot/python
export COOT_SBASE_DIR="$CCP4/share/sbase"
export PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library/Coot/lib/python2.7/site-packages/gtk-2.0:/Library/Coot/share/coot/python:$PYTHONPATH
/Library/Coot/bin/coot-real "$@"
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax)
email: [log in to unmask]
On Mar 29, 2012, at 8:55 AM, Longfei Wang wrote:
> Hi William,
>
> Thank you for your suggestion. Another question, how to import the whole
> dictionary into coot?
>
> Best
> Longfei
>
> On Tue, Mar 27, 2012 at 5:09 PM, William G. Scott <[log in to unmask]> wrote:
>
>> Try this:
>>
>>
>> http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
>>
>> It seems to behave with nucleic acids correctly, at least in my hands.
>>
>> There is also a newer one (March 10, 2012). Maybe you should try that
>> first.
>>
>>
>> http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.35.tar.gz
>>
>>
>> William G. Scott
>> Professor
>> Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> 228 Sinsheimer Laboratories
>> University of California at Santa Cruz
>> Santa Cruz, California 95064
>> USA
>>
>> phone: +1-831-459-5367 (office)
>> +1-831-459-5292 (lab)
>> fax: +1-831-4593139 (fax)
>> email: [log in to unmask]
>>
>> On Mar 27, 2012, at 1:29 PM, Longfei Wang wrote:
>>
>>> Hi there,
>>>
>>> I've received a bug report about coot. I think this is a good place to
>>> report.
>>> Here is the summary of the problem. If open a molecule and try to build a
>>> new nucleotide, Coot crashes. This happened for the version of Coot 3936,
>>> both in Linux and WinCoot. A labmate suspects that there are library
>> issues
>>> with regards to PDB version between Coot and REFMAC. An additional issue:
>>> Protein residues with hydrogens present can be real space refined in
>> Coot.
>>> However, nucleic acid residues with hydrogens present cannot be real
>> space
>>> refined in Coot. Attempting to do this results in exploding hydrogens.
>>>
>>>
>>> Best
>>> Longfei
>>>
>>> --
>>> *Longfei Wang
>>> *
>>> Postdoctoral Fellow
>>> Harvard Medical School
>>> 250 Longwood Ave
>>> Boston, MA 02115
>>
>>
>
>
> --
> *Longfei Wang
> *
> Postdoctoral Fellow
> Harvard Medical School
> 250 Longwood Ave
> Boston, MA 02115
|