I get the dirty mmcif message in the terminal window.
This is the message I get:
dirty mmCIF file? /Users/.../r-pento.cif
Bad CIFRC_Ok on ReadMMCIFFile
init_refmac_mon_lib /Users/.../r-pento.cif had no bond restraints
Thanks!
On Wed, Mar 18, 2009 at 11:08 AM, Sangeetha Vedula
sangeetha...@gmail.comwrote:
Hello
I am experiencing the same problem as the person who emailed this initially
(pasted below; the entire thread that I found in the archive is pasted after
my email, for reference).
*Hello, *
* I modelled a small molecule with the dundee prodrg server *
* and can read the pdb without any problems into Coot. But *
* when I try to import the cif.dictionary I only get the *
* message: ooops, cif dictionary contains no restraints. (to *
* create this file I copied and pasted the refmac5 file from *
* prodrg into a new file). *
* Can anyone please explain to me what this error message *
* means? *
Reading the responses, it appears that there are some empty loops in the
cif file generated by proDRG that this user had to remove and all was well.
However, I looked at my cif file and none of the loops are empty. When I
compare this file to one that coot accepts, the only difference is that the
coot-accepted version has xyz values for the ligand:
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
The last three lines are absent in proDRG cif file. I removed these lines
as well as the coordinates from the coot-accepted version but coot reads the
file anyway. Clearly, this isn't the problem. What could it be?
I am unable to use sketcher/libcheck or a refmac5 generated cif file for
the ligand. Sketcher/libcheck won't work (but that is a different problem,
which I have to fix separately, as sketcher doesn't recognize even a plain
old cyclohexanol), and refmac5 adds and deletes double bonds randomly, and
messes the geometry up completely.
Any help with the proDRG cif file will be appreciated!!
Thanks,
Sangeetha.
From: Paul Emsley
Date: Thu Dec 01 2005 - 04:29:05 GMT
On Wed, 2005-11-30 at 19:14 -0500, Joel Bard wrote:
* Usually this means that there is some sort of little error in the *
* format of the cif file and it gives up reading before it gets to the *
* restraints. *
Exactly. Mareike send me her cif file and there was indeed a syntax
error in it. The thing to look for is dirty mmCIF file? xxx.cif
in the console.
We've had this problem before in fact. IIRC we contacted the authors of
PRODRG about it - they seem not to have fixed the problem yet.
To fix PRODRG cif files then:
At the end of PRODRG cif files we can get empty geometry description
loops. In this case we have:
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
#
# ---
#
This causes the mmdb's mmCIF parser to choke. Simply remove these
lines and the file can be parsed.
Paul.
* You can try manually comparing it with a cif file that coot likes. An *
* easier thing to do might be to read your monomer (as a pdb) into the *
* ccp4 monomer sketcher and have it generate a new cif file. Coot *
* usually likes the cif files from the monomer sketcher. *
* *
* Good Luck, *
* *
* Joel *
* *
* Mareike Kurz m.k...@imb.uq.edu.au 11/30/2005 5:41:26 PM *
* *
* *
* Hello, *
* I modelled a small molecule with the dundee prodrg server *
* and can read the pdb without any problems into Coot. But *
* when I try to import the cif.dictionary I only get the *
* message: ooops, cif dictionary contains no restraints. (to *
* create this file I copied and pasted the refmac5 file from *
* prodrg into a new file). *
* Can anyone please explain to me what this error message *
* means? *
I suppose that such a question means that i) it should be in the FAQ and
ii) I should propagate the dirty cif message to the gui. Hmmm...
