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
<[email protected]>wrote:
> 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" <[email protected]> 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...
