At this stage only the viewing of the molecule is a problem but I
failed to point out that I leave the ChemCompVar to the default input
value ('neutral') upon importing using FormatConverter since I am
simply assuming it is in the free form. Ultimately I want to have
these carbohydrates linked together but at this stage I am content
with simply assigning a free form.
I noticed however that a ChemComp xml file for GalNAc from the
euroCarb database that Wim provided me with contains information for
chemBonds and chemCompVars not present in the one I generated using
FormatConverter which I found confusing but I am not sure this has
anything to do with not being able to view my imported molecule.
Regards,
Henry
On 11 Jul 2010, at 21:12, Rasmus Fogh wrote:
> Dear All,
>
> The error message "No atom coordinates are available for chemical
> compound ..." normally means that the oordinates simply are not
> available in the reference data. This is normal, many ChemComps do
> not have coordinates, and the only difference it makes is that you
> cannot view it in the molecular viewer. The message should be a
> 'warning' rather than an error, tight? Warnings are for things where
> you can safely continue working afterwards.
>
> The second half sounds weird. You can not have a functional
> ChermCOmp without bonds (unless it is somethign like Zn++). Are you
> sure that there is a problem, apart from the fact that you cannot
> view the molecule?
>
> One owuld have to check, but a possible explanation would be taht
> there are no known CHemCompCOords, that this means you cannot view
> the CHemComp in the small molecue viewer, and that *evrything* else
> works as it should.
>
> Someone else would have to check, though, as I do not have time
> before going on holiday.
>
> Yours,
>
> Rasmus
>
> ---------------------------------------------------------------------------
> Dr. Rasmus H. Fogh Email: [log in to unmask]
> Dept. of Biochemistry, University of Cambridge,
> 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
>
> On Thu, 8 Jul 2010, Henry Hocking wrote:
>
>> Hello,
>>
>> I am wanting to add the small compound D-Galactose to my project.
>> First I select Ccp code Gal in Small Compounds and I am told it is
>> not available locally so I accept the download to local database.
>> This downloads "other+Gal
>> +msd_ccpnRef_2007-12-11-10-16-35_00023.xml" file to my ChemComp
>> folder however, nothing gets downloaded to my ChemCompCoord folder
>> and indeed I get the message "No atom coordinates are available for
>> chemical compound Gal". Is this because there are no atom
>> coordinates available to download or that it simply cannot find it
>> in my ChemCompCoord folder?
>>
>> I then tried Import>Single files>Chemical Compounds> pdb on a
>> galactose.pdb file (attached) using FormatConverter. This creates
>> two associated xml files (attached), one in the ChemComp folder and
>> one in ChemCompCoord folder. I can add this compound as a new chain
>> in my Molecular System and all atoms appear in atom browser so in
>> terms of assignment it works, however I cannot visualise it in the
>> Small Compounds molecular viewing window. I noticed that there were
>> no chemBonds info in these xml files and chemCompVarCoords is
>> always _3? Could it be I am missing bond information? Is there a
>> way to import CNS topology files into Analysis? How would one go
>> about generating the necessary bonding information (assuming this
>> is the problem) from an imported pdb file?
>>
>> Cheers,
>>
>> Henry
>>
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