Dear Henry,
We are looking at providing more ChemComps and more ChemCompVars, and
making sur you cna link these carbohydrates.
If the two different GalNAc files are different that is worth taking a
look at. I am off on holiday tomorrow, though, so I'll leave it to my
colleagues.
I think the only reason for the viewing problem is likely to be that the
ChemCompCoords were never enerated in the refernce data, and that the
differences in the ChemComp is another matter.
That is all from me.
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 Mon, 12 Jul 2010, Henry Hocking wrote:
> 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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