Hi all,
I noticed some strange behaviour while adding a new small chemical
compound to CCPNMR.
I want to include the molecule cholic acid in my CCPNMR assignment,
assign my spectra and use them later for structure calculation in Aria2.
First of all, when I try to select cholic acid (CHD) from the small
chemical compound browser it is greyed out and I cannot download it.
Suggestions for that?
Second, I built cholic acid and used the pdb import and assigned my
spectra - fine.
Third, I noticed I'll need force field parameters for Aria2 and for
quick-and-dirty I used the PRODRG server to generate some. PRODRG
changes the atom names so I had to import my compound again (PDB import)
and assign it again (done).
Now, after some trial and error runs with the same pdb file my atom
names in the atom browser have suddenly changed. Only protons are
affected, e.g. HAA is not found anymore, howewever, the assigned peak
still carries the assignment HAA. Moreover, there are now 4-letter atom
names which do not appear in the uploaded pdb data and the small
compound window. I assume this has something to do with automated
H-assignments of the corresponding heavy atoms?
What I would like to know is: I am 100% certain that I have assigned the
correct atom names - how can they change? Even in earlier project
backups the names have suddenly changed and I do not understand the
reason for that.
How can I delete entries from the small chemical compound list?
And can I assign a three-letter PDB code to my "OTHER" chemical
compound? I'm pretty sure I'll need that later in Aria :)
Help is much appreciated!
Best wishes,
Vanessa
--
Vanessa Granitzka, M.Sc.
Biomolecular NMR-Spectroscopy
NC 5/173
Faculty of Chemistry and Biochemistry
Ruhr-University Bochum
Universitaetsstr. 150
D-44801 Bochum
Tel.: +49 234 32-26246
########################################################################
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
|