Hi Christina,
I think the tutorial on the ARIA website is now superseded by better functionality in both CCPN analysis and ARIA 2.3 that doesn't require the modified ChemComps. (The error you're seeing is because the ChemComp naming system got stricter at some point and the file name has to be very particularly constructed with "+" as the separator). I'm sure this is written up somewhere, but I can't lay my hands on it just now.
With Analysis 2.4 you should archive your project and then create a new version of your molecule and deprotonate the Zn ligand residues before it gets locked - keep this possible by keeping “Destination Mol System:” set to "<None>".
Add a template molecule for your Zn ion.
Create a MolSystem with a new chain from your modified protein template (e.g. chain A) and a new Zn ion or ions in the same MolSystem (e.g. chain Z).
Transfer your assignments to the new protein chain. Regenerate your restraints if you're using analysis rather than ARIA to make them.
In ARIA 2.3 specify the new molecular system and choose the option containing both chains.
Now add Zinc Coordination entries for each Zinc site and enter the appropriate residue numbers from chains Z and A.
I think that's it.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
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The University of Glasgow, charity number SC004401
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From: CcpNmr software mailing list [[log in to unmask]] on behalf of Christina Redfield [[log in to unmask]]
Sent: 24 July 2018 17:56
To: [log in to unmask]
Subject: Re: Zinc ion coordination in structure calculations
Hello,
I'm trying to use CCPN Analysis and Aria to calculate the structure of a zinc containing domain. I've followed the quite old instructions on the Aria web site about modifying Aria and CCPN Analysis but I'm getting the following error when I try to load a project:
/Users/christinaredfield/Programs/ccpnmr_2/ccpnmr2.2/data/ccp/molecule/ChemComp/CYO.xml lacks field separators +
I've put the CYO.xml and CZN.xml files into a slightly different directory from the one suggested in the Aria tutorial because the directory they suggest doesn't exist. Have I put the files in the wrong place? Do they need to be renamed or edited?
Others have posted similar messages in the past relating to this error message but I couldn't find the answer posted by anyone.
Thanks in advance for any help.
Best wishes,
Christina
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