Hi Wim,
Thank you so much. I'm afraid there are some more problems:
1. cyana2 and later do no longer have the charge in the residue name. So GLU,ASP,LYS,ARG and not GLU-,ASP-,LYS+,ARG+ .
2. The N-terminal amide is just N and H (although a valence problem) not N, H1, H2, H3
3. The C-Term has just an O not O' and O'' (The present version of CYANA does not allow for special endgroups at the N- or C-terminus of the polypeptide chain. http://www.cyana.org/wiki/index.php/Residue_library_file )
4. The 5'-end of RNA has an phosphate in cyana library. If we have a structure without 3'phosphate one would have to remove the HO5' when exporting with cyana naming.
5. The 3'end of RNA does not have an HO3' in cyana --> have to remove.
Applying all this I can read the pdb in cyana
Regards
Markus
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Blatter Markus
ETH Zurich
Institute of Molecular Biology & Biophysics
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-----Original Message-----
From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Wim Vranken
Sent: Montag, 5. November 2012 16:28
To: [log in to unmask]
Subject: Re: exporting coordinates in cyana format
Hi Markus,
> 1. Although I select all 20 models only one model is written
Thanks for sending me the file - the format is what the FC considers as 'pseudoPdb', which encompasses any kind of PDB formatted file which is not officially from the PDB (and so does not have full header information). Dyana (and Cyana?) used to have its own format for coordinates, this is what the FC will try to write out if you select that format for the coordinates.
In any case, *after* updating from the server (thanks Wayne!), try:
Export->PseudoPdb->Coordinates
and select the 'CYANA2.1' naming system. The FC should write out a file with HIST, RADE, . residue names. Let me know if that works.
Best regards,
Wim
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Dr. Wim Vranken [log in to unmask]
Jean Jeener NMR Center, Structural Biology Brussels - VUB Molecular Recognition Unit, Department of Structural Biology - VIB
Building E, 5th Floor, E5.05
Pleinlaan 2, 1050 Brussels
Belgium
Tel: +32 (0)2 6291025 http://more.vub.ac.be/
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