[RASMB] Mistakes in US-SOMO reference tables

[Mattia Rocco]

Dear UltraScan SOMO Users,

Peter Zipper has recently discovered some errors in the distributed version 
of the somo.residue file of US-SOMO. I paste below his comments:

In my recent tests using Ultrascan 9.9 Rev. 1831 I encountered a 
discrepancy between the molecular weights of RNA chains as reported by 
Ultrascan and the results obtained from my programs. When I analyzed the 
discrepancy in more detail I could localize its origin very soon. I 
detected that in the Ultrascan file somo.residue the nucleobases are not 
represented with the correct number of hydrogen atoms but are lacking 
between 1 and 3 hydrogens.
In detail:
in adenine one hydrogen is missing at C2;
in cytosine one hydrogen is missing at C5 and one at C6;
in guanine one hydrogen is missing at N1 and two are missing at N2;
in uracil one hydrogen is missing at N3, C5, and C6, respectively;
in thymine one hydrogen is missing at N3 and one at C6.
I do not understand why these hydrogens are not taken into account in your 
somo.residue file. But perhaps you can give me a simple explanation.

Matter of fact, Peter was absolutely correct, and I take full 
responsibility for that, it was sloppy entering on my part. I apologize for 
any inconvenience this might have caused, and I am grateful to Peter for 
having uncovered these mistakes. I have now corrected them, and new 
versions of the somo.residue and somo.atom files are made available for 
downloading (see http://somo.uthscsa.edu). Beside the corrections,the new 
somo.residue now contains hydroxyproline, more alternate names for 
nucleotides (wish there was a strict convention on PDB atoms naming that 
all software adhered to... ), Triton X-100 (with different chain lengths), 
Mn and Mg ions, AMP, ATP, ATF, and explicit water of hydration (for SAXS 
simulations, the structures must be hydrated using available external 
programs). If you have coded for new atoms/residues using US-SOMO, you 
should pick those bits from your current tables and add them to the new 
tables, an operation that can be done using any text editor. However, 
should anyone feel uneasy to do so, you can send me your somo.atom and 
somo.residue files, and I will insert the extra residues/atoms in either 
the current distribution, or, if you want to keep it private, I will email 
the corrected files back to you.

Best wishes to you all, and happy hydrodynamic/SAS modeling with US-SOMO!

Mattia





Dr. Mattia Rocco
Biopolimeri e Proteomica
IRCCS Azienda Ospedaliera Universitaria San Martino - IST - Istituto 
Nazionale per la Ricerca sul Cancro
c/o Centro per le Biotecnologie Avanzate (CBA)
Largo Rosanna Benzi 10
I-16132 Genova, Italy

Phone: +39-0105737-310
Fax: +39-0105737-325
e-mail: mattia.rocco at istge.it

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