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Dear UltraScan SOMO Users,<br><br>
Peter Zipper has recently discovered some errors in the distributed
version of the somo.residue file of US-SOMO. I paste below his
comments:<br><br>
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. <br>
In detail: <br>
in adenine one hydrogen is missing at C2; <br>
in cytosine one hydrogen is missing at C5 and one at C6; <br>
in guanine one hydrogen is missing at N1 and two are missing at N2;
<br>
in uracil one hydrogen is missing at N3, C5, and C6, respectively; <br>
in thymine one hydrogen is missing at N3 and one at C6. <br>
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.<br><br>
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
<font color="#0000FF"><u>http://somo.uthscsa.edu)</u></font>. 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.<br><br>
Best wishes to you all, and happy hydrodynamic/SAS modeling with
US-SOMO!<br><br>
Mattia<br><br>
<br><br>
<br>
<x-sigsep><p></x-sigsep>
Dr. Mattia Rocco<br>
Biopolimeri e Proteomica<br>
IRCCS Azienda Ospedaliera Universitaria San Martino - IST - Istituto
Nazionale per la Ricerca sul Cancro<br>
c/o Centro per le Biotecnologie Avanzate (CBA)<br>
Largo Rosanna Benzi 10<br>
I-16132 Genova, Italy<br><br>
Phone: +39-0105737-310<br>
Fax: +39-0105737-325<br>
e-mail: mattia.rocco@istge.it<br><br>
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