Thanks everyone. I did two things:
1. Extract the MW from the cif file as suggested by David (see below)
2. I extracted the RNA sequence from the cif file and ran it through an
oligo calculator with ssRNA as the option
Both give similar results.
Best wishes,
Reza
Reza Khayat,
There is a CCP4 basic program rwcontents
Run it as
rwcontents xyzin rna.pdb
It lists no_of_C m no_of_O etc.. and sums their mass
If you have the H atoms in the pdb that will give you the total mass.
If not you will have to estimate the no of H yourself..
Eleanor
On Fri, 16 Nov 2018 at 16:46,
Dear Reza,
The calculated molecular weight for each molecule in a PDB entry is
given in the archive PDBx/mmCIF file. The weight in Daltons is given in
the _entity.formula_weight category. Please see
http://www.ebi.ac.uk/pdbe/entry-files/4tna.cif for an example file.
Kind Regards,
David
I’m guessing you need to be closer than ~320 atomic mass units per
ribonucleobase? (Which neglects modified bases and counter ions and assumes 25%
each of ACGU?)
On Nov 16, 2018, at 10:19 AM, Reza Khayat
mailto:rkha...@ccny.cuny.edu>> wrote:
Hi,
I’m not an RNA person. Can anyone suggest a
Hi,
I'm not an RNA person. Can anyone suggest a method to calculate the mass of a
RNA PDB? I'd like the protons to also be considered in the calculation. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
85 Saint Nicholas Terrace,
