Re: [ccp4bb] RNA pdb molecular weight
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, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, November 16, 2018 12:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] RNA pdb molecular weight 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, David Armstrong mailto:dav...@ebi.ac.uk>> wrote: 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ebi.ac.uk_pdbe_entry-2Dfiles_4tna.cif&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5itxEGXDI6EW8_C_MVWsmgoRHhNnrOxgjPKbNUqqCzQ&s=nYiEO2JLKYNAkliZUFwcaU3u07gcmV5ow99_BJl3KhE&e=> for an example file. Kind Regards, David On 16/11/18 16:19, Reza Khayat wrote: 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, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5itxEGXDI6EW8_C_MVWsmgoRHhNnrOxgjPKbNUqqCzQ&s=wFjZkIMrlyTPrQL2Ru2KdEVYyDSeelB34KTeiS9qvz0&e=> 212-650-6070 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5itxEGXDI6EW8_C_MVWsmgoRHhNnrOxgjPKbNUqqCzQ&s=qNuYPtejzx6z_s-sGGpeW1kJ7kX8BePZgNYE5OlAitk&e=> -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5itxEGXDI6EW8_C_MVWsmgoRHhNnrOxgjPKbNUqqCzQ&s=qNuYPtejzx6z_s-sGGpeW1kJ7kX8BePZgNYE5OlAitk&e=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5itxEGXDI6EW8_C_MVWsmgoRHhNnrOxgjPKbNUqqCzQ&s=qNuYPtejzx6z_s-sGGpeW1kJ7kX8BePZgNYE5OlAitk&e=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] RNA pdb molecular weight
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, David Armstrong wrote: > 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 > > On 16/11/18 16:19, Reza Khayat wrote: > > 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, CDI 2.318 > > New York, NY 10031 > > http://www.khayatlab.org/ > > 212-650-6070 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > -- > David Armstrong > Outreach and Training Coordinator > PDBe > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD UK > Tel: +44 1223 492544 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] RNA pdb molecular weight
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 On 16/11/18 16:19, Reza Khayat wrote: 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, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] RNA pdb molecular weight
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 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, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] RNA pdb molecular weight
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, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
