Tried the homologues thing. There are homologues and I've done the fitting, but this is what I consider to be subjective. I'm certain the referee will ask: Given the quality of density for the nucleotide, how certain are the authors that a different fit is not possible? Have other fit poses been considered?
Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, July 23, 2020 1:07 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? Coot is pretty good at fitting known ligands, and unknown ones, too! -------- Original Message -------- On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote: Hi, Can folks suggest programs for objectively docking ATP/ADP molecules into density? Our density is not so good, probably because of occupancy, and we'd like a less subjecting approach for modeling. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=NCJxuuXUzKYpS2Tc2Ny_3kYinX8Cg20Y5D9elTGcnRE&s=cyXoGwvleVJhuJ6PhFggTxLK0WJTnvvxFxlc-U1A0iQ&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=NCJxuuXUzKYpS2Tc2Ny_3kYinX8Cg20Y5D9elTGcnRE&s=cyXoGwvleVJhuJ6PhFggTxLK0WJTnvvxFxlc-U1A0iQ&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
