Joel You'll need to be more specific than ".cif" files. CIF can be used for models, data and restraints. Read more here.
http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6 If you are referring to the restraints CIF, it is possible but I'm not sure which software uses it. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > Does the Schrodinger software read a .cif file? The bond order should be > embedded in there. > > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Nigel > Moriarty > *Sent:* Friday, 8 July 2022 7:47 am > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Missing double bonds in the ligand > > > > Further reading > > > > https://en.wikipedia.org/wiki/The_Treachery_of_Images > <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FThe_Treachery_of_Images&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=W1W38k1ojjAqhp3ZjM81dMP86UMlp8bnnOYLg%2Bnk5AU%3D&reserved=0> > > > > > https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10 > <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fphenix-online.org%2Fphenixwebsite_static%2Fmainsite%2Ffiles%2Fnewsletter%2FCCN_2016_01.pdf%23page%3D10&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MuwAXaUsqCI4G6yAyVJimLn3I2JoX7JcFWlx4zIGFIE%3D&reserved=0> > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : nwmoria...@lbl.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > <https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.lbl.gov%2F&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qFlMWmLOXzftylRuD%2BaySZgplAegttraaWnZA9Uaccw%3D&reserved=0> > > ORCID : orcid.org/0000-0001-8857-9464 > <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0001-8857-9464&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VXj9S5lltBHJubLfsQrPhvfTz8eOdhXwhOrtn7oCLHw%3D&reserved=0> > > > > > > On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten <robbie_joos...@hotmail.com> > wrote: > > Dear Anil, > > > > Bond orders are not captured in PDB files explicitly. The way bonds are > shown depends on the program and possibly additional information sources > (i.e. molecular restraint or topology files). > > So this is just a "problem" with Schrödinger. > > > > Cheers, > > Robbie > > > > On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" <anilmarap...@gmail.com> > wrote: > > Dear CCP4 Users, > > We are working on a ligand-bound structure and would like to look at > protein-ligand interactions using Schrodinger. > > Molecule structure is: > > When we load the ligand-fitted PDB file into Schrodinger, the molecule > appears to be flat like it should be in the structure but it removed all > the double bonds in the ligand where the above shown original molecular > structure has double bonds in it. > > When we load the same PDB file into pymol and look at the ligand it shows > correctly > > > > We would appreciate if any insight or suggestions for why this may be > happening and how to ensure the ligand shows properly when the PDB is > loaded into Schrodinger. Would this be an issue with Schrodinger software > or with the PDB file? > > I can be available by direct email for troubleshooting at > amara...@purdue.edu. > > > > -- > > > *Anil Kumar Marapaka, Ph.D. Post-Doctoral Research Associate * > > *Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),* > > *Purdue University, West lafayette,* > > *Indiana-47907, USA.* > > *Mobile 1: +1-765-409-6245 (USA)* > > *Mobile 2: +91-995-998-5571 (India)* > > *Email 1: amara...@purdue.edu <amara...@purdue.edu>* > > *Email 2: anilmarap...@gmail.com <anilmarap...@gmail.com>* > > > > > ------------------------------ > > 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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qCEjT8kiKSV2n%2BMFyJ0D6cqGN5Ob2EIWfDxI7XuLSts%3D&reserved=0> > > > > > ------------------------------ > > 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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qCEjT8kiKSV2n%2BMFyJ0D6cqGN5Ob2EIWfDxI7XuLSts%3D&reserved=0> > > > ------------------------------ > > 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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qCEjT8kiKSV2n%2BMFyJ0D6cqGN5Ob2EIWfDxI7XuLSts%3D&reserved=0> > ######################################################################## 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/
