Re: [ccp4bb] Missing double bonds in the ligand
Thanks Nigel, I meant the mmcif coordinate file format as an alternative to the pdb file. I am now not convinced it contains the bond order etc Alternatively, saving as a .mol2 file should save atom types and bond order From: Nigel Moriarty Sent: Friday, 8 July 2022 12:31 pm To: Joel Tyndall Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Missing double bonds in the ligand 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<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fphenixwebsite_static%2Fmainsite%2Ffiles%2Fnewsletter%2FCCN_2013_01.pdf%23page%3D6=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=b2fkWsdF77efNj%2FGHsKZJwizq%2FwZXC6elTwyl6HULhA%3D=0> 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<mailto: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=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iPFj31dUns0UNyytIR%2B3k15CYHTBqi%2FW%2FXSjCK0jtGY%3D=0> ORCID : orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=woV4FlAu6cCBn1YLMHScdFaesiLF8H5aFZuqeVi7v0M%3D=0> On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall mailto: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 mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Nigel Moriarty Sent: Friday, 8 July 2022 7:47 am To: CCP4BB@JISCMAIL.AC.UK<mailto: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=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=B46a7oKJkysY0BAH9MVj5hsmmNavmdkPmDDCsqnkmzI%3D=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=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=xSoheHtkA8vI65EnwOuIUkqj277TLJMusGiTJU15d68%3D=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<mailto: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=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=iPFj31dUns0UNyytIR%2B3k15CYHTBqi%2FW%2FXSjCK0jtGY%3D=0> ORCID : orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9c43f4426e5142e2c8b608da60792337%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928371203272374%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=woV4FlAu6cCBn1YLMHScdFaesiLF8H5aFZuqeVi7v0M%3D=0> On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten mailto:robbie_joos...@hotmail.com>>
Re: [ccp4bb] Missing double bonds in the ligand
The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do your PDB atom names match the CCD? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] [External] Re: [ccp4bb] Missing double bonds in the ligand
You can make molecule in chemdraw or chemdraw 3d with proper bond order and save it in sdf or .mol format or any other format compatible with schrodinger. Schrodinger should be able to read .sdf or .mol format. Dhiraj From: CCP4 bulletin board on behalf of Nigel Moriarty Sent: Thursday, July 7, 2022 7:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [External] Re: [ccp4bb] Missing double bonds in the ligand 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<http://CCI.LBL.gov> ORCID : orcid.org/-0001-8857-9464<https://orcid.org/-0001-8857-9464> On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall mailto: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 mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Nigel Moriarty Sent: Friday, 8 July 2022 7:47 am To: CCP4BB@JISCMAIL.AC.UK<mailto: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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=W1W38k1ojjAqhp3ZjM81dMP86UMlp8bnnOYLg%2Bnk5AU%3D=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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=MuwAXaUsqCI4G6yAyVJimLn3I2JoX7JcFWlx4zIGFIE%3D=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<mailto: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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=qFlMWmLOXzftylRuD%2BaySZgplAegttraaWnZA9Uaccw%3D=0> ORCID : orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VXj9S5lltBHJubLfsQrPhvfTz8eOdhXwhOrtn7oCLHw%3D=0> On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten mailto: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" mailto: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 P
Re: [ccp4bb] Missing double bonds in the ligand
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/-0001-8857-9464 On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall wrote: > Does the Schrodinger software read a .cif file? The bond order should be > embedded in there. > > > > *From:* CCP4 bulletin board *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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=W1W38k1ojjAqhp3ZjM81dMP86UMlp8bnnOYLg%2Bnk5AU%3D=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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=MuwAXaUsqCI4G6yAyVJimLn3I2JoX7JcFWlx4zIGFIE%3D=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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=qFlMWmLOXzftylRuD%2BaySZgplAegttraaWnZA9Uaccw%3D=0> > > ORCID : orcid.org/-0001-8857-9464 > <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VXj9S5lltBHJubLfsQrPhvfTz8eOdhXwhOrtn7oCLHw%3D=0> > > > > > > On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten > 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" > 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
Re: [ccp4bb] Missing double bonds in the ligand
Does the Schrodinger software read a .cif file? The bond order should be embedded in there. From: CCP4 bulletin board 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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=W1W38k1ojjAqhp3ZjM81dMP86UMlp8bnnOYLg%2Bnk5AU%3D=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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=MuwAXaUsqCI4G6yAyVJimLn3I2JoX7JcFWlx4zIGFIE%3D=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<mailto: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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=qFlMWmLOXzftylRuD%2BaySZgplAegttraaWnZA9Uaccw%3D=0> ORCID : orcid.org/-0001-8857-9464<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F-0001-8857-9464=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VXj9S5lltBHJubLfsQrPhvfTz8eOdhXwhOrtn7oCLHw%3D=0> On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten mailto: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" mailto: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<mailto: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<mailto:amara...@purdue.edu> Email 2: anilmarap...@gmail.com<mailto: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=1<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7Ca5e0b49c210e4696b81b08da605198a8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637928201266212076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=qCEjT8kiKSV2n%2BMFyJ0D6cqGN5Ob2EIWfDxI7XuLSts%3D=0> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww
Re: [ccp4bb] Missing double bonds in the ligand
Further reading https://en.wikipedia.org/wiki/The_Treachery_of_Images https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10 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/-0001-8857-9464 On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 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" > 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: > [image: image.png] > > 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. > [image: image.png] > > When we load the same PDB file into pymol and look at the ligand it shows > correctly > [image: image.png] > > > 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 * > *Email 2: 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=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Missing double bonds in the ligand
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,RobbieOn 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 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 correctlyWe 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.eduEmail 2: 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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
