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/0000-0001-8857-9464 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: > [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 <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 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
