1. Are you sure it is a bond and not merely a rendering artifact with two hydrogens superimposed on each other? Have you tried flipping through rotamers for either side chain to see if this resolves the clash?
1. If it is a "real" bond intended by those who created the model, then there may be information describing it in the pdb header. 1. You can submit your pdb to molprobity. It will give a list of contacts and clashes: http://molprobity.biochem.duke.edu/ ________________________________ From: Joel Tyndall <joel.tynd...@otago.ac.nz> Sent: Tuesday, September 6, 2022 21:09 To: Timofey Tyugashev <tyugas...@niboch.nsc.ru>; pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] Solid stick between two residues? [EXTERNAL SENDER - PROCEED CAUTIOUSLY] I agree with Tim, PyMOL simply adds bonds based on the geometry of the structure. The salt bridge is very close. The "problem" (if any) lies with the crystal structure coordinates -----Original Message----- From: Timofey Tyugashev <tyugas...@niboch.nsc.ru> Sent: Tuesday, 6 September 2022 3:17 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Solid stick between two residues? > Dear pymol users, > does anybody recognize this type of bond and can explain me what this is? It > appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but > for some reason PyMol connects the two amino acids with a stick? > > Kind regards, > Matthias > PyMOL generally draws covalent bonds based on geometric distances between atoms. Probably in this case the salt bridge between two residues was tight enough for the software to mislabel it. _______________________________________________ PyMOL-users mailing list Archives: https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OAqKEUr1ACgF%2FrgK1lQe%2FswrIoeJy6rsDmAkIRaEy94%3D&reserved=0 Unsubscribe: https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QzrVv6%2FuYKyvSB%2B0y1y4JbtPTCEO18UFfuimnuW3PH0%3D&reserved=0 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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