Re: [PyMOL] Solid stick between two residues?
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 Sent: Tuesday, September 6, 2022 21:09 To: Timofey Tyugashev ; 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 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.netdata=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=OAqKEUr1ACgF%2FrgK1lQe%2FswrIoeJy6rsDmAkIRaEy94%3Dreserved=0 Unsubscribe: https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=QzrVv6%2FuYKyvSB%2B0y1y4JbtPTCEO18UFfuimnuW3PH0%3Dreserved=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 ___ 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
Re: [PyMOL] Solid stick between two residues?
> On 5 Sep 2022, at 16:39, Bruhn, Matthias wrote: > > 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? Pymol will create a bond if the distance between the hydrogen of this lysine and the aspartate is too short. I guess that the protonation of this protein was not properly done. Florian ___ 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
Re: [PyMOL] Solid stick between two residues?
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 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.netdata=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=OAqKEUr1ACgF%2FrgK1lQe%2FswrIoeJy6rsDmAkIRaEy94%3Dreserved=0 Unsubscribe: https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=05%7C01%7Cjoel.tyndall%40otago.ac.nz%7C8a1a7fcbb53243802a3508da8fbc7829%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637980336904146409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=QzrVv6%2FuYKyvSB%2B0y1y4JbtPTCEO18UFfuimnuW3PH0%3Dreserved=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
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: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Solid stick between two residues?
One possibility is that it could be a duplicated hydrogen atom where each has connectivity to either residue. I can't say for sure without seeing the original file. Best, Jarrett J On Mon, Sep 5, 2022 at 11:37 AM Bruhn, Matthias wrote: > 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 > > > > > > -- > > TWINCORE GmbH I Feodor-Lynen-Str. 7 I 30625 Hannover I > https://www.twincore.de > > Geschäftsführer: Prof. Dr. Ulrich Kalinke > Aufsichtsratsvorsitzender: Prof. Dr. med. Michael P. Manns > HRB 203373, Amtsgericht Hannover > > Hinweise zur Erfüllung unserer Informationspflichten zur Verarbeitung > personenbezogener Daten gemäß Art. 13, 14 DSGVO finden Sie unter: > https://www.twincore.de/datenschutz/ > ___ > 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 > -- *Jarrett Johnson* | Senior Developer, PyMOL ___ 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
