Re: [PyMOL] Solid stick between two residues?

[Kelvin B. L. <Kel...@ug...>]

  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 <joe...@ot...>
Sent: Tuesday, September 6, 2022 21:09
To: Timofey Tyugashev <tyu...@ni...>; pym...@li... <pym...@li...>
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 <tyu...@ni...>
Sent: Tuesday, 6 September 2022 3:17 PM
To: pym...@li...
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.


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