Hi Jiri, A low-tech solution that will certainly work, is just to manually show the relevant distances. In coot under measure there is an option to show distances, just by clicking on the two atoms involved.
Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von chemocev marker Gesendet: Samstag, 9. Dezember 2017 16:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Van der waals force Hi Thanks for your good help and I am wondering is there clear way to show these forces like H-bond. I tried KING and can see the VDW radii but not the visual representation. Does coot has any option for this. best Jiri On Fri, Dec 8, 2017 at 8:57 AM, HERMAN VAN TILBEURGH <herman.van-tilbeu...@u-psud.fr<mailto:herman.van-tilbeu...@u-psud.fr>> wrote: jiri, VDW forces are always acting and between any pair of atoms the optimal distance (most favourable interaction energy) depends on the pair of atoms involved in the interaction, but is a big bitter than the sum of atomic radii all the best herman Herman van Tilbeurgh Professor structural biology Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à l'appliqué Institut de Biologie Intégrative de la Cellule - I2BC UMR 9198 CNRS- Université Paris Sud Team: Fonction et Architecture des Assemblages MacroMoléculaires http://www.i2bc.paris-saclay.fr/spip.php?article256<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.i2bc.paris-2Dsaclay.fr_spip.php-3Farticle256&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=VVWto30xREVhv0uIO_VEafCPsMB9i3sakwUMTjBoNoY&s=gGmsG2cs9BqkBu-Er1nFhvTN3cxzLE4i0yyk1D2HdFc&e=> Batiment 430 91405 Orsay France Tel: 33 1 69 15 31 55 fax: 33 1 69 85 37 15 herman.van-tilbeu...@u-psud.fr<mailto:herman.van-tilbeu...@u-psud.fr> Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <klah...@igbmc.fr<mailto:klah...@igbmc.fr>> a écrit : Hello, van der Waals interactions are very weak, this is why we usually speak about van der Waals contacts rather than interactions. These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate a close contact or steric clash of an atomic model under refinement), corresponding to the packing of the van der Waals spheres of the individual atoms. In hydrogen bond interactions, the term “interaction” normally implies sharing a hydrogen atom between two polar residues, for example between the hydroxyl group of a threonine side chain with a carbonyl group of the main chain peptide backbone; in there one should take into account the geometry as well (e.g. ~120°-180° is favorable, 90° is not). Note that some positions such as Calpha-H can be slightly polarized (these contribute to bifurcated H-bonds in beta sheets for example, see e.g. https://www.ncbi.nlm.nih.gov/pubmed/12220491<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_12220491&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=VVWto30xREVhv0uIO_VEafCPsMB9i3sakwUMTjBoNoY&s=weI-inGLqAXhJ_EhaGFFo4ERu_6o45Y3YItvWvc89Po&e=> ). In the context of series of van der Waals contacts between hydrophobic residues there can be additive effects of the weak interactions with then sum up, but in this context one should also consider entropic effects such as de-solvatation which becomes favorable energetically. Hope this helps. Best regards, Bruno ########################################################################### Bruno P. Klaholz Centre for Integrative Biology Institute of Genetics and of Molecular and Cellular Biology 67404 ILLKIRCH FRANCE http://igbmc.fr/Klaholz<https://urldefense.proofpoint.com/v2/url?u=http-3A__igbmc.fr_Klaholz&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=VVWto30xREVhv0uIO_VEafCPsMB9i3sakwUMTjBoNoY&s=65zyao0Xoc2AosXmLz88UG14E4bjRtbZSi1-C4ZnDBk&e=> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of chemocev marker Sent: 08 December 2017 07:55 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Van der waals force Hi I just have a basic question if the Van der waals interaction will exist between the hydrophobic residues or it can also be contributed by the polar residues as well. What distance is required for the Van der waals interaction. best Jiri
