Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, Here are those references: for CH...O hydrogen bonds I'd recommend our review: "Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function" (2012) http://www.jbc.org/content/287/50/41576.full for chalcogen bonds, I don't know of a great recent review, but this recent article

Re: [ccp4bb] Atom clashes in active site?

Hi Scott, That would be great if you have some references handy? Thanks very much, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz

Re: [ccp4bb] Atom clashes in active site?

Hi Pavel, That worked a treat! Thanks again for your help, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Tue, Dec 20, 2016 at 3:18 PM, Pavel Afonine

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, Based on the atoms and distances you are mentioning, these don't sound like steric clashes, but like a chalcogen bond between the S and O atoms, and CH...O hydrogen bonds between the O and CH3. These are common and well-accepted interactions, but unfortunately aren't usually treated as

Re: [ccp4bb] Atom clashes in active site?

Hi Pedro, quick answer: no. Longer answer: see article "13 typical occupancy refinement scenarios and available options in phenix.refine" here: http://phenix-online.org/newsletter/ Pavel On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias wrote: > Hi Pavel, > > If the

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, One of the atoms should be in altconf A and the other in B. Otherwise the problem remains. Pedro Às 01:48 de 20/12/2016, Andrew Marshall escreveu: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein

Re: [ccp4bb] Atom clashes in active site?

Hi Pavel, If the occupancies are 1 does phenix still refine them? Anyway, they can be explicitly fixed if necessary. Pedro Às 03:00 de 20/12/2016, Pavel Afonine escreveu: > Hi Perdo, > > technically this should work too with the caveat that non-blanc altid > will trigger occupancy refinement

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, yes, exactly as you describe: set distance_ideal to a meaningful value (approx. distance between density peaks, doesn't have to be very accurate), and set sigma to some large number, say 1 or so. Pavel On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall <

Re: [ccp4bb] Atom clashes in active site?

Hi Pavel, To define a weak bond, would you use "geometry_restraints.edits { ... bond {... " , and just set a rough distance_ideal and a very high sigma (like say 5A)? Or are you referring to something different? Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of

Re: [ccp4bb] Atom clashes in active site?

Hi Perdo, technically this should work too with the caveat that non-blanc altid will trigger occupancy refinement for corresponding atoms which may not be desired. Pavel On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias wrote: > Hi Andrew, > > The simplest way would be to

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, you can define a weak bond between clashing atoms which will disable repulsion. A weak bond should not introduce any bias. Pavel On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall < andrew.c.marsh...@adelaide.edu.au> wrote: > Hi all, > > I have a structure of a condensing enzyme with

Re: [ccp4bb] Atom clashes in active site?

Could this be a covalent interaction? Difficult to judge without seeing anything From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew Marshall Sent: Tuesday, 20 December 2016 2:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Atom clashes in active site? Hi all

Re: [ccp4bb] Atom clashes in active site?

Hi all, Thank you for your suggestions. I tried the pdb file edit (making the offending atoms of both the ligand and the protein 'B' altconf), but it didn't seem to make any difference to their positions after a single round of refinement..? The atoms in the active site concern two acetyl groups

[ccp4bb] AW: [ccp4bb] Atom clashes in active site?

[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Andrew Marshall Gesendet: Montag, 19. Dezember 2016 06:39 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Atom clashes in active site? Hi all, I have a structure of a condensing enzyme with substrate bound. The active site is very tight, requiring some

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, The simplest way would be to place the "offending" atoms in separate conformers as used to refine alternate conformations. This is a 1-letter code that goes just before the 3-letter residue name: > ATOM139 SG *B*CYS A 21 -20.620 4.518 34.501 0.39 > 12.23 AS

[ccp4bb] Atom clashes in active site?

Hi all, I have a structure of a condensing enzyme with substrate bound. The active site is very tight, requiring some of the substrate atoms to clash with a catalytic cysteine. This means that although the substrate fits the density nicely upon manual real-space refinement, phenix recognises the