Re: [ccp4bb] Phenix / Coot neutron queries.
Hi Jonathan, send me files off list and I will have a look. From your description it isn't clear to me what the problem is. You need to add H or D or H and D only once (and phenix.ready_set is the right tool to do it!), then just do refinement and all should work. Coot indeed may not play well with some of exotic scenarios but so far that hasn't been a huge issue as phenix.refine can handle this mostly automatically. Pavel On Thu, Jun 20, 2019 at 5:44 PM Jonathan Cooper < 0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: > I am trying to refine a neutron structure for someone and I have come > across a couple of things which I need help with. > > I am struggling to get the occupancy refinement of the > hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of > them get deleted by readyset but the trick seems to be to call them > hydrogen in the atom name field yet say they are D in the element symbol > field. Is that the best way? Also, readyset seems to delete the D's in D2O? > > I would appreciate any tips on what is the best 'strategy' for refining > with neutron data i.e. reciprocal- versus real-space or both, etc, because > my R-free just seems to go up. > > Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it > stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond > angle from ~110 to about 120 degrees so it seems to be picking-up wrong > geometry info from somewhere. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Phenix / Coot neutron queries.
Dear Jonathan, since structure for neutron data are usually pre-refined and you are only interested in the small print, you can also use SHELXL for refinement (https://doi.org/10.1107/S1600576713027659). That gives you full control over what you want to achieve. With PDB2INS (https://doi.org/10.1107/S1600576719005478) it is very simple to get the starting ins-file from a PDB entry (it may even take care of the NEUT command). Coot works pretty well with SHELXL files, too. Best, Tim Am 21.06.2019 00:44, schrieb Jonathan Cooper: I am trying to refine a neutron structure for someone and I have come across a couple of things which I need help with. I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of them get deleted by readyset but the trick seems to be to call them hydrogen in the atom name field yet say they are D in the element symbol field. Is that the best way? Also, readyset seems to delete the D's in D2O? I would appreciate any tips on what is the best 'strategy' for refining with neutron data i.e. reciprocal- versus real-space or both, etc, because my R-free just seems to go up. Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond angle from ~110 to about 120 degrees so it seems to be picking-up wrong geometry info from somewhere. - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Phenix / Coot neutron queries.
On 20/06/2019 17:44, Jonathan Cooper wrote: I am trying to refine a neutron structure for someone and I have come across a couple of things which I need help with. I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of them get deleted by readyset but the trick seems to be to call them hydrogen in the atom name field yet say they are D in the element symbol field. Is that the best way? Also, readyset seems to delete the D's in D2O? I would appreciate any tips on what is the best 'strategy' for refining with neutron data i.e. reciprocal- versus real-space or both, etc, because my R-free just seems to go up. Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond angle from ~110 to about 120 degrees so it seems to be picking-up wrong geometry info from somewhere. Not helpful but related: It has been a while since I looked at this, I recall that Coot and Phenix disagree about neutron-refinement restraints usage on a quite fundamental level which means they practically don't work together. (I'd like them to work together, but this issue has not reached the top of the todo list.) Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Phenix / Coot neutron queries.
I am trying to refine a neutron structure for someone and I have come across a couple of things which I need help with. I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of them get deleted by readyset but the trick seems to be to call them hydrogen in the atom name field yet say they are D in the element symbol field. Is that the best way? Also, readyset seems to delete the D's in D2O? I would appreciate any tips on what is the best 'strategy' for refining with neutron data i.e. reciprocal- versus real-space or both, etc, because my R-free just seems to go up. Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond angle from ~110 to about 120 degrees so it seems to be picking-up wrong geometry info from somewhere. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
