RE: OMIT-map
This seems to be another name for a difference Fourier map, calculated from F_obs - F_calc; the term omit map being used in the macromolecular community. It shows scattering density missing in the model, i.e. from omitted atoms. *Von:* davide.lev...@gmail.com *Gesendet:* Sonntag, 18. August 2024 um 8:01 AM MESZ *An:* rietveld_l@ill.fr *Betreff:* OMIT-map Dear All, I received the answer from a referee for an article about an organic structure I determined. The referee asks for An omit map (including contour level) for all ligand-bound crystal structures. I searched about omit-map, but I did not find a clear how to calculate this map. Can anyone send me something about the omit-map or explain me how to obtain these maps with GSAG or TOPAS? Thanks Davide Levy ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the subject with no body text The Rietveld_L list archive is onhttp://www.mail-archive.com/rietveld_l@ill.fr/ ++ smime.p7s Description: Kryptografische S/MIME-Signatur
Re: OMIT-map
It should be slightly different (https://doi.org/10.1107/S0021889887012755), see slide 9 here: https://brockhouse.lightsource.ca/media/uploads/xrd-school-2024/introduction_to_gsas-ii.pdf The calculation appears to be here: https://github.com/AdvancedPhotonSource/GSAS-II/blob/0b735da79488087ee5bc7b3159c82f90a5697dc2/GSASII/GSASIImath.py#L3720 Best, Jon On 2024-08-19 09:16, Többens wrote: This seems to be another name for a difference Fourier map, calculated from F_obs - F_calc; the term omit map being used in the macromolecular community. It shows scattering density missing in the model, i.e. from omitted atoms. *Von:* davide.lev...@gmail.com *Gesendet:* Sonntag, 18. August 2024 um 8:01 AM MESZ *An:* rietveld_l@ill.fr *Betreff:* OMIT-map Dear All, I received the answer from a referee for an article about an organic structure I determined. The referee asks for An omit map (including contour level) for all ligand-bound crystal structures. I searched about omit-map, but I did not find a clear how to calculate this map. Can anyone send me something about the omit-map or explain me how to obtain these maps with GSAG or TOPAS? Thanks Davide Levy ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the subject with no body text The Rietveld_L list archive is onhttp://www.mail-archive.com/rietveld_l@ill.fr/ ++ ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: OMIT-map
The OMIT map is calculated like a normal map, but with a certain region of the structure being omitted when calculating Fcalc. A usual electron density map in macromolecular crystallography is calculated from both experimental (Fobs) and calculated (Fcalc) structure factors. Fcalc (structure factors calculated from the model) are necessary to get approximate phases. This causes model bias - the obtained electron density is skewed toward the model and might seem to confirm a model that's not truely supported by the experimental data. The idea of the OMIT map is that you exclude a certain region when calculating structure factors (this region can be modelled as bulk solvent instead – a flat electron density). If the region is relatively small, it won't degrade the overall map quality too much, but it will remove the bias in this particular region. It's a trick to validate if a ligand is really there. Marcin ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
