Re: [COOT] RSR weight estimate really high
On 17/09/18 19:49, Robert Grant wrote: > I have been using the Phenix-linked Coot to modify a MR solution calculated > from a rather poor data set, with high merging Rs and very low absolute > intensities. I have observed what I consider bizarre behavior in the real > space refinement function. My original observation was that very often RSR > would actually make the model look less like the density. I generally use > the default matrix weight (60) or reduce it to 20. When I let coot estimate > the weight it came up with 65446. That seems like a high number - and maybe coincidentally close to 65536. > With that value the RSR seems to behave normally. How is this weight > calculated? What kind of data pathology would produce the results I am > seeing? Is it related to the low intensity values in the data? > The "Estimate" button give a value that is proportional to the inverse of the rmsd of the map (so, yes) - if you don't have an average sized protein at average resolution with structure factors for the map more or less on the absolute scale, then your initial estimate will be a bit off. (after having selected a reasonably well-fitting part of the structure) you can also use Extensions -> Settings -> Autoweight Refinement. In my hands refinement is not very sensitive to the weight - as long as you are within a factor of ~5, it seems OK. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
[COOT] RSR weight estimate really high
I have been using the Phenix-linked Coot to modify a MR solution calculated from a rather poor data set, with high merging Rs and very low absolute intensities. I have observed what I consider bizarre behavior in the real space refinement function. My original observation was that very often RSR would actually make the model look less like the density. I generally use the default matrix weight (60) or reduce it to 20. When I let coot estimate the weight it came up with 65446. With that value the RSR seems to behave normally. How is this weight calculated? What kind of data pathology would produce the results I am seeing? Is it related to the low intensity values in the data? To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
[COOT] Problem with FLEV in COOT 0.8.9.1 EL (ccp4)
Dear All, The Ligand -> FLEV_this_residue option doesn't seem to work - I get an error message: No set_atom_type() for this build/compiler WARNING:: failure to construct rdkit molecule However, using Extensions -> Lidia -> view in LIDIA does work, provided the 3-character residue code is unique, i.e., it does not exist in the CCP4 library. If I have created and loaded a CIF dictionary with the a code that already existis in the CCP4 library, this works fine for real space refinement but not here, because LIDIA appears to pick the CCP4 dictionary and then there is an atom name mismatch. For protein-ligand complexes, DRG or INH are cases in point. Is there a way to tell LIDIA to use the loaded CIF dictionary instead of the CCP4 one? Best regards, Pedro -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
