[COOT] Coot 9.8.91 is still broken
Dear Paul, I just had the chance to try out the new Coot version 9.8.91 from CCP4 and I would like to report that RSR of ribosomes is still broken (albeit not as severely as before). You can have a look at PDB-7K00 for examples: https://www.rcsb.org/structure/7K00 https://www.ebi.ac.uk/emdb/EMD-22586 I went through the model with sphere refine to check for broken areas and identified many, here are a few: G533 in chain a C823 in chain A G1186 in chain A C1147 in chain A A614 in chain a In addition, there are three modified residues in that model that still require edited restraints to make them work in Coot: D2T 3TD 6MZ Here, the group name is "NON-POLYMER", I changed that to RNA (3TD+6MZ) or L-peptide (D2T) which makes it work in Coot. Is that ok to do? Many regards, Helge To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Map rotation and translation
Thank you Paul for the explanation/clarification. Indeed, it would be enough for me at the moment if I could align maps according to the fit I get in ChimeraX. The "transform_map() function" sounds exactely like what I was looking for! Could you perhaps elaborate if I filled in the parameters correctly (see below)? ChimeraX output: Fit map job122_class1 in map job145_class1+3 using 378391 points correlation = 0.9626, correlation about mean = 0.8182, overlap = 1.076e+04 steps = 40, shift = 0.009, angle = 0.00377 degrees Position of job122_class1 (#1) relative to job145_class1+3 (#4) coordinates: Matrix rotation and translation 0.3251 -0.00473394 -0.01060925 2.07918736 0.00471099 0.8651 -0.00218664 -0.57281865 0.01061946 0.00213651 0.4133 -1.65452589 Axis 0.18292243 -0.89823687 0.39963723 Axis point 165.64873479 0. 190.89655799 Rotation angle (degrees) 0.67707290 Shift along axis 0.23364667 Coot command: Based on |(transform-map /imol/ /rotation-matrix/ /trans/ /point radius/)| from the user manual: (transform-map 1 (list 0.3251 -0.00473394 -0.01060925 0.00471099 0.8651 -0.00218664 0.01061946 0.00213651 0.4133) (list 2.07918736 -0.57281865 -1.65452589) (list 181.1739959716797 205.94700622558594 198.18699645996094) 10) The value for "point" I took from running |(rotation-centre)| in Coot, is that correct? The resulting map fragment seems to be aligned quite well to the resampled map.| | I set the radius to 10 for testing purposes, is there a way to use the full map by default? Best, Helge To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] Map rotation and translation
Dear all, Continuing from this topic over at the ChimeraX user list: http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2022-January/003177.html I would like to ask if it is possible currently (or to introduce) the ability in Coot to rotate and translate a cryo-EM map according to the output of the ChimeraX "fitmap" command. This would be very useful in comparing the map quality of volumes e. g. from the same classification. Resampling the volumes in ChimeraX changes the map and is therefore not a good option when one wants to compare subtle differences in the densities. I believe the information provided by "fitmap" adheres to the ChimeraX Positions Format described here: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html The output from "fitmap" to the log appears a bit different though, so I am not sure which one would be useable in the end: Example: tool show 'Fit in Map'Fit map run_class001.mrc in map run_class001.mrc using 159932 points correlation = 0.9589, correlation about mean = 0.5393, overlap = 82.65 steps = 48, shift = 2.47, angle = 0.571 degrees Position of run_class001.mrc (#1) relative to run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.5193 -0.00918946 0.00341831 2.19650599 0.00918323 0.5615 0.00183397 -4.59169731 -0.00343502 -0.00180249 0.9248 1.52902230 Axis -0.18233729 0.34363524 0.92123175 Axis point 479.76292846 225.20927991 0. Rotation angle (degrees) 0.57135182 Shift along axis -0.56979010 Many thanks for reading, Helge To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] RSR of tRNA with nascent chain
Dear all, I have what feels like a trivial question about modelling in coot, but unfortunately I have not managed to solve it myself. I would like to create a bond between a P-tRNA and nascent chain and then subsequently use RSR in Coot for modelling. What I gathered so far is that I should use acedrg to create the restraints of the linked unit (in my case "A" to "VAL"). Therefore, I first followed the tutorial in the Coot development blog which worked well. But when I try to do the "real world" example with my model, acedrg crashes (and I could not find a useful error message). What I could figure out is that it has something to do with the RNA-nucleotide being referred to as "A", because linking an imported "AMP" molecule to valine as well as my whole nascent chain works as it should. Therefore, I wanted to ask if you could briefly tell me what is the correct way to achieve this type of linkage in Coot? Many thanks for reading and best wishes, Helge P. S. I have modified Oli Clarke's trimmings to automatically load the "Restraints" menu with "add_module_restraints()", but this is only partially working as the menu is not showing all entries upon starting coot. I have to still manually load "Calculate -> Modules -> Restraints" to get the rest of the entries to show. Is there something I could do to have the full menu from the get go? To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
