Re: [COOT] Mask the map
pebbleped...@gmail.com wrote: hi all, I have a question about how does coot mask the electron density map. I have a ccp4 electron density map file with parameters like this: Parameters as read from the map file Origin .. -167 -36 -35 Extent ..10974 113 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z OK, so right there is the problem. Coot uses clipper's crystallographic maps - using maps that are not the asymmetric unit can be confusing, there are 2 copies of symmetry-related density. So this electron density map has 109*74*113=911458 grid points and its origin located at point -167 -36 -35 After I mask part of the density map (around chain B) and only leave electron density around chain A, I export it. Now its parameters are like this: Parameters as read from the map file Origin .. 0 0 0 Extent ..15652 112 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z OK, so a P1 asymmetric unit. So now the masked map has 156*52*112=908544 grid points with origin locate at point 0 0 0 Before I do tests, I guess how coot to do mask is: to find out grid points around selected atoms from model and set the density value to be zero then save the map like this: 1.11.1 2.12.1 3.1 0.0 4.14.1 5.15.1 Yes, if I understood correctly. So then I can compare the two maps to check out at which point the mask is placed. But actually, the masked map have different points with the initial map. Symmetry-related density, I would guess. Does anyone know how can I get a masked map with same grid points as the initial map and the only differences are density values at some grid point were set to be zero? The first map should be the asymmetric unit (again, if I understood correctly). Paul..
Re: [COOT] Mask the map
Yes, Paul's analysis of the problem is correct. Coot is the wrong tool for this job. You can do the job in CCP4 using NCSMASK and MAPMASK. Open Map Mask Utilities. Use Create/Edit Mask to make a mask about your model. Enter the grid and extent values from your current map. Use a pdb file containing only chain B. Turn off the 'trim mask' option. Use Edit/Rotate maps and masks and select 'solvent flatten a map using a mask' to flatten the unmasked region. Kevin pebbleped...@gmail.com wrote: hi all, I have a question about how does coot mask the electron density map. I have a ccp4 electron density map file with parameters like this: Parameters as read from the map file Origin .. -167 -36 -35 Extent ..10974 113 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z So this electron density map has 109*74*113=911458 grid points and its origin located at point -167 -36 -35 After I mask part of the density map (around chain B) and only leave electron density around chain A, I export it. Now its parameters are like this: Parameters as read from the map file Origin .. 0 0 0 Extent ..15652 112 Grid 15652 112 Cell axes ... 100.74 32.81 72.69 Cell angles . 90.00 90.71 90.00 UVW (fast, medium, slow) Y X Z So now the masked map has 156*52*112=908544 grid points with origin locate at point 0 0 0 Before I do tests, I guess how coot to do mask is: to find out grid points around selected atoms from model and set the density value to be zero then save the map like this: 1.11.1 2.12.1 3.1 0.0 4.14.1 5.15.1 So then I can compare the two maps to check out at which point the mask is placed. But actually, the masked map have different points with the initial map. Does anyone know how can I get a masked map with same grid points as the initial map and the only differences are density values at some grid point were set to be zero?
Re: [COOT] Release 0.6
Maia Cherney wrote: I suggested some time ago to include Go to atom button in the bar beside Display manager, as this is one of the most used buttons. Paul liked the idea, but I don't see it in the new release. For the record, I should reply to this. I did consider this option. I thought that it would be a useful addition. But only marginally so, seeing as there is already a menu item and a keyboard accelerator (F6) to show the dialog. Added to that, I rarely close (and then re-open) the go to atom dialog. Therefore it got shelved. It may well appear in 0.6.1. Paul.
