Re: [COOT] to separate levels of positive and negative density
Why not read the diff map in twice? You can have diff contour levels for each copy of the map.. Paul Emsley wrote: Maia Cherney wrote: If I use a *map_coeffs.mtz file from the phenix.refine, how can I turn off the negative density? ??? Confusing question. By unclicking the "is difference map?" button (you can't do this in auto-read mode, of course). Paul.
Re: [COOT] to separate levels of positive and negative density
Maia Cherney wrote: If I use a *map_coeffs.mtz file from the phenix.refine, how can I turn off the negative density? ??? Confusing question. By unclicking the "is difference map?" button (you can't do this in auto-read mode, of course). Paul.
Re: [COOT] to separate levels of positive and negative density
Hi Paul, If I use a *map_coeffs.mtz file from the phenix.refine, how can I turn off the negative density? Maia Paul Emsley wrote: chern wrote: Hi all, Is it possible to separately adjust the levels of positive and negative electron density? No (and yes). When I try to build a fragment with a poor density I want to decrease the level of positive density from 3 sigma to 2 or even 1 sigma to see more positive density, but then the whole map becomes red with negative density. That is supposed to indicate something to you. Can I shut off the negative density at all, leaving only the positive density in the PHFOFCWT maps? Yes - sort of. When you read in the mtz file, uncheck the "is difference map?" check box, then you will not get a negative level. You will have to colour the new map "by hand" though. ( I would like also to color them separately). It is possible to do so in xtalview. As above - if you want scroll negative levels then you will need to do something like: (set-stop-scroll-diff-map-level -5) Paul.
Re: [COOT] to separate levels of positive and negative density
Thank you, Paul. I understand now that if I want positive and negative densities at different levels, I will need to load the PHFOFCWT map twice, with checked and unchecked "is difference map?" and have negative density at 3sigma (with checked diff.map) and positive density at 1 sigma (with unchecked diff.map). Maia Paul Emsley wrote: chern wrote: Hi all, Is it possible to separately adjust the levels of positive and negative electron density? No (and yes). When I try to build a fragment with a poor density I want to decrease the level of positive density from 3 sigma to 2 or even 1 sigma to see more positive density, but then the whole map becomes red with negative density. That is supposed to indicate something to you. Can I shut off the negative density at all, leaving only the positive density in the PHFOFCWT maps? Yes - sort of. When you read in the mtz file, uncheck the "is difference map?" check box, then you will not get a negative level. You will have to colour the new map "by hand" though. ( I would like also to color them separately). It is possible to do so in xtalview. As above - if you want scroll negative levels then you will need to do something like: (set-stop-scroll-diff-map-level -5) Paul.
Re: [COOT] to separate levels of positive and negative density
chern wrote: Hi all, Is it possible to separately adjust the levels of positive and negative electron density? No (and yes). When I try to build a fragment with a poor density I want to decrease the level of positive density from 3 sigma to 2 or even 1 sigma to see more positive density, but then the whole map becomes red with negative density. That is supposed to indicate something to you. Can I shut off the negative density at all, leaving only the positive density in the PHFOFCWT maps? Yes - sort of. When you read in the mtz file, uncheck the "is difference map?" check box, then you will not get a negative level. You will have to colour the new map "by hand" though. ( I would like also to color them separately). It is possible to do so in xtalview. As above - if you want scroll negative levels then you will need to do something like: (set-stop-scroll-diff-map-level -5) Paul.
Re: [COOT] to separate levels of positive and negative density
Hi all, Is it possible to separately adjust the levels of positive and negative electron density? When I try to build a fragment with a poor density I want to decrease the level of positive density from 3 sigma to 2 or even 1 sigma to see more positive density, but then the whole map becomes red with negative density. Can I shut off the negative density at all, leaving only the positive density in the PHFOFCWT maps? ( I would like also to color them separately). It is possible to do so in xtalview. Maia
