Re: [ccp4bb] visual mask editor - why

az Shaanan <mailto:bshaa...@bgu.ac.il> Sent: Thursday, May 28, 2020 11:59 To: b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> Cc: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] visual mask editor - why Hi Bernhard, Did you consider trying

Re: [ccp4bb] visual mask editor - why

genration, etc.  Run the script with no arguments to get a list. Oh, but don't try it on an mtz file!  mtz files are not maps. -James Holton MAD Scientist On 5/28/2020 12:11 PM, Bernhard Rupp wrote: Yes I have already pilfered useful parts of it in the scripts… Thx, BR *From:* Boaz Shaanan

Re: [ccp4bb] visual mask editor - why

Dear Bernand, In MAIN embedded map algebra can probably vover all what you need. If you want to go along this path, please, let me know and I will help you. best, dusan > On 30 May 2020, at 01:00, CCP4BB automatic digest system > wrote: > > > Date:Fri, 29 May 2020 00:02:11 -0700 >

Re: [ccp4bb] visual mask editor - why

Wont mapmask do that? Find the fraction coordinate of the blob extent then carve that section out of the map? Eleanor >From documentation: *XYZLIM [ASU] [CELL] [MATCH] **Set the output map extent as `extend'. - are given in grid units or in fractional coordinates. It is possible to

Re: [ccp4bb] visual mask editor - why

Hi Bernhard, "Like comparing these map regions, excluding intrusion of a solvent mask, etc.": You didn't say much about the context.. So I'd say Polder map approach comes to mind first based on these keywords. Next is "map comparison" ( https://doi.org/10.1107/S1399004714016289). If none of

Re: [ccp4bb] visual mask editor - why

Yes I have already pilfered useful parts of it in the scripts. Thx, BR From: Boaz Shaanan Sent: Thursday, May 28, 2020 11:59 To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor - why Hi Bernhard, Did you consider trying 'polder' in the phenix

Re: [ccp4bb] visual mask editor - why

Hi Bernhard, Did you consider trying 'polder' in the phenix package? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On May 28, 2020 21:17, Bernhard Rupp wrote: Maybe I should explain an example: Say coot detects an unmodelled

Re: [ccp4bb] visual mask editor - why

Looks like the density manipulation/carving tools might be useful. Thx, BR From: CCP4 bulletin board On Behalf Of Jurgen Bosch Sent: Thursday, May 28, 2020 11:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor - why Give this a shot: https://www.eyesopen.com/afitt

Re: [ccp4bb] visual mask editor - why

Give this a shot: https://www.eyesopen.com/afitt At least in Vida from the same suite of programs, you can select such a blob as you describe and export it in a useful way. Jürgen ___ Jürgen Bosch, Ph.D. Division of