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 > <lists...@jiscmail.ac.uk> wrote: > > > Date: Fri, 29 May 2020 00:02:11 -0700 > From: Pavel Afonine <pafon...@gmail.com> > Subject: Re: 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 the above: what we (or you) are missing? > > Pavel > > On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp <hofkristall...@gmail.com> > wrote: > >> Maybe I should explain an example: Say coot detects an unmodelled blob >> (maybe a ligand). Now, I would like to do >> >> a number of things without biasing towards a model. Like comparing these >> map regions, excluding >> >> intrusion of a solvent mask, etc. >> >> >> >> Now could coot for example just generate a mask around what it already >> knows are blobs? >> >> Possible useful items could be a solvent mask not including that regions, >> or a density map >> >> that includes only features with a certain boundary around that blob. >> >> >> >> I pilfered some kludges together from different sources, but let’s just >> say inelegant would be a compliment. >> >> >> >> Best, BR >> >> ------------------------ >> >> Brief question: Does something like a visual density mask editor exist? >> >> Thx, BR >> >> ------------------------------------------------------ >> >> Bernhard Rupp >> >> http://www.hofkristallamt.org/ >> >> b...@hofkristallamt.org >> >> +1 925 209 7429 >> >> +43 676 571 0536 >> >> ------------------------------------------------------ >> >> Many plausible ideas vanish >> >> at the presence of thought >> >> ------------------------------------------------------ >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > ------------------------------ > > Date: Fri, 29 May 2020 09:34:23 +0100 > From: Harry Powell - CCP4BB <hrp-ccp...@virginmedia.com> > Subject: Re: Strange Pseudosymmetry Effects > > Hi Tim > > You could send out an SOS to some of the other authors in the same issue, who > might have kept a copy - several are “regular" posters on this forum, e.g. > > Sacha Urzhumtsev > Gerard Kleywegt > Eleanor Dodson > > There’s a good chance they’ll be stuck at home at the moment with plenty of > time to search through old boxes… > > Harry > >> On 28 May 2020, at 21:04, Tim Gruene <tim.gru...@univie.ac.at> wrote: >> Dear Eddie, dear all >> >> According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article >> appeare in Newsletter June 95. It is mentioned in the table of contents, >> "Correction on perfection: primary extinction correction in protein >> crystallography" by Polykarpov and Sawyer. >> Unfortunately, the article itself is not there >> >> Extinction is not the same as the dynamic effects that James mentioned, >> but this seems the closest match. >> >> Would anyone have a copy they can share with me? >> >> Thanks a lot! >> >> Best, >> >> Tim > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > ------------------------------ > > Date: Fri, 29 May 2020 10:49:03 +0100 > From: Eleanor Dodson <eleanor.dod...@york.ac.uk> > Subject: Re: 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] <x1> <x2> <y1> <y2> <z1> <z2>**Set the output > map extent as `extend'. <x1>-<z2> are given in grid units or in fractional > coordinates. It is possible to automatically extend to the CCP4 default > asymmetric unit, or a whole unit cell, by specifying `XYZLIM ASU' or > `XYZLIM CELL'. It is also possible to extend the map to match another map > (given as MAPLIM) by specifiying `XYZLIM MATCH'. The default is to keep the > extent of the input map.* > > On Fri, 29 May 2020 at 08:03, Pavel Afonine <pafon...@gmail.com> wrote: > >> 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 the above: what we (or you) are missing? >> >> Pavel >> >> On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp <hofkristall...@gmail.com> >> wrote: >> >>> Maybe I should explain an example: Say coot detects an unmodelled blob >>> (maybe a ligand). Now, I would like to do >>> >>> a number of things without biasing towards a model. Like comparing these >>> map regions, excluding >>> >>> intrusion of a solvent mask, etc. >>> >>> >>> >>> Now could coot for example just generate a mask around what it already >>> knows are blobs? >>> >>> Possible useful items could be a solvent mask not including that regions, >>> or a density map >>> >>> that includes only features with a certain boundary around that blob. >>> >>> >>> >>> I pilfered some kludges together from different sources, but let’s just >>> say inelegant would be a compliment. >>> >>> >>> >>> Best, BR >>> >>> ------------------------ >>> >>> Brief question: Does something like a visual density mask editor exist? >>> >>> Thx, BR >>> >>> ------------------------------------------------------ >>> >>> Bernhard Rupp >>> >>> http://www.hofkristallamt.org/ >>> >>> b...@hofkristallamt.org >>> >>> +1 925 209 7429 >>> >>> +43 676 571 0536 >>> >>> ------------------------------------------------------ >>> >>> Many plausible ideas vanish >>> >>> at the presence of thought >>> >>> ------------------------------------------------------ >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 Dr. Dusan Turk, Prof. Head of Structural Biology Group http://stef.ijs.si/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
