[COOT] How to mask a map considering the symmetric operations?
Hi all, I am looking for a strategy to obtain a density map which only contain densities where no assignment was made in the model. When I load a PDB file and its corresponding density map to coot, I can mask all regions contain the model. And then several parts were left around the edge of the model. However, these parts are not totally the one where no assignments was made, because some of them belong to the adjacent asymmetric unit part. I can display these parts by using " cell and symmetry" function in coot and can see the model overlap with the map. But how can I also make masks on them and let only the part where no assignments was made left from the whole map. That is how to mask the model and also its images. Thanks
Re: [COOT] How to mask a map considering the symmetric operations?
Thanks. But there will still be the parts from other adjacent asymmetric unit as the whole electron density map contain a whole specific asymmetric unit and some parts from its adjacent asymmetric units. I only want the information form one asymmetric unit in the model. 2009/12/17 Christina Bourne : > Can't you see what you want in an Fo-Fc map? > > > From: "pebbleped...@gmail.com" > To: COOT@JISCMAIL.AC.UK > Sent: Thu, December 17, 2009 11:57:41 AM > Subject: [COOT] How to mask a map considering the symmetric operations? > > Hi all, > > I am looking for a strategy to obtain a density map which only contain > densities where no assignment was made in the model. > > When I load a PDB file and its corresponding density map to coot, I > can mask all regions contain the model. And then several parts were > left around the edge of the model. > > However, these parts are not totally the one where no assignments was > made, because some of them belong to the adjacent asymmetric unit > part. I can display these parts by using " cell and symmetry" function > in coot and can see the model overlap with the map. > > But how can I also make masks on them and let only the part where no > assignments was made left from the whole map. That is how to mask the > model and also its images. > > Thanks > >
Re: [COOT] How to mask a map considering the symmetric operations?
Hi, you dont say how you obtained you map. Usually in Coot, thanks to clipper, the maps extend over the whole "crystal space", i.e. you have the same map in all asu. However this only works if the map is either generated by Coot itself (from an mtz file) or if you read a map file which covers only/exactly the asu (or unit cell). I assume you didnt use either of these. So, please try that and you will get the same, masked map around all molecules incl the symmetry related ones. Alternatively you could write out the symmetry related molecules and masked them again. B Hi all, I am looking for a strategy to obtain a density map which only contain densities where no assignment was made in the model. When I load a PDB file and its corresponding density map to coot, I can mask all regions contain the model. And then several parts were left around the edge of the model. However, these parts are not totally the one where no assignments was made, because some of them belong to the adjacent asymmetric unit part. I can display these parts by using " cell and symmetry" function in coot and can see the model overlap with the map. But how can I also make masks on them and let only the part where no assignments was made left from the whole map. That is how to mask the model and also its images. Thanks -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] How to mask a map considering the symmetric operations?
Or to put it slightly differently: the masking of symmetry-related density works (only) when the cell and symmetry of the map is the same as the cell and symmetry of the atoms for the mask. Paul. Bernhard Lohkamp wrote: Hi, you dont say how you obtained you map. Usually in Coot, thanks to clipper, the maps extend over the whole "crystal space", i.e. you have the same map in all asu. However this only works if the map is either generated by Coot itself (from an mtz file) or if you read a map file which covers only/exactly the asu (or unit cell). I assume you didnt use either of these. So, please try that and you will get the same, masked map around all molecules incl the symmetry related ones. Alternatively you could write out the symmetry related molecules and masked them again. B Hi all, I am looking for a strategy to obtain a density map which only contain densities where no assignment was made in the model. When I load a PDB file and its corresponding density map to coot, I can mask all regions contain the model. And then several parts were left around the edge of the model. However, these parts are not totally the one where no assignments was made, because some of them belong to the adjacent asymmetric unit part. I can display these parts by using " cell and symmetry" function in coot and can see the model overlap with the map. But how can I also make masks on them and let only the part where no assignments was made left from the whole map. That is how to mask the model and also its images. Thanks
