[ccp4bb] Map Alignment
Dear Chen you can use the Matrix Copy command in pymol to align maps. Check the pymol wiki for details and an example how to use: http://pymolwiki.org/index.php/Matrix_copy. Best regards Florian Date:Thu, 21 Mar 2013 23:29:31 -0400 From:Chen Zhao chenzhaoh...@gmail.com Subject: Map Alignment Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the Superpose maps utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen - Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland Tel.: +41-(0)56-310-2332 Email: florian.brueck...@psi.ch
Re: [ccp4bb] Map Alignment
On Thu, 2013-03-21 at 23:29 -0400, Chen Zhao wrote: Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I have learned to take a few seconds to double check the parameters (the reference model, the 'moving' model, the screen centre and the refinement map) when using map transformations in Coot. Paul. attachment: Transform-map-by-LSQ.png
[ccp4bb] Map Alignment
Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the Superpose maps utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen
Re: [ccp4bb] Map Alignment
If I understand your question correctly, you have a couple of atoms which you could align to get the rotation translation then you can use these values with maprot (CCP4) or mama (USF) to actually superimpose maps. Jürgen On Mar 21, 2013, at 11:29 PM, Chen Zhao wrote: Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the Superpose maps utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Map Alignment
Hi Chen, I also tried the Superpose maps utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. I'm not aware of such problem. If it does exist and you want me to fix it please send me the files and I'll have a look. Pavel
