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Dear all, Thank you for your replies, I actually saw the options in coot that Chris and others suggested and I already tried it before, but for some reason it did not work for me. Maybe I`m doing something wrong. So I open in coot pdb1 and map1 for mutant 1 and pbd2 and map2 for mutant 2. Then I go to extension map, transform by LSQ model fit, I specify the reference (pdb1) and moving (pdb2) structures, specify the residue and the radius (by the way there is no option to specify the map). I assume coot does it automatically, since I specify the moving and reference structures. Then, all coot is doing, is creating transformed copy of pdb2 (which is in alignment with pdb1), and a transformed map. But this transformed map does not match the transformed copy of pdb2. Actually it does not match any of the pdbs? Thank you, Milya. Quoting [log in to unmask]: > Dear Milya, > > Last year, we were facing the exact problem you mentioned. > > I contacted Paul Emsley (author of COOT) who programmed a little routine > wich is part of the general release of the program: > > In COOT version 0.5.2, go to > Extensions > Maps ... > Transform map by LSQ model fit ... > You will need to specify two structures (Reference and Moving), as well > as the map to be transformed. > > That should do the trick. > > Thanks, > Chris > > > > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Milya Davlieva > Sent: Mon, September 07,2009 6:28 > To: [log in to unmask] > Subject: [ccp4bb] Alignment of Electron Density Map for structures that > have different space groups > > Dear all, > I need to make a figure which needs to consist of 2 aligned pdb files > and their electron density maps for the structures of two mutants (with > different space groups). I'm able to do this when there are two > structures that have the same space group. Could, you, please, help me > to find a way to do this for structures with different space groups? > Thank you very much for your help, > Dr. Milya Davlieva > Rice University > > -------------------------------------------------------- > > UCB Celltech is the UK branch of UCB Pharma S.A., a company > registered in Belgium with registered offices at Allee de la > Recherche 60, 1070 Brussels, Belgium, KBO/BCE nr. 0403.096.168, > RPR/RPM Brussels. > UCB Celltech's UK branch registration number is BR009137 and its UK > representative office is at 208 Bath Road, Slough, Berkshire SL1 3WE. > -------------------------------------------------------- > > Legal Notice: This electronic mail and its attachments are intended > solely for the person(s) to whom they are addressed and contain > information which is confidential or otherwise protected from > disclosure, except for the purpose for which they are intended. > Dissemination, distribution, or reproduction by anyone other than > the intended recipients is prohibited and may be illegal. If you are > not an intended recipient, please immediately inform the sender and > return the electronic mail and its attachments and destroy any > copies which may be in your possession. UCB screens electronic mails > for viruses but does not warrant that this electronic mail is free > of any viruses. UCB accepts no liability for any damage caused by > any virus transmitted by this electronic mail. (Ref: #*CUK0308) > -------------------------------------------------------- > >