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Unfortunately there isn't really such a thing as an "aligned .map and .pdb" unless you are talking about one specific software package. .map files (also known as .mrc files) live in pixel space, and unfortunately the interpretation of the origin isn't completely self-consistent among software packages. So, you could make, for example, a Chimera session where a map and model are nicely overlaid on top of each other for visualization purposes, but if you then tried to convert the PDB to a density map for computing the FSC or somesuch, unless you generate the density map within Chimera, you are unlikely to see the same alignment. Some software packages have put a bit of effort into synchronizing these things, and there ARE some published standards, but the practical reality is that it's a bit of a mess. -------------------------------------------------------------------------------------- Steven Ludtke, Ph.D. <[log in to unmask]<mailto:[log in to unmask]>> Baylor College of Medicine Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>) Academic Director, CryoEM Core (cryoem.bcm.edu<http://cryoem.bcm.edu>) Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu>) On May 22, 2018, at 5:56 PM, Tamas Hegedus <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi, I have an aligned .map and .pdb. I translate the all atom structure by (-100,-100,-100). I also try to translate the map using python mrcfile by setting the mrcf.header.nxstart = mrcf.header.nxstart - 100 (and also for nystart and nzstart). mrcf.close() The translation is done, however, the new .map and new .pdb are significantly off. I think that I miss something in .map file format and/or mrcfile usage. I appreciate any suggestion, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:[log in to unmask] Budapest, 1094, Hungary | https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hegelab.org&d=DwICaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=TFAc6Gfuna0piV5mZyGJz7JXbihKV29TbKTM8jSuJ3s&s=JZmBsCAMgKq7MNEgE9LZhzb8liwEgqIhPvA2ZXXwHag&e=