fitting a protein inside an EM reconstruction
hi! I am having a small problem in fitting crystal structures into the EM reconstruction. Problem definition When I open the protein that I am trying to fit into the EM map along side the EM map, the Em Map shrinks. The EM map which is the super set, which holds 3 proteins appears shrunk with respect to the protein that I am trying to fit inside the EM Map and the crystal structure How am I to overcome this hurdle? thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790
Hi Jayant, The problem with the EM map being too small for the crystal model is that the SPIDER map header does not say the grid plane spacing. Chimera is giving it a default grid plane spacing of 1 angstrom. To fix this you need to know the grid plane spacing, also called "voxel size" in Angstroms. Then enter this value in volume dialog, using volume dialog menu entry Features / Origigin and Scale. Probably the plane spacing is the same along the x, y and z axes, so you will enter the same number in the 3 voxel size fields, and press the Return key to then have the map displayed at the new scale. Unfortunately the above change does not modify your SPIDER file so it will still have the wrong scale the next time you open it in Chimera. Two solutions are to write the SPIDER map out in MRC format using the volume dialog menu entry File / Save As, or save a Chimera session using the main Chimera window menu entry File / Save Session As. Chimera is not able to write out new SPIDER format maps. Tom
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Thomas Goddard