locating models in maps by unit cell transformations
Hi, It often turns out that the atomic model you create in O needs to be transformed by a crystallographic symmetry operation in order to fit into the map created by refmac. In O this is no problem because the map automatically covers the bit of model you put in the center of your screen. However this does not seem to happen in Chimera. Is there an easy way to make the map cover the model (i.e. without working out what the transformation is and then creating a transformed pdb file)? Many thanks Trevor
Hi Trevor, I don't know whether this will meet your needs or not, but you could try using Unit Cell (under Tools... Higher-Order Structure): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ unitcell.html It will generate additional copies using MTRIX, SMTRY and/or CRYST1 matrices. I am hoping the refmac map will go along with one of those copies, but a disadvantage of the approach is that you will have the other copies too (could tax the system depending on number/size). The extras could be removed after you get the copy you want, however. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 4, 2008, at 6:36 AM, Trevor Sewell wrote:
Hi,
It often turns out that the atomic model you create in O needs to be transformed by a crystallographic symmetry operation in order to fit into the map created by refmac. In O this is no problem because the map automatically covers the bit of model you put in the center of your screen. However this does not seem to happen in Chimera. Is there an easy way to make the map cover the model (i.e. without working out what the transformation is and then creating a transformed pdb file)?
Many thanks
Trevor
Hi Trevor, Chimera doesn't move a crystallography unit cell map around to cover the PDB model you are looking at, as does O and Coot. Basically Chimera map capabilities were created primarily for electron microscopy maps that are not periodic. Still I agree that is useful for many people and we should add that to Chimera and I'll put it on our requested feature list. http://www.cgl.ucsf.edu/chimera/plans.html There are harder ways currently in Chimera to get the PDB model and map to coincide in cases where they don't when they are first opened. One is to shift the map by hand. Use the volume dialog Coordinates panel and add an integral number of unit cell shifts to the x, y, or z axes. You'd have to look at the CRYST1 record in the PDB file to know the unit cell size, or show the Unit Cell dialog (menu Tools / Higher-Order Structure / Unit Cell). If the cell angles are not 90,90,90 then it is trickier to figure out the xyz translations. Coot and maybe O too also will "wrap" the periodic map if the PDB crosses the map unit cell box into the next unit cell. In Chimera two copies of the map could be made (volume dialog menu file / duplicate), one translated by a unit cell size, and turning off "cap box faces" in the volume dialog surface and mesh options. Actually I see this does not work since Chimera knows that the two maps are the same and applies the same translation to both. That needs fixing. Even if it worked it is a lot of trouble. Again Chimera should do the wrapping. Since most Chimera map users look at electron microscopy it will need to be an optional behavior when added to Chimera. I will add this too the requested features page. Tom
Hi Trevor, Terry, The method of duplicating the unit cell map and shifting one copy to have the density cover a PDB model that straddles the boundary can be made to work with difficulty. Since Chimera is currently too "smart" and decides to translate both copies of the map in the same way, you would need to copy the map on disk and open the two files so that Chimera does not know they are the same. These are of course desperation measures that we hope to make unnecessary in the future. Tom
participants (3)
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Elaine Meng -
Thomas Goddard -
Trevor Sewell