From: Albion B. <ba...@ms...> - 2006-09-22 01:04:19
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I am experiencing a strange phenomenon when I open maps in Pymol. I have a Chimera session with a PDB file docked into a CCP4 map. If I display the unit cell in Chimera the density is centered in the unit cell. If I open the exact same map and PDB file in Pymol, the model and map are no longer in agreement, and when I display the unit cell in Pymol the map is situated at the corner of the unit cell rather than in the center. I have found that if I translate the PDB model by _roughly_ half the unit cell length (in all dimensions) I arrive at where it is normally situated in Chimera. But even this is not exact, and it appears to be half the unit cell dimensions + ~10A. I am just trying to understand how this map is being interpreted by Pymol and what known ambiguities or assumptions are made when it is loaded that might cause this behavior. Thanks Albion Here is the maps info from MAPMAN Grid = 96 96 96 Origin = -48 -48 -48 Extent = 96 96 96 Cell = 213.423 213.423 213.423 90.000 90.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 884736 Density min = -6.915E-01 Max = 2.397E+00 Average = 7.247E-11 Sigma = 2.290E-01 Variance = 5.243E-02 Mappage Prod= 8.257E+01 Plus = 57 Dyn. range = -6.903E-01 To = 2.398E+00 Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 Grid vol. = 9.721E+06 %Cell vol. = 100.00 Origin frac = -0.50000 -0.50000 -0.50000 Origin Cart = -106.712 -106.712 -106.712 Top frac = 0.48958 0.48958 0.48958 Top Cart = 104.488 104.488 104.488 Spacing = 2.223 2.223 2.223 Top = 47 47 47 Changes = F |
From: Peter A. M. <pa...@co...> - 2006-09-22 13:34:53
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Hi, Based on your mapman info, it looks like this map is centered on the origin of your unit cell. One possibly explaination is that your model is in the center of the unit cell, and that Chimera is using symmetry to generate density around the region you are centered on (I have never used Chimera, so I could be wrong about this...but this behavior is fairly common). Pymol (as far as I know) does not currently do symmetry expansion of the map; so you'd need to use your favorite map manipulation program to extract a region covering your model. Pete > I am experiencing a strange phenomenon when I open maps in Pymol. > > I have a Chimera session with a PDB file docked into a CCP4 map. If I > display the unit cell in Chimera the density is centered in the unit > cell. > > If I open the exact same map and PDB file in Pymol, the model and map > are no longer in agreement, and when I display the unit cell in Pymol > the map is situated at the corner of the unit cell rather than in the > center. > > I have found that if I translate the PDB model by _roughly_ half the > unit cell length (in all dimensions) I arrive at where it is normally > situated in Chimera. But even this is not exact, and it appears to be > half the unit cell dimensions + ~10A. > > I am just trying to understand how this map is being interpreted by > Pymol and what known ambiguities or assumptions are made when it is > loaded that might cause this behavior. > > Thanks > > Albion > > Here is the maps info from MAPMAN > > Grid = 96 96 96 > Origin = -48 -48 -48 > Extent = 96 96 96 > Cell = 213.423 213.423 213.423 90.000 90.000 > 90.000 > UVW = 1 2 3 > Spcgrp = 1 Nr of points = 884736 > Density min = -6.915E-01 Max = 2.397E+00 > Average = 7.247E-11 Sigma = 2.290E-01 > Variance = 5.243E-02 > Mappage Prod= 8.257E+01 Plus = 57 > Dyn. range = -6.903E-01 To = 2.398E+00 > Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 > Grid vol. = 9.721E+06 %Cell vol. = 100.00 > Origin frac = -0.50000 -0.50000 -0.50000 > Origin Cart = -106.712 -106.712 -106.712 > Top frac = 0.48958 0.48958 0.48958 > Top Cart = 104.488 104.488 104.488 > Spacing = 2.223 2.223 2.223 > Top = 47 47 47 > Changes = F > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > Pete Meyer Fu Lab BMCB grad student Cornell University |