Greg and Eric, Thank you. I installed the build and it works great. The default offset when using thermal ellipsoids is very nice. I haven't figured out how to drag individual labels but that may be me or that I'm using a trackball, but the labeloffset command works well. I'm getting very positive feedback from my users! Thanks. New question, Is it possible to calculate electron density maps from a standard PDB format fcf file with the structure factors in it? SHELX is the small molecule standard and it will output reflection files. I know COOT will calculate the maps on the fly from this format but figures from COOT are NO MATCH for Chimera. It would be nice to be able to read the .fcf file and get maps back. If I try to use COOT calculated maps I have no control over the position of the map and it can be the same for trying to use CCP4 maps. Maps calculated in Chimera centered on the molecule would be useful beyond description. From the SHELX manual m = 6:Write a free-format CIF file containing h,k,l, Fo, σ(Fo), Fc and φ (phase angle in degrees) for the reflection list as defined for m = 1. This is the recommended format for the deposition of reflection data with the PDB, and is also the format required for the generation of refinement statistics and electron density maps using SHELXPRO An actal file # # h,k,l, Fo-squared, sigma(Fo-squared), Fc and phi(calc) # data_ta36 _shelx_title ' ta36 in P-1' _shelx_refln_list_code 6 _shelx_F_calc_maximum 147.61 _exptl_crystal_F_000 628.00 _reflns_d_resolution_high 0.7205 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, -z' _cell_length_a 10.9827 _cell_length_b 11.4038 _cell_length_c 12.1961 _cell_angle_alpha 65.918 _cell_angle_beta 73.507 _cell_angle_gamma 76.655 loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_meas _refln_F_squared_sigma _refln_F_calc _refln_phase_calc 1 0 0 548.13 8.13 23.91 0.0 2 0 0 713.05 6.90 27.04 0.0 3 0 0 4487.70 36.52 61.90 0.0 4 0 0 5185.71 41.46 70.98 0.0 And the relevant part of the corresponding SHELX ins file TITL ta36 in P-1 CELL 0.71073 10.9827 11.4038 12.1961 65.918 73.507 76.655 ZERR 1.00 0.0005 0.0006 0.0006 0.003 0.003 0.003 LATT 1 SFAC C H N O F S Cu UNIT 52 45 9 8 6 2 2 WGHT 0.000000 FVAR 0.66533 0.53147 CU1 7 -0.011240 0.599643 0.665074 11.00000 0.02325 0.03784 = 0.02594 -0.00922 -0.00439 -0.00980 O1 4 0.323760 0.794114 0.628981 11.00000 0.02076 0.03749 = 0.07654 -0.03652 -0.01288 -0.00180 Cheers, Mike <<< ------------------------------------------------------------------------>
Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>
On Aug 7, 2009, at 2:44 PM, Greg Couch wrote: On Thu, 6 Aug 2009, Michael Day wrote:
How does one change the position of atom labels? For small coordination complexes the default atom labels land on the atom and it would be nice to move them as a whole or individually so they are alongside the atom ball or anisotropic ellipsoid.
Cheers, Mike
In the next daily build, we will have interactive label moving, where you can pick a label and drag it around, and if you hold down the shift key, it will move in Z. It will default to the Control-button-3 mouse mode, but can be reassigned using the mouse mode preferences. You will also be able to change the label offsets using the command line, the "labeloffset x y z atom-spec" and "rlabeloffset x y z atom- spec" commands to set the offsets and "~labeloffset" and "~rlabeloffset" to reset them to the default behavior of adjusting the offset with the representation. For users with existing saved preferences, you might need to turn label dragging on by resetting the mouse mode preferences or by explicitly assigning it to Control-button-3. There's no icon for it yet in the mouse modes interface, but it will be the rightmost column for now. Since the label moving code is new, please send me feedback about how well it works for you. - Greg