[Chimera-users] Moving atom labels

Michael Day mikeday at caltech.edu
Mon Aug 10 18:05:42 PDT 2009

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!


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  

An actal file
# h,k,l, Fo-squared, sigma(Fo-squared), Fc and phi(calc)
_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

  '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

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
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 


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 at 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

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