[Chimera-users] Moving atom labels

Tue Aug 11 11:22:05 PDT 2009

Hi Michael,

  How difficult would it be for Chimera to compute x-ray maps from 
structure factors?  For deposited Protein Databank models with structure 
factors, the Uppsala Electron Density Server (EDS) provides maps.

    http://eds.bmc.uu.se/eds/

These maps can be fetched by Chimera (File / Fetch by ID).  The 
procedure the describe for computing 2fo-fc maps is quite intricate

    http://eds.bmc.uu.se/eds/eds_help.html#NITTY_GRITTY

They are trying to verify the reported R-factor and do other sanity 
checks.  Still it may be too complex a procedure even without the 
quality controls for us to put into Chimera.  But we don't know much 
about crystallographic refinement software.  Maybe you could provide 
more details to show us that it is in fact easy to compute the maps?

  It may be there are easy solutions to get externally generated maps to 
align with the models in Chimera.  Both COOT and CCP4 know how to 
correctly align the PDB models and maps they calculate so that should be 
possible in Chimera too.  I am not very knowledgable about COOT or CCP4 
and any information about the alignment they use that you could provide 
might help us improve use of those maps in Chimera.

    Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Moving atom labels
From: Michael Day <mikeday at caltech.edu>
To: Greg Couch <gregc at cgl.ucsf.edu>, Eric Pettersen <pett at cgl.ucsf.edu>
Date: 8/10/09 6:05 PM
> 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 at caltech.edu <mailto: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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