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@caltech.edu>
To: Greg Couch <gregc@cgl.ucsf.edu>, Eric Pettersen <pett@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
<<< ------------------------------------------------------------------------>>>

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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