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Hi Michael,<br>
<br>
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.<br>
<br>
<a class="moz-txt-link-freetext" href="http://eds.bmc.uu.se/eds/">http://eds.bmc.uu.se/eds/</a><br>
<br>
These maps can be fetched by Chimera (File / Fetch by ID). The
procedure the describe for computing 2fo-fc maps is quite intricate<br>
<br>
<a class="moz-txt-link-freetext" href="http://eds.bmc.uu.se/eds/eds_help.html#NITTY_GRITTY">http://eds.bmc.uu.se/eds/eds_help.html#NITTY_GRITTY</a><br>
<br>
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?<br>
<br>
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.<br>
<br>
Tom<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Moving atom labels<br>
From: Michael Day <a class="moz-txt-link-rfc2396E" href="mailto:mikeday@caltech.edu"><mikeday@caltech.edu></a><br>
To: Greg Couch <a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a>, Eric Pettersen
<a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu"><pett@cgl.ucsf.edu></a><br>
Date: 8/10/09 6:05 PM<br>
<blockquote cite="mid:37A69CAD-83BF-4BD7-B82D-8385A35E5DDF@caltech.edu"
type="cite">Greg and Eric,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I'm getting very positive feedback from my users! </div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>New question,</div>
<div><br>
</div>
<div>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.</div>
<div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b><br>
</b></div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>From
the SHELX manual</b></div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>m
= 6</b>:Write a free-format CIF file containing h,k,l, F<span
style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7px; line-height: normal; font-size-adjust: none; font-stretch: normal;">o</span>,
<span
style="font-family: Symbol; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">σ</span>(F<span
style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7px; line-height: normal; font-size-adjust: none; font-stretch: normal;">o</span>),
F<span
style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7px; line-height: normal; font-size-adjust: none; font-stretch: normal;">c</span>
and <span
style="font-family: Symbol; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">φ</span>
(phase angle in </div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">degrees)
for the reflection list as defined for m = 1. This is the recommended
format for </div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">the
deposition of reflection data with the PDB, and is also the format
required for the </div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">generation
of refinement statistics and electron density maps using SHELXPRO</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>An
actal file</b></div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">#</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">#
h,k,l, Fo-squared, sigma(Fo-squared), Fc and phi(calc)</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">#</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">data_ta36</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_shelx_title
' ta36 in P-1'</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_shelx_refln_list_code
6</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_shelx_F_calc_maximum
147.61</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_exptl_crystal_F_000
628.00</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_reflns_d_resolution_high
0.7205</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">loop_</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _symmetry_equiv_pos_as_xyz</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> 'x,
y, z'</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> '-x,
-y, -z'</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_length_a
10.9827</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_length_b
11.4038</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_length_c
12.1961</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_angle_alpha
65.918</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_angle_beta
73.507</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">_cell_angle_gamma
76.655</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">loop_</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_index_h</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_index_k</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_index_l</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_F_squared_meas</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_F_squared_sigma</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_F_calc</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"> _refln_phase_calc</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">1
0 0 548.13 8.13 23.91 0.0</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">2
0 0 713.05 6.90 27.04 0.0</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">3
0 0 4487.70 36.52 61.90 0.0</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">4
0 0 5185.71 41.46 70.98 0.0�</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>And
the relevant part of the corresponding SHELX ins file</b></div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">TITL
ta36 in P-1</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">CELL
0.71073 10.9827 11.4038 12.1961 65.918 73.507 76.655</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ZERR
1.00 0.0005 0.0006 0.0006 0.003 0.003 0.003</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">LATT
1</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">SFAC
C H N O F S Cu</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">UNIT
52 45 9 8 6 2 2</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">WGHT
0.000000</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">FVAR
0.66533 0.53147</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">CU1
7 -0.011240 0.599643 0.665074 11.00000 0.02325
0.03784 =</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
0.02594 -0.00922 -0.00439 -0.00980</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">O1
4 0.323760 0.794114 0.628981 11.00000 0.02076
0.03749 =</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
0.07654 -0.03652 -0.01288 -0.00180�</div>
<div
style="margin: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</div>
</div>
</div>
<div><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true"> <span class="Apple-style-span"
style="font-family: 'Bradley Hand ITC TT'; font-size: 20px;">
<div style="">
<div>
<div>
<div>
<div>
<div>
<div>
<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
------------------------------------------------------------------------>>></div>
<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab & Molecular Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<div><br>
</div>
<div><>< <>< <>< <>< <><
<>< <>< <>< <>< <><</div>
<div><br>
</div>
<div>Beckman Institute, Room 116</div>
<div>Phone: (626) 395-2734</div>
<div>Fax: (626) 449-4159</div>
<div>e-mail: <a moz-do-not-send="true"
href="mailto:mikeday@caltech.edu">mikeday@caltech.edu</a></div>
<div><<<
------------------------------------------------------------------------>>></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</span> </div>
<br>
<div>
<div>On Aug 7, 2009, at 2:44 PM, Greg Couch wrote:</div>
<br class="Apple-interchange-newline">
<div>On Thu, 6 Aug 2009, Michael Day wrote:<br>
<br>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Cheers,<br>
</blockquote>
<blockquote type="cite">Mike<br>
</blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
Since the label moving code is new, please send me feedback about how
well it works for you.<br>
<br>
<span class="Apple-tab-span" style="white-space: pre;"> </span>- Greg<br>
</div>
</div>
<br>
</div>
<pre wrap="">
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</pre>
</blockquote>
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