Hi Tom, Your script does exactly what I needed. I tend to forget how easy it is to add a piece of code to Chimera when the behaviour I want is not available. Though, I think it would have taken me awhile to sort this one out. Many Thanks, Ingvar On 2013-05-21 18:24, Tom Goddard wrote:
Hi Ingvar,
You're right there is no command option to dump text output about the map fits found during a search when you are not using the graphical user interface. But from Python you have access to all the results. I've attached a Python script that fits one map in another and prints out correlation, and the positioning matrix and other info, for example,
16 fits correlation = 0.99998944748 ave map value = 1.83066447933 points inside = 0.978085351788 times found 1 Matrix rotation and translation 0.99999654 -0.00109470 0.00239128 -0.06929400 0.00109836 0.99999823 -0.00153028 0.16076910 -0.00238960 0.00153290 0.99999597 0.01414383 Axis 0.50324711 0.78544818 0.36029640 Axis point -8.71411462 0.00000000 49.27362380 Rotation angle (degrees) 0.17437486 Shift along axis 0.09649976
correlation = 0.946936951988 ave map value = 1.39059352115 points inside = 0.21107266436 times found 1 Matrix rotation and translation -0.88578783 -0.46402579 -0.00774527 -84.25465980 -0.45395343 0.86978824 -0.19337708 -3.14068125 0.09646870 -0.16777507 -0.98109394 67.13834146 Axis 0.23752992 -0.96687475 0.09344922 Axis point -43.46328686 0.00000000 32.27793387 Rotation angle (degrees) 176.91070890 Shift along axis -10.70233149
[14 more fits]…
I made this script by looking at Chimera Python code
chimera/share/FitMap/fitcmd.py
which implements the fitmap command. And also I looked at search.py and fitlist.py in the same directory to figure out the Python functions I needed to call. It is not easy to figure that out. There is a page of Chimera Python example scripts
http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
Tom
On May 21, 2013, at 5:21 AM, ingvar wrote:
Hello,
I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution.
I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage.
Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option.
I am on RHEL 6.2/6.3 if that matter.
Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out.
Kind Regards, Ingvar
Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now")
Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid
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