[Chimera-users] Fitmap in batch mode
ingvar at ebi.ac.uk
Tue May 21 05:21:48 PDT 2013
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.
Typical python script:
from chimera import runCommand as rc
rc("volume #0 level 1.34 transparency 0.5")
rc("volume #1 level 0.58 transparency 0.5")
rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2
#rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2")
Setup to run with Xvfb (in bash):
while [ -f /tmp/.X$i-lock ]
Xvfb :$i &
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