[Chimera-users] Fitmap in batch mode

ingvar ingvar at ebi.ac.uk
Wed May 22 06:16:21 PDT 2013


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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>> 


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