Hi,
I have some problem in understanding how the new writers work.
I'm using the CMMwriter like, writing out only the final model (frame): > # Setup a CMM writer > writer = IMP.display.CMMWriter("model.%1%.cmm") > log = IMP.display.WriteOptimizerState(writer) > g = IMP.display.XYZRsGeometry(ps) > log.add_geometry(g) > log.update()
This generates the model file with the coordinates (each line is a chimera marker) and a file called "model.%1%.cmm", which only contains the header line: <marker_set name="model.0.cmm">
This header should be in the model file, but since it is missing it causes a problem with chimera. Is there a way to get rid of the model.%1%.cmm file so that to have just one file containing all the informations? I've tried without the %1% string: > writer = IMP.display.CMMWriter("model.1.cmm")
but that rises the error: > e = o.do_optimize(steps) > File "/usr/src/imp/trunk/build/lib/IMP/core/__init__.py", line 4338, in do_optimize > return _IMP_core.MonteCarlo_do_optimize(self, *args) > _IMP.InternalException: Cannot set frame on writer without file name pattern.
Thanks, Davide
-- Davide Baù Structural Genomics Laboratory Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler 16, 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/
*** http://www.saveaswwf.com ***
I just fixed the bug that was causing the headers to not be added to all the files and the %1% file to be created. Sorry about that. The test cases were a bit too simple to catch the bug. They have been improved and hopefully will catch such problems better in the future.
On Jun 13, 2011, at 9:46 AM, Davide Baù wrote:
> Hi, > > I have some problem in understanding how the new writers work. > > I'm using the CMMwriter like, writing out only the final model (frame): >> # Setup a CMM writer >> writer = IMP.display.CMMWriter("model.%1%.cmm") >> log = IMP.display.WriteOptimizerState(writer) >> g = IMP.display.XYZRsGeometry(ps) >> log.add_geometry(g) >> log.update() > > > This generates the model file with the coordinates (each line is a chimera marker) and a file called "model.%1%.cmm", which only contains the header line: > <marker_set name="model.0.cmm"> > > This header should be in the model file, but since it is missing it causes a problem with chimera. Is there a way to get rid of the model.%1%.cmm file so that to have just one file containing all the informations? I've tried without the %1% string: >> writer = IMP.display.CMMWriter("model.1.cmm") > > but that rises the error: >> e = o.do_optimize(steps) >> File "/usr/src/imp/trunk/build/lib/IMP/core/__init__.py", line 4338, in do_optimize >> return _IMP_core.MonteCarlo_do_optimize(self, *args) >> _IMP.InternalException: Cannot set frame on writer without file name pattern. > > Thanks, > Davide > > > -- > Davide Baù > Structural Genomics Laboratory > Bioinformatics & Genomics Department, Prince Felipe Research Center > Avda. Autopista del Saler 16, 46012 Valencia, Spain > Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 > email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ > > *** http://www.saveaswwf.com *** > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Thanks Daniel!
Davide
On Jun 13, 2011, at 9:14 PM, Daniel Russel wrote:
> I just fixed the bug that was causing the headers to not be added to all the files and the %1% file to be created. Sorry about that. The test cases were a bit too simple to catch the bug. They have been improved and hopefully will catch such problems better in the future. > > > On Jun 13, 2011, at 9:46 AM, Davide Baù wrote: > >> Hi, >> >> I have some problem in understanding how the new writers work. >> >> I'm using the CMMwriter like, writing out only the final model (frame): >>> # Setup a CMM writer >>> writer = IMP.display.CMMWriter("model.%1%.cmm") >>> log = IMP.display.WriteOptimizerState(writer) >>> g = IMP.display.XYZRsGeometry(ps) >>> log.add_geometry(g) >>> log.update() >> >> >> This generates the model file with the coordinates (each line is a chimera marker) and a file called "model.%1%.cmm", which only contains the header line: >> <marker_set name="model.0.cmm"> >> >> This header should be in the model file, but since it is missing it causes a problem with chimera. Is there a way to get rid of the model.%1%.cmm file so that to have just one file containing all the informations? I've tried without the %1% string: >>> writer = IMP.display.CMMWriter("model.1.cmm") >> >> but that rises the error: >>> e = o.do_optimize(steps) >>> File "/usr/src/imp/trunk/build/lib/IMP/core/__init__.py", line 4338, in do_optimize >>> return _IMP_core.MonteCarlo_do_optimize(self, *args) >>> _IMP.InternalException: Cannot set frame on writer without file name pattern. >> >> Thanks, >> Davide >> >> >> -- >> Davide Baù >> Structural Genomics Laboratory >> Bioinformatics & Genomics Department, Prince Felipe Research Center >> Avda. Autopista del Saler 16, 46012 Valencia, Spain >> Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 >> email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ >> >> *** http://www.saveaswwf.com *** >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Hi Daniel,
the headers are now added to the coordinate files but the files containing the header are still generated, e.g. setting "writer = IMP.display.CMMWriter("model.%1%.cmm")" generates a file named "model.1.-1.cmm" which contains the following lines:
<marker_set name="model.1.0.cmm"> <marker_set name="model.1.0.cmm"> </marker_set>
Davide
On Jun 13, 2011, at 9:14 PM, Daniel Russel wrote:
> I just fixed the bug that was causing the headers to not be added to all the files and the %1% file to be created. Sorry about that. The test cases were a bit too simple to catch the bug. They have been improved and hopefully will catch such problems better in the future. > > > On Jun 13, 2011, at 9:46 AM, Davide Baù wrote: > >> Hi, >> >> I have some problem in understanding how the new writers work. >> >> I'm using the CMMwriter like, writing out only the final model (frame): >>> # Setup a CMM writer >>> writer = IMP.display.CMMWriter("model.%1%.cmm") >>> log = IMP.display.WriteOptimizerState(writer) >>> g = IMP.display.XYZRsGeometry(ps) >>> log.add_geometry(g) >>> log.update() >> >> >> This generates the model file with the coordinates (each line is a chimera marker) and a file called "model.%1%.cmm", which only contains the header line: >> <marker_set name="model.0.cmm"> >> >> This header should be in the model file, but since it is missing it causes a problem with chimera. Is there a way to get rid of the model.%1%.cmm file so that to have just one file containing all the informations? I've tried without the %1% string: >>> writer = IMP.display.CMMWriter("model.1.cmm") >> >> but that rises the error: >>> e = o.do_optimize(steps) >>> File "/usr/src/imp/trunk/build/lib/IMP/core/__init__.py", line 4338, in do_optimize >>> return _IMP_core.MonteCarlo_do_optimize(self, *args) >>> _IMP.InternalException: Cannot set frame on writer without file name pattern. >> >> Thanks, >> Davide >> >> >> -- >> Davide Baù >> Structural Genomics Laboratory >> Bioinformatics & Genomics Department, Prince Felipe Research Center >> Avda. Autopista del Saler 16, 46012 Valencia, Spain >> Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 >> email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ >> >> *** http://www.saveaswwf.com *** >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
participants (3)
-
Daniel Russel -
Davide Baù -
Davide Baù