As I said, if you print the profile after fitting, everything works. I attached the modified script.

Dina

On Sun, Dec 12, 2010 at 3:21 PM, Robert Brynmor Fenwick robert.fenwick@irbbarcelona.org wrote: > It would be great if you could try this out. > > The files that I sent yesterday should work the pdbs have the > extension .fit. The code should run. The input fitting file is > saxs.dat > > Bryn > > Sent from my iPod > > On 12/12/2010, at 20:45, Dina Schneidman duhovka@gmail.com wrote: > >> Robert, >> >> In case you didn't get my yesterday answer: >> >> you have to run fit_profile function before printing out the profile: >> >> chi = saxs_score.fit_profile(sum_profile) >> >> it will sum up the partial profiles into a single one. >> >> After fit_profile you can write the profile into file >> >> sum_profile.write_SAXS_file('out.dat') >> >> so just move this line to the end of your script. >> >> If you want me to try to run it, please attach your input PDBs. >> >> Dina >> >> On Sun, Dec 12, 2010 at 7:02 AM, Robert Fenwick >> robert.fenwick@irbbarcelona.org wrote: >>> >>> Hi, >>> I am having a bit of a tough time with writing a script and wondered if >>> someone could help. >>> I have installed the latest nightly builds and am trying to write the >>> following: >>> I wish to loop over n structures, calculate the summed partial saxs profile. >>> I hope to achieve this using the attached code and example structures. >>> I think that I should use the add_partial_profiles function, however I can >>> not get it to work the way that I would like. Is there a way to access the >>> values in the predicted saxs profiles using the python interface? >>> Here is my current code, but it does not work as I would expect. >>> Bryn >>> >>> >>> R. Bryn Fenwick >>> robert.fenwick@irbbarcelona.org >>> Post-doctoral fellow >>> Chemistry and Molecular Pharmacology Programme >>> Institute for Research in Biomedicine (IRB Barcelona) >>> Parc Científic de Barcelona >>> Baldiri Reixac 10, 08028 Barcelona, SPAIN >>> Tel. (+34) 9340 20460 >>> >>> >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >

This is the code tat I have been trying to compile:

svn checkout -r 7371 http://svn.salilab.org/imp/trunk imp

B.

On 21 January 2011 10:26, Robert Brynmor Fenwick < robert.fenwick@irbbarcelona.org> wrote:

> Can you send me a tar file of some imp code that compiles the python > interface and works with the script that you sent previously. I am sorry to > bother you, I am getting amazing results from your program but I have had a > fatal crash on a machine here that has robbed me of the code that I was > using. I have tried various builds and none seem to work. > > Regards, > > Bryn > > > On 13 December 2010 20:52, Dina Schneidman dina@salilab.org wrote: > >> As I said, if you print the profile after fitting, everything works. I >> attached the modified script. >> >> Dina >> >> On Sun, Dec 12, 2010 at 3:21 PM, Robert Brynmor Fenwick >> robert.fenwick@irbbarcelona.org wrote: >> > It would be great if you could try this out. >> > >> > The files that I sent yesterday should work the pdbs have the >> > extension .fit. The code should run. The input fitting file is >> > saxs.dat >> > >> > Bryn >> > >> > Sent from my iPod >> > >> > On 12/12/2010, at 20:45, Dina Schneidman duhovka@gmail.com wrote: >> > >> >> Robert, >> >> >> >> In case you didn't get my yesterday answer: >> >> >> >> you have to run fit_profile function before printing out the profile: >> >> >> >> chi = saxs_score.fit_profile(sum_profile) >> >> >> >> it will sum up the partial profiles into a single one. >> >> >> >> After fit_profile you can write the profile into file >> >> >> >> sum_profile.write_SAXS_file('out.dat') >> >> >> >> so just move this line to the end of your script. >> >> >> >> If you want me to try to run it, please attach your input PDBs. >> >> >> >> Dina >> >> >> >> On Sun, Dec 12, 2010 at 7:02 AM, Robert Fenwick >> >> robert.fenwick@irbbarcelona.org wrote: >> >>> >> >>> Hi, >> >>> I am having a bit of a tough time with writing a script and wondered >> if >> >>> someone could help. >> >>> I have installed the latest nightly builds and am trying to write the >> >>> following: >> >>> I wish to loop over n structures, calculate the summed partial saxs >> profile. >> >>> I hope to achieve this using the attached code and example structures. >> >>> I think that I should use the add_partial_profiles function, however I >> can >> >>> not get it to work the way that I would like. Is there a way to access >> the >> >>> values in the predicted saxs profiles using the python interface? >> >>> Here is my current code, but it does not work as I would expect. >> >>> Bryn >> >>> >> >>> >> >>> R. Bryn Fenwick >> >>> robert.fenwick@irbbarcelona.org >> >>> Post-doctoral fellow >> >>> Chemistry and Molecular Pharmacology Programme >> >>> Institute for Research in Biomedicine (IRB Barcelona) >> >>> Parc Científic de Barcelona >> >>> Baldiri Reixac 10, 08028 Barcelona, SPAIN >> >>> Tel. (+34) 9340 20460 >> >>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> IMP-users mailing list >> >>> IMP-users@salilab.org >> >>> https://salilab.org/mailman/listinfo/imp-users >> >>> >> >>> >> >> >> >> _______________________________________________ >> >> IMP-users mailing list >> >> IMP-users@salilab.org >> >> https://salilab.org/mailman/listinfo/imp-users >> > >> > _______________________________________________ >> > IMP-users mailing list >> > IMP-users@salilab.org >> > https://salilab.org/mailman/listinfo/imp-users >> > >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> > > > -- > R. Bryn Fenwick > robert.fenwick@irbbarcelona.org > Post-doctoral fellow > Chemistry and Molecular Pharmacology Programme > Institute for Research in Biomedicine (IRB Barcelona) > Parc Científic de Barcelona > Baldiri Reixac 10, 08028 Barcelona, SPAIN > Tel. (+34) 9340 20460 >