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 > >

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 >