Hello,
Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that IMP.display.ChimeraWriter does not exist anymore and rmf needs to be used to write the geometry to chimera format. I have been searching for examples and I think I need to use rmf_display and give "chimera" as a parameter, but I did not find any example, all the examples are with PymolWriter. Can anyone help me writing in chimera format using the rmf? And do I need to change more lines of code with this change or can I just replace "w = IMP.rmf.ChimeraWriter(storage_folder+"/"+chimera_file)" with a similar line??
thanks a lot
Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summar...
On 5/26/16 8:18 AM, Ibai Irastorza wrote: > Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that > IMP.display.ChimeraWriter does not exist anymore and rmf needs to be > used to write the geometry to chimera format.
That's not correct. IMP does not use RMF to write Chimera format; IMP no longer writes Chimera format. This is because Chimera format is not very flexible or general. Write your structures out as RMF files instead (there are several examples in the IMP.rmf module) and Chimera can read those.
Ben
thanks! now I get it.
The problem is that I am only able to get videos when trying to save in the rmf format and I am only interested in the final models, not all the frames, because of the post analysis of these models.
Isn't there a way to get only the rmf format of the final model with IMP? or I have to manage to get the rmf file, open with chimera and save the session or the pdb with it?
Thanks for ur time and trouble Ben
Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summar...
2016-05-26 23:18 GMT+02:00 Ben Webb ben@salilab.org:
> On 5/26/16 8:18 AM, Ibai Irastorza wrote: > >> Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that >> IMP.display.ChimeraWriter does not exist anymore and rmf needs to be >> used to write the geometry to chimera format. >> > > That's not correct. IMP does not use RMF to write Chimera format; IMP no > longer writes Chimera format. This is because Chimera format is not very > flexible or general. Write your structures out as RMF files instead (there > are several examples in the IMP.rmf module) and Chimera can read those. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
On 5/26/16 4:07 PM, Ibai Irastorza wrote: > The problem is that I am only able to get videos when trying to save in > the rmf format and I am only interested in the final models, not all the > frames, because of the post analysis of these models.
I don't follow you. By "videos" you mean you're saving a trajectory? Just modify your script to only write out the final model (essentially, a trajectory with a single frame in it) by only calling IMP.rmf.save_frame() once.
Ben