March 2019 - Chimera-dev - RBVI Mailing Lists

About Chimera Extension Permission
by Yuhong Zha 25 Mar '19

25 Mar '19

Dear Sir or Madam, This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are currently developing a Chimera extension to implement our MAINMAST algorithm. However, when I update my Chimera to the newest version, I started to get permission errors. I'm using a Mac. In our extension, we have some code involving editing files like "os.remove(filename)". However, after the update, the extension receives error "Operation not permitted" when executing those lines. I think one possible reason might be improper updating steps. After the update, I started Chimera directly from installer instead of drag the icon to my folder. Then this error occurs. Later, even when I deleted the Chimera by dragging it to trash and deleting trash, and then re-download and install Chimera, the error still occurs. We have 2 Mac made the update but only one of them has this error. Do you have any clue why this happens? Thank you in advance for your help and looking forward to your reply! If there is any question regarding our extension, please let me know! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Re: [chimera-dev] Retrieving model_id / model_name via API
by Tom Goddard 07 Mar '19

07 Mar '19

Oops. Should be v.new_region(ijk_step = (1,1,1), adjust_step = False) Chimera automatically adjust the step size to stay within a maximum total number of voxels. The adjust_step = False means not to do that automatic changing of the specified step. Tom > On Mar 7, 2019, at 2:57 PM, Lars Hangartner <lhangart(a)scripps.edu> wrote: > > Hi Tom. > > Thanks for the reply. Unfortunately, this did not work. My implementation was as follows and did not change anything. > Best, > Lars > > for vol in openModels.list(modelTypes=[Volume]): > vol.new_region(ijk_step = (1,1,1)) > > > >> On Mar 7, 2019, at 1:07 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> To set the step of a Volume model v in Chimera in Python code >> >> v.new_region(ijk_step = (1,1,1)) >> >> Tom >> >> >>> On Mar 6, 2019, at 8:42 PM, Lars Hangartner <lhangart(a)scripps.edu <mailto:lhangart@scripps.edu>> wrote: >>> >>> Hi Eric, >>> >>> Thanks for the swift response, worked like a charm. May I also ask how to set the ’step’ property value from the volume viewer GUI pop-up from a script? >>> >>> Thanks, >>> >>> Lars >>> >>>> On Mar 6, 2019, at 3:40 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Lars, >>>> The model attributes for the ID are ‘id’/‘subid’ for the parts before and after any ‘.’ respectively, and the ‘name’ attribute has the model name. You would loop through all volume models with something like: >>>> >>>> from chimera import openModels >>>> from VolumeViewer import Volume >>>> for vol in openModels.list(modelTypes=[Volume]): >>>> print “%d.%d %s” % (vol.id <http://vol.id/>, vol.subid, vol.name) >>>> >>>> We realize the programmer documentation isn’t great. What little we have you can find here: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> . One of our objectives for ChimeraX is much better programmer documentation. >>>> >>>> —Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> >>>> >>>>> On Mar 6, 2019, at 10:40 AM, Lars Hangartner <lhangart(a)scripps.edu <mailto:lhangart@scripps.edu>> wrote: >>>>> >>>>> Hi guys, >>>>> >>>>> I am desperately looking to get the model_id / model name from all open volume objects. I have tried openModel.list()[0].model_id in many iterations but no success… I would like to iterate through models and identify the resampled ones. >>>>> >>>>> Can anybody help? >>>>> >>>>> Thanks, >>>>> >>>>> Lars >>>>> >>>>> >>>>> P.S: API documentation would really be helpful. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-dev mailing list >>>>> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> >>>>> >>>> >>> >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> >> >

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Retrieving model_id / model_name via API
by Lars Hangartner 07 Mar '19

07 Mar '19

Hi guys, I am desperately looking to get the model_id / model name from all open volume objects. I have tried openModel.list()[0].model_id in many iterations but no success… I would like to iterate through models and identify the resampled ones. Can anybody help? Thanks, Lars P.S: API documentation would really be helpful.

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Chimera-dev March 2019