- Chimera-dev - RBVI Mailing Lists

Loop refinement in chain A and Chain B
by Aashish Bhatt 06 May '19

06 May '19

Dear Sir/ Ma'am I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. Can you please give me an idea of how to build the complete structure? Best regards Aashish INST-Mohali India

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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 08 Mar '19

08 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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rc(command): save session command problem
by Yuhong Zha 28 Feb '19

28 Feb '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, we encountered a problem of using Chimera's command line "rc("save current_session.py")" to save current session. This problem only happens in some Mac system. In our extension, we want to save the whole session after open some files. So we first do "os.chdir(path)" to where we want to store the file. Then we use "rc("save current_session.py")" to save the current session info to a file. However, after we changed the current working directory correctly, "rc("save current_session.py")" still fails and displays error message of "Directory () does not exists". I have attached the code and error we encounter. I checked the current working directory right before calling "rc("save current_session.py)" and I am sure the current working directory is correct and is not (). Is there any settings we missed that result in rc(command) only execute at directory ()? Or is there any way that we can specify which directory we want to save the session using rc(command)? We tried it on 2 Mac but only one of them has this problem. I am thinking maybe some preference setup would cause this problem? Also, we encountered a problem of "Access Denied" when modifying the files from Chimera. On one Mac, we updated to the latest version chimera. But when we run our extension, we get "Access Denied" error when try to remove some files. No such error occurs within the same Mac before updating the version. Do you have any clue why that happens. If there is any question regarding our extension, please let me know! For more information about our lab, here is the link to our website: http://www.kiharalab.org/index.php. Kihara Bioinformatics Laboratory, Purdue University<http://www.kiharalab.org/index.php> www.kiharalab.org Area of Research Dr. Daisuke Kihara Principal Investigator. Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. Thank you in advance for your help and looking forward to your reply! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Summit supercompuer
by Victor Padilla-Sanchez 22 Jan '19

22 Jan '19

Dear Chimera, Would you tell me if someone has developed/ported Chimera to Summit supercomputer at Oak Ridge National Laboratory ? Please let me know, Thank you very much, Victor Padilla-Sanchez, PhD

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Auto-start extension in the Chimera
by Yuhong Zha 11 Jan '19

11 Jan '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, we encountered a problem of how to automatically start our extension when opening the Chimera. Now we have to go to IDLE and manually type "import our_extension.gui" to import our extension. Is there a way in the Chimera that could allow us to automatically open the extension every time we start the Chimera? Our current Chimera version is UCSF Chimera, production version 1.12 . If there is any question regarding our extension, please let me know! For more information about our lab, here is the link to our website: http://www.kiharalab.org/index.php. Kihara Bioinformatics Laboratory, Purdue University<http://www.kiharalab.org/index.php> www.kiharalab.org Area of Research Dr. Daisuke Kihara Principal Investigator. Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. Thank you in advance for your help and looking forward to your reply! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Chimera orbitals alias question
by Benjamin Looker 16 Oct '18

16 Oct '18

Hello! My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function? An alias such as: alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. Any help would be greatly appreciated! Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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Freeing chimera memory after combining two molecules
by Daniel VH 05 Oct '18

05 Oct '18

Hi, In my python script I'm using the combine() function to merge a protein and a molecule into one model and since I'm doing this multiple times and only use the combined result to save it with pdbWrite I want to free the memory of the object combination right after that, but after the instructions chimera.openModels.close(combination), del combination, chimera.update.checkForChanges(), gc.collect(), chimera.closeSession() the memory is not freed. This is the code that reproduces the problem, it uses the molecules in the zipfile I have attatched. import chimera from Combine import combine import zipfile import time import gc import os #from memory_profiler import profile for itemnum in range(3): #@profile def pathmaker(itemnum): dirpath = os.path.dirname(os.path.realpath(__file__)) zippath=dirpath+'/'+'test1_000.zip' torsionpath=zipfile.ZipFile(zippath).extract('Pathway_000_Pathway.txt') proteinpath=zipfile.ZipFile(zippath).extract('Protein_000_Protein.mol2') ligandpath=zipfile.ZipFile(zippath).extract('Ligand_000_Ligand.mol2') opened = chimera.openModels.open(proteinpath) protein = opened[0] opened1 = chimera.openModels.open(ligandpath) mol=opened1[0] combination=combine([mol,protein],protein) totalnum=str(itemnum).zfill(3)+'_'+str(i).zfill(3) chimera.pdbWrite([combination], chimera.Xform(), 'testpdb%s.pdb' %totalnum) print('writing testpdb%s.pdb' %totalnum) chimera.openModels.close(combination) del combination chimera.update.checkForChanges() gc.collect() chimera.closeSession() for i in range(20): pathmaker(itemnum) #this stops the code and shows memory increase for each iteration print('pause 6 seconds...') time.sleep(6)

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Auto set threshold boundaries and colors
by Benjamin Looker 24 Sep '18

24 Sep '18

Hello! My name is Benjamin Looker, and I have recently become acquainted with your software for visualization of molecular orbital calculations that my group does with some regularity. I was wondering whether the statement on this page refers to a specific preferences file in the Chimera program files. : ( http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/… ) "For unsigned data types, an initial threshold is set so that 1% of voxels" The reason I ask is because it would be much simpler, given a known color code and level, to standardize the import of files into Chimera for any sort of publication, especially in the event that many molecular orbitals needed to be visualized at once for a project. Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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