- Chimera-users - RBVI Mailing Lists

segment and group density together
by Yangqi Gu 21 Jun '19

21 Jun '19

Hi Chinera users, I have a density map of a filament. After I segmented the map, I want to group all the outer globular domain (which is part of a monomer) together. Instead of group them one by one, is there a quicker way to do this? I have the helical symmetry of the filaments. Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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chimera help in spacing out two structures within the same session
by #LAI KEI ONN# 21 Jun '19

21 Jun '19

Dear Chimera team would appreciate if you have any advice in spacing out two/or more structures within the same chimera session (e.g. the green structure away from the beige ones) so as to clearly visualise the intercrosslinks (red and blue sticks) between two different structures. Currently everything is superimposed with one another and i tried separating all the structures into different sessions and recombining it again but it didnt work. I am using xlinkanalyzer plugin with chimera. Would appreciate your kind advice, [cid:a79ad9c6-047a-493c-abc9-3ac3d537f4df] thank you! Best Regards Kei Onn LAI|黎啟諳 Phd Student Lee Kong Chian School of Medicine

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Chimera - mask after vop
by Ryan Harlich 18 Jun '19

18 Jun '19

Hi Chimera team, Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth: WORKING SOLUTION #chimera_script.write('open ' + paths['input'] + '\n' # 'open ' + paths['ground_truth'] + '\n' # 'molmap #1 6 gridSpacing 1\n' # 'volume #1.1 level 0.1\n' # 'mask #0 #1.1\n' # 'vop resample #2 onGrid #1.1\n' # 'volume #3 save ' + paths['cleaned_map']) NEW SOLUTION chimera_script.write('open ' + paths['input'] + '\n' 'vop gaussian #0 sDev 2\n' 'vop median #1 iterations 5 modelId #2.1\n' 'volume #2.1 level 0.1\n' 'mask #0 #2.1\n' 'vop resample #3 onGrid #2.1\n' 'volume #4 save ' + paths['cleaned_map']) While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes. [cid:image001.png@01D525AB.830ADC20] Thank you, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Chimera local resolution color
by Dmitry Semchonok 14 Jun '19

14 Jun '19

Dear colleagues, I have a cryo-em map after resmap local resolution. I would like to see not just the 2D colored slices but the hole model (not in the movie mode). How to color the model model in chimera based o remap? I would like the final result be similar to https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu… <https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu…> Thank you. Sincerely, Dmitry

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Stereo glasses
by Jonathan Sheehan 14 Jun '19

14 Jun '19

Hi all, What stereo setup are people recommending these days? It seems that NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there something else that is available and works well? Thanks for any advice! -Jonathan

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Script to generate and fit structures
by Ahmad Khalifa 12 Jun '19

12 Jun '19

I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place. Is it feasible, how can I do it? Regards.

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counter ions
by patrizio.arrigo＠ge.ismac.cnr.it 12 Jun '19

12 Jun '19

Dear All I would like to use counter ions of nucleic acids not included in the default list of Chimera. I do not know how to perform this action. The option add ions offers only a limited set of ionic species I guess that is necessary to use amber18. Can you give me some suggestions Dr. Patrizio Arrigo CNR SMAC

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Chimera silent installer options for RHEL 7.6
by Darin Lory 11 Jun '19

11 Jun '19

Chimera Gurus, Are there linux silent install options for the Chimera so I can specify the installation directory, etc. I have chimera working via the regular installation method. My team and I are trying to automate the installation via Ansible playbook. Kindly advise, -Darin "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'" -Issac Asimov [image: --] Darin S. Lory [image: https://]about.me/darin.lory <https://about.me/darin.lory?promo=email_sig&utm_source=email_sig&utm_medium…>

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Chimera - can I tweak the red color on the Red-cyan stereo view
by Tweten, Rodney K. (HSC) 11 Jun '19

11 Jun '19

We are displaying our protein structures on a large TV in the Red-Cyan stereo view, which works pretty good for 3D viewing (except the required loss of specific colors). We tend to see a bit of ghosting of the red structure, which I suspect is that the red color lens of the Red-Cyan glasses we have (we’ve tried a few with the same results) is not quite matched to that being used by Chimera in its Red-Cyan stereo view. I was wondering if there is any way the user could tweak the red color being used by chimera in this stereo view to more closely match that of the glasses (assuming that this is responsible for the ghosting of the red structure). Thanks! Rodney Tweten George Lynn Cross Professor "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” Isaac Asimov BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1

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APBS
by Karl R Voigtritter 11 Jun '19

11 Jun '19

Hello, I am trying to display an APBS surface. I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1 server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the "color" nothing happens. -Karl Voigtritter, Ph.D. California State University, Chico

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