August 2021 - Chimera-users - RBVI Mailing Lists

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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(no subject)
by Thirumurugan Prakasam 30 Oct '21

30 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Copy protein orientation
by SANDOVAL, KENNETH 06 Sep '21

06 Sep '21

Hello, I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following: 1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation Thank you, Kenneth Sandoval

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Making oligomers from Alphafold predictions
by tim smith 01 Sep '21

01 Sep '21

Hi All, Apologies for the nonrelated question!! Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you Best Smith

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Capture click event
by jeni_zen2004＠yahoo.co.in 30 Aug '21

30 Aug '21

Hi, Is there a way to capture the Chimera click event or a way to work around?I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid. Thanks,Catherine

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ITasser model looks different once PDB opened in UCSF Chimera
by Athena Andreosso 26 Aug '21

26 Aug '21

Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands. When I clicked on model 2 it was better but there's still a visible discrepancy. Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ? Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso(a)qimrberghofer.edu.au<mailto:AthenaAndreosso@qimrberghofer.edu.au> | www.qimr.edu.au<http://www.qimr.edu.au/> 300 Herston Road, Herston QLD 4006

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3D Visualization
by Song, David 25 Aug '21

25 Aug '21

Hi, My name is Dave Song, and I am a graduate student interested in visualizing protein structures in 3D. I was wondering if you had any recommendations in regards to computer hardware requirements for maximum performance while using Chimera/ChimeraX. Additionally, do you have any suggestions on monitors and 3D glasses that work well with Chimera? Thank you for your time, and I look forward to hearing from you. Best, Dave

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Chimera not responding
by Pritam Dey 23 Aug '21

23 Aug '21

Cannot execute 'gzip': no automatic decompression of .Z files Return code: -1073741819 Press return or enter to to exit

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Hollow Sticks When Exporting as STLs?
by Josh Moon 17 Aug '21

17 Aug '21

Hello, I hope to make this question as direct and simple as I can! When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my "stick" portions are hollow. This creates thin, weak walls for 3D printing. I've included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure. What am I doing incorrectly? Is there something I can do in Chimera to export a solid object with no "hollow tubes." Fixing this with 3d programs can be time consuming. Sincere thanks, Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

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Fc dimer fall apart after fusion with a GS linker
by tiger wang 16 Aug '21

16 Aug '21

Dear Ms/Mr helper: I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? Thanks very much for your help Sincerely TW

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Chimera-users August 2021