- Chimera-users - RBVI Mailing Lists

Creating discs
by Prathvi Singh 14 Mar '23

14 Mar '23

Hi Elaine, Is it possible in chimera or chimeraX to create such planes for membrane proteins which show the plasma membrane boundaries as shown in: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html If yes, then kindly tell me how to do it. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

Query colors?
by Esser, Lothar (NIH/NCI) [E] 13 Mar '23

13 Mar '23

Hi, in my current project I am reading about 50 pdb files. Chimera does a good job at assigning pleasant colors automatically and I would like to get access to the chosen colors to write 2dlabels with the same color. How do I get access to the molecular (ribbon color) ? It's probably trivial but well, I somehow could not figure this out. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

3 3

Selecting planes using command line
by Prathvi Singh 13 Mar '23

13 Mar '23

Hi Elaine, I see that after defining a plane, it gets listed in the "Axes/Planes/Ellipsoids" section with each plane having a unique ID. However, I am unable to use these IDs to select planes individually via command line. Moreover, when I hover my mouse over a plane, it displays: #0:? How to select the planes using the command line? And, can I move these planes independent of the protein model? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

export stl file
by Yifan Wang 08 Mar '23

08 Mar '23

Hi Chimer team, I have a question about exporting stl files. Because I load one pdb file in chimera and export as a stl file then I load in a CAD based software to compare with another stl file I generated through another software. So the input to generate the stl file are the same, but the results are different. The results show that two different stl files in the same 3D quadrant but it got rotated at different angles. What may cause this issue? Thank you so much! Yifan

3 2

Issue with MD movie
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users ! I am working on visualization of MD trajectory dealing with the multi-model pdb composed of 3000 snapshots. First of all, there are no problems with this file in other software like vmd or even Chimera-X. But when I load it into the Chimera (I use context menu tools ... / MD movie), I get three times more frames (9000 !) and the overall dynamics looks very unnatural when I try to play it as a movie. Any possibilities how could I fix it ? Many thanks in advance Best regards Enrico

2 1

Questions about cartoon visualisation
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users! I have several basic commands related to the visualization of cartoon models: 1) Is it possible to color secondary structure elements (normally integrated in the context menu by means of tools -> depiction) via some command called from command line / script ? 2) how could I change the representation style of the cartoon diagrams e.g. radius of loops or introducing some artistic elements in alpha-helixes / B-sheets ? Is it possible to modify it via commands ? Many thanks in advance Best wishes Enrico

2 2

Hydrogen issue with minimization
by Guillaume Grataloup 08 Feb '23

08 Feb '23

Dear support, I currently trying to perform a minimization on a hERG canal pdb file but I run into an issue I didn't manage to solve: "Residue #0:23.A (GLU/glutamic_acid) should have either atom HB1 or HB3, but not both" Maybe the problem comes from the pdb file, I put it in attachment just in case it can help understand the issue. Also my Chimera version is 1.16 and I'm on Windows Thank you in advance Guillaume Grataloup 5th year bioengineering studient at Polytech Nice Sophia, France

2 1

A question abount "define axis"
by squirrel 07 Feb '23

07 Feb '23

Dear Chimera list, I'm Interested in finding and showing the distance of N-terminal and C-terminal between two proteins. As I can't download GUI so I use "chimera --nogui" to compute them. That's my command: open protein.pdb sel:1.Ln; measure center sel mark True radius 0.3 color cyan modelId 1; sel:1.S2; measure center sel mark True radius 0.3 color cyan modelId 2; sel:390.Lz; measure center sel mark True radius 0.3 color cyan modelId 3; sel:44.LH; measure center sel mark True radius 0.3 color cyan modelId 4; distance #1 #3; define axis name Ln_N_Lz_C #1 #3; distance #1 #4; define axis name Ln_N_LH_C #1 #4; distance #2 #3; define axis name S2_N_Lz_C #2 #3; distance #2 #4; define axis name S2_N_LH_C #2 #4; stop But I found that when I input "distance" and "define axis" the terminal shows that "Must specifiy at least two atoms/centroids to define an axis". I am puzzle because I can see the #1,#2,#3，#4 in the list. Can you give me some guidance? Thanks in advance

4 3

Conference Announcement: 35th MMWS in Erlangen, Germany
by Harald Lanig 07 Feb '23

07 Feb '23

1 0

A question about "Distance Measure"【2】
by squirrel 05 Feb '23

05 Feb '23

Dear Ms/Mr： Thanks to your reply. In the last mail, I ask for your help and I am appreciate your detailed description. This is the content of last mail: "I meet a problem recently. Every proteins have N-terminations and C-terminations, and I want to measure the distance between all proteins at each other's N-C, N-N, and C-C terminals by using UCSF Chimera. But there are too many proteins for me to start.I've read Chimera's tutorials and searched my questions online. But I didn't find the answer I needed.Can you please give me some guidance or tips？" Now I would like to add some new information and have two new questions I would like to consult you. I want to measure the end distances of many proteins within a model. Because there are so many proteins, it is not practical to measure them one by one. So I want to ask if you use the command line method to measure the distance of multiple proteins. In addition, I tried to follow your guidance and found that the measured atoms name showed -1, so I couldn't confirm which atom was the distance between them, and I am puzzled how I should change the name. Looking forward to your reply.♥

2 1