- ChimeraX-users - RBVI Mailing Lists

Can ChimeraX morph between two surfaces?
by Steve Chou 14 Feb '19

14 Feb '19

Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou

2 5

bug report: hide with silhouettes
by Alexis Rohou 11 Feb '19

11 Feb '19

Hi Elaine, ChimeraX team, When silhouettes is set to true, hiding all models causes a bug whereby the display panel is not responsive / redrawn. As far as I can tell other parts of the GUI are still working. Below is a minimal reproducer. Attached are screenshots of what I'm seeing when silhouettes true (bug) or silhouettes false (no bug). I am running this on MacOS 10.13.6 on a MBP with graphics "Intel Iris Plus Graphics 650 1536MB" (sorry not sure what might be relevant here), and the Chimera version is: UCSF ChimeraX version: 0.8 date: 2018-12-17 22:26:30 UTC branch: v0.8 commit: 412d62d1949722ed7f52b3e515ec0f3b70b6b7af Python: 3.6.4 Obviously there's a workaround to avoid this but this caught me a few times in the last couple of days and it'd be nice to not have to watch out for it because the only solution I've found so far is to quit ChimeraX and start again. Cheers, Alexis PS. here's the reproducer: open pdb:1tbq set silhouettes true # Hide stuff hide #!1 models # Wait a bit (alternatively stop here and return to interactive use before doing the next step) wait 100 # print version out version verbose # Try to show it again. This should work (and does if silhouettes false) show #!1 models

3 4

volume zone - unexpected behavior when newMap false
by Alexis Rohou 11 Feb '19

11 Feb '19

Hello, I've been playing with volume zone and having good fun, but... I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true). When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation. Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis

3 4

Can ChimeraX add noise (Brownian-like motion) in morphing?
by Steve Chou 11 Feb '19

11 Feb '19

Dear ChimeraX support, When morphing from one structure to another unaligned structure, ChimeraX follows a smoothly curved path? Can it add noise (Brownian-like motion) to the path? All the best, Steve -- Steve Chou

2 3

equivalent to "move cofr"
by Alexis Rohou 08 Feb '19

08 Feb '19

Hello, Switching to ChimeraX, I find myself looking for an equivalent to "move cofr <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html#cofr>". Is there one? The use case is: I'm working on a particular part of a map & structure, I open a structure of a homologuous domain from the PDB, but its coordinates are way off, and I want to move it to the region I'm working on without having to zoom out and drag it. My apologies if this is in the documentation somewhere, I'm still finding my way around. Cheers, Alexis

2 2

Output motion prickle magnitude
by Scott, Brandon L. 08 Feb '19

08 Feb '19

Using the measure motion command I am able to generate the prickles on the surfaces correctly, which is great for visualization. Is it possible to write the magnitude of those prickles, and the index to a file so we can do further analysis on the distributions? Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

How to align two molecules using a subset of atoms in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX support team, I tried the following command first - it worked well. ================== match #1/A to #2/A ================== Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix." ================== matchmaker #1/A:10-20@CA to #2/B:10-20@CA ================== System Info: ================== Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo ChimeraX version: 0.9 (2019-02-05) ================== Thank a bunch! Steven -- Steve Chou

2 3

How to re-define the secondary structure info in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX developers and users, In Chimera, I can use the following commands to redefine the secondary structure info. ============================ setattr r isHelix false : setattr r isSheet false : setattr r isSheet true :8-12,16-21 setattr r isHelix true :55-61,78-92 ============================ What's the ChimeraX equivalent? By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX? Many thanks in advance! Steve -- Steve Chou

2 1

Bio-Formats with ChimeraX?
by Matthew Akamatsu 07 Feb '19

07 Feb '19

Hi, I just started using ChimeraX to render and save 3D time lapse microscopy data as a high-performance replacement of Fiji. I am wondering how flexible ChimeraX can be in opening different TIF-derived file formats - particularly hyperstacks (multi color, multi Z, multi time). Other desired formats would be proprietary formats like .nd2 and .sld . Bio-Formats does all of this in an open-source manner - how feasible would it be to have bio-formats type functionality in ChimeraX? Thanks, Matt

2 3

VR in ChimeraX and Dell Visor
by Lewandowski, Jozef 24 Jan '19

24 Jan '19

Hi, Has anyone tested Dell Visor for VR in ChimeraX? If yes are there any issues you have run into? I am assuming that the experience should be similar to what Tom has described for Samsung Odyssey but I would appreciate if anyone had specific feedback on this particular piece of hardware. Thanks, Józef

2 1