January 2025 - ChimeraX-users - RBVI Mailing Lists

Confirming coordinate axis
by Abhinaba Das 24 Jan '25

24 Jan '25

Dear ChimeraX-users, I'm writing to ask if there is a way to view the x,y,and z axis live while model building. I've a helical map generated in CryoSPARC which has a D1 symmetry. I could generate the asymmetric unit (ASU) for the corresponding C1 reconstruction but having issues applying D1 symmetry. The approach I've taken is to make a diheral copy of the C1 ASU (turn y 180 center <mapId> coordinateSystem <mapId> model <modelid>; followed by combine command). This should generate the dihedral ASU, and if the helical symmetry is applied should generate the symmetric copies (?). But seems not to be working.. I've assumed that the dyad axis is along the y-axis (cryosparc says for its output map). Just wondering if the axes are aligned.. Thanks, Abhi

3 2

openmmforcefields
by Lewandowski, Jozef 24 Jan '25

24 Jan '25

Hi, I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX? Thanks, Józef

3 2

Surface Color
by Hansen, Bryan (NIH/NIAID) [E] 24 Jan '25

24 Jan '25

Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

2 3

Assigning a custom net charge for a ligand using dockprep
by Jade Shi 24 Jan '25

24 Jan '25

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly? Thanks a lot! Jade

2 1

Draw and build secondary structures interactively
by Roden Deng Luo 22 Jan '25

22 Jan '25

Hi, I know there is a tool and command "build". But it is not that interactive. I wonder if there is a feature in ChimeraX (or any other tools) that can allow the user to draw in 3D space (or 2D) lines and then specify some segments as alpha-helices and some other segments as beta-sheets. I imagine the generated structure can be a backbone populated with G (glycine). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

"forEach" command to open multiple pdb from multiple directories and save images there ?
by Vincent CHAPTAL 21 Jan '25

21 Jan '25

Hi, I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. I'm using the forEach command to open all the results and run the script to create an image, and it works very well: open script.cxc forEach /PATH*/ranked_*.pdb script.cxc: open reference-structure.pdb match #1 to #2 color #*/B green color #*/C red color #*/D blue view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41 I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location: save /PATH*/$file.png doesn't work because the /PATH*/ is not recognized as an existing directory. save /$PATH*/$file.png gives the same error. If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. Could you let me know how to save in the folder where the .pdb was read from? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 2

UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

2 2

Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

2 2

No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

2 1

Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

2 2