- ChimeraX-users - RBVI Mailing Lists

Save Session
by F.Xavier Gomis-Rüth 12 Sep '24

12 Sep '24

Dear Elaine, I am trying to save the session under ChimeraX v. 1.8 but the program refuses to do so with the message below. Any suggestion is welcomed. Best, Xavier --

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Chimerax's download link is no longer working
by 卢健之 11 Sep '24

11 Sep '24

Hello, I tried to dowonload the chimerax from the link https://www.rbvi.ucsf.edu/chimerax/download.html. But it seems the server is down. I wonder if you could provide me with a new download link. I would really appreciate it.

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no template at MD forcefield
by Dmitry Semchonok 11 Sep '24

11 Sep '24

Dear Tristan and colleagues, I hope you are doing well. I have a question about the cofactors and residues that ISOLDE cannot see immediately. [cid:17de3c4d-4ac6-471b-b5b9-ecaa4e534d18] What is the proper way to treat them? The program proposes that I do a search and then give the options. Shall I select the most probable one out of the list? And how do we deal with Chlorophylls (Chl a; Chl b) and carotenoids (car)? And sometimes, even with regular ones like ARG [cid:8ff9222b-feb1-47b3-9b5e-a52e714e2355] Thank you in advance. Kind regards, Dmitry

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Select all connected atoms to selection
by Alexander Lee 10 Sep '24

10 Sep '24

Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command select @{atom_name}; select zone select 2 It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks!

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atoms.scene_coords inconsistency before and after saving
by Roden Deng Luo 10 Sep '24

10 Sep '24

Hi, With version 1.7.1 (2024-01-23), if I open a structure (tested with 6MEO and 6ARA), select the whole molecule, change "Right Mouse" to "Rotate model", rotate the model by dragging with the right mouse, save the model into a .cif file (uncheck "Use untransformed coordinates"), and then type the following python script in the Shell in the session performed the rotation and in a new session/launch of ChimeraX and opening of the saved file, the results are different, see the attached screenshots. ======= from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] mol.atoms.scene_coords ======= For 6ARA, if I do not change the camera setting before rotation (drag the left mouse), only rotate in the original camera setting, this is not reproduced. But if I change the camera setting, this is reproduced. For 6MEO, I always reproduce the described behavior. From https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi… , *property *scene_coords <https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi…> Atoms’ coordinates in the global scene coordinate system. This accounts for the Drawing positions for the hierarchy of models each atom belongs to. Either I misunderstood the whole scene and camera system, or this should not have happened. Why is this the case? How can I access from the session performed the rotation the coords as in a new session? Many 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.

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license for university students
by Angel David Montijo Valdés 09 Sep '24

09 Sep '24

Good afternoon, I am writing to you in the kindest way to request a free use license for the chimera X program. Because I am a student at the National Autonomous University of Mexico (UNAM), within the Faculty of Sciences, and it would be a great opportunity to use your tool in different molecular biology analyses. If you need a proof of my identity as a student, you can ask me for it without any problem. I look forward to hearing from you. Best regards.

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Select multiple rotamer conformations for a single amino acid
by Alexander Lee 09 Sep '24

09 Sep '24

Hi! I was able to select and use multiple rotamer conformations simultaneously for a single amino acid using the Rotamers tool, saved as alternate locations within a pdb file. Is there a way to do that using swapaa or from the command line?

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Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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Re: [Chimera-users] morph command in chimerax
by Elaine Meng 09 Sep '24

09 Sep '24

Hi Bryan, Since this is a ChimeraX question, I've CC'd chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> --- in the future please use that mailing list for ChimeraX questions, because we don't want to confuse users between the two programs, for which the answers may be different. This answer is for ChimeraX: The "morph" command is for atomic structures, not maps. That's why it keeps saying you need structures! This is mentioned in the first sentence of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> To instead morph maps, see the "volume morph" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 9, 2024, at 7:29 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I’m using ChimeraX v 1.8 (2024-06-10) and I’m having a problem with the morph command. No matter how I format the command I’m getting the same error message of “Require at least 2 structures for morph” I’ve tried > morph #3,4 core 0.1 frames 75 wrap t > and > morph #3#4 core 0.1 frames 75 wrap t > These are 2 electron density maps so there’s no sequence info docked in yet. Thanks for any tips or advice on what I’m doing wrong. > Bryan Hansen

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MD Trajectory
by Mcguire, Kelly 06 Sep '24

06 Sep '24

What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories? Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego

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