- ChimeraX-users - RBVI Mailing Lists

Optimizing ChimeraX Performance for Multiple Subtomo Maps
by 王光磊 05 Sep '24

05 Sep '24

Hi, I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. My system specifications are as follows: Dual Intel Xeon 5317 processors(a)3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions. Thanks, Wang GuangLei

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Discrepancy: plDDT laphafold3 and ChimeraX version 1.9.dev202405310031 (2024-05-31)
by Khawar Siddiqui 03 Sep '24

03 Sep '24

Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence). Thanks again for the help. sohail Dr Khawar Sohail Siddiqui, [cid:3f847f24-9a1b-47bc-bb56-1704e8bd8ac3] [cid:2c952f1f-e76e-458e-a444-8242f6bdab3a] [cid:0089dce1-a9be-4009-93b9-d158c31cee29]hoo.com

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I found that the phosphodiester bond has broken.
by Yan ZHANG 张艳 03 Sep '24

03 Sep '24

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible. [cid:image001.png@01DAFDEC.77532DA0]

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Purchase license
by Lili Ye 03 Sep '24

03 Sep '24

Hello, I am from Sironax(Beijing)Co.,Ltd. We want to buy two licenses now, how to buy? Thanks! Lili Ye 叶丽丽 Sironax (Beijing) Co., Ltd. 维泰瑞隆（北京）生物科技有限公司 Add: Building 2, No.9 Yike Road, Zhong-Guan-Cun Life Science Park, Changping district, Beijing, China 102206 北京市昌平区生命科学园医科路9号院2号楼8层 Tel: （+86）15201581663 Email: Lili.Ye(a)sironax.com<mailto:Lili.Ye@sironax.com> [1534753277(1)]

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Inquiry About Building Molecular Structures in ChimeraX
by 化工化工 02 Sep '24

02 Sep '24

Dear Professor, I hope this message finds you well. I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library. At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work. I would greatly appreciate any guidance or suggestions you might have. Thank you very much for your time and assistance. Best regards, Youcai Zhu 化工化工 1366924572(a)qq.com  

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Re: color bfactor by alphafold palette
by Elaine Meng 02 Sep '24

02 Sep '24

To summarize for users, the ChimeraX alphafold coloring to show pLDDT values is continuously shaded, whereas the coloring shown at the AlphaFold database is similar but discontinuous, and differences may be evident. The reasoning behind the ChimeraX alphafold coloring palette is that it may be more informative about the specific values. However, it may be confusing that it looks similar, yet not the same, as the AlphaFold database pLDDT coloring. A few months ago, Abnieszka Obarska (thank you!) helpfully provided a command to match the coloring shown at the AlphaFold database. Since it was in an image, however, it is not convenient for cut and paste, so I have copied it here: color bfactor palette 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 Although I did not check if the color hex codes exactly match the AlphaFold database colors, I tried it on a couple of examples at least to my eye, it reproduced the coloring of structures shown at the database. 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

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AlphaFold PAE plot not generated
by Catrin McHugh 30 Aug '24

30 Aug '24

Good morning Having successfully generated a PAE plot (and coloured the model accordingly) with data generated by AF3, I am getting an error message when I try to do the same using a JSON file generated by ColabFold for AF2. The error message is: 'is not AlphaFold predicted aligned error data, expected a top level list". I attach the JSON file, and the relevant structure PDB. Many thanks in advance Catrin

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Random residue colors?
by Daniel Asarnow 30 Aug '24

30 Aug '24

Hi all, In the color command documentation, it says 'color random' can per atom or per residue. How can random residue colors be specified? I can only get random atom colors. Thanks! -da

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CIMERAX 64BIT FOR WIN 10
by Lee, Yong Sok (NIH/NIAID) [E] 29 Aug '24

29 Aug '24

I AM LOOKING A FOR A 64BIT VERSION OF CHIMERAX FOR WINDOWS 10. TRED DOWLOANDING AND INSTALLING CHIMERAX 1.8 BUT IT WOULD NOT LAUNCH ON MY WINDOWS 10 64 BIT SYSTEM. LET ME KNOW IF YOU HAVE A SOLUTION FOR THIS ISUUE. LOOKING FORWARD TO HEARING FROM YOU.

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Invitation to conduct a UCSF Chimera Workshop at Purdue University
by Ferdausi, Nourin 29 Aug '24

29 Aug '24

Dear Team, I hope this email finds you well. My name is Nourin Ferdausi and I am a graduate student at the Department of Biological Sciences in Purdue University. My colleague, Priyanka Naik (cc’d here) and I are writing to you on behalf of the Structural Biology and Biophysics Club (SBBC). We are hoping to organize a virtual workshop focused on UCSF Chimera, and we would be honored if one of your team members could conduct this workshop. The graduate students and researchers of our structural biology group use a wide variety of experimental approaches like cryo-electron microscopy and X-ray crystallography for determining molecular structures. Consequently, the Chimera software is integral to our research, and we believe your insights would be of great impact to our community. We are flexible with the format of this virtual workshop, which is tentatively scheduled for mid-September; however, we are open to adjusting the date based on your availability. Your participation will provide our members with a unique opportunity to learn directly from a developer of UCSF Chimera. Please let me know if we can have a quick Zoom call to discuss the event in detail. We look forward to your reply at your earliest convenience! Thank you, Nourin Ferdausi Ph.D. Candidate, Noinaj Lab Supporting officer, Structural Biology and Biophysics Club Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology West Lafayette, IN-47907-2054

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