September 2024 - ChimeraX-users - RBVI Mailing Lists

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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