Hi Yan, PDB 4ola is an X-ray structure so you could fetch PDB and the X-ray map (from the Electron Density Server) using ChimeraX commands open 4ola open 4ola from EDS The map is a unit cell and does not cover the PDB atom coordinates. To use the crystal symmetry to extend the map to cover the atom coordinates use ChimeraX command volume cover #2 atomBox #1 The x-ray map of course has other copies of the molecules packed together and if you want to see just the x-ray density near the atom coordinates you could use volume zone #3 near #1 range 3 For PDB 7sva which is a cryoEM structure with map at the EMDB with id 25446 you can open both with open 7sva open 25446 from emdb Converting the PDB files to maps gives a different result than looking at experimental results, and I'm not sure why you want to do that. But the ChimeraX molmap command will do that by adding up Gaussians at the atom positions. That does not give a good approximation to the experimental maps in most cases. All these commands are fully documented in the ChimeraX User Guide. Tom
On Sep 25, 2024, at 1:54 AM, Yan ZHANG 张艳 <zhangyan30@westlake.edu.cn> wrote:
Hi Tom,
Thank you for your response. I'll try to explain my situation more clearly.
I am comparing two structures (PDB IDs: 4ola and 7sva). I want to use the "color near atoms" feature in ChimeraX to color the maps of both structures. However, 4ola is a crystal structure and is in MTZ format. I would like to display it in the same way as an MRC file.
I hope this is clearer. My current solution is to convert the PDB file of 4ola to an MRC file directly. This approach seems to work, but I am unsure if it is acceptable.
Thank you for your help.
Best regards, Yan
发件人: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> 日期: 星期三, 2024年9月25日 14:16 收件人: Yan ZHANG 张艳 <zhangyan30@westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn>> 抄送: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> 主题: Re: [chimerax-users] Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
You don't often get email from goddard@sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> Hi Yan,
We might have advice if you can explain what you are doing more clearly. MRC files are real space maps and MTZ files contain Fourier space coefficients.
Tom
On Sep 24, 2024, at 9:57 PM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
I hope this message finds you well.
I am writing to inquire whether it is possible to selectively choose individual electron density maps of a single model from the MTZ files containing crystallographic data. This capability would enable me to perform comparative analyses of the same structure obtained through different methods. Currently, I am facing a challenge as the MRC files cannot be aligned with the MTZ files. I am seeking your guidance on whether there is a solution or tool within ChimeraX that can assist me in this process.
Your expertise and support in this matter would be greatly appreciated. I am looking forward to hearing from you at your earliest convenience. Thank you very much for your attention to this inquiry.
Best regards,
Yan Zhang Westlake University Email: zhangyan30@westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn>
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