How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.
Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover> 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match?
Thank you for your attention. I'm looking forward to your reply.
For X-ray data, usually it could be the conversion from mtz to ccp4/map format, one loses the origin of a reference is not given. Make sure to convert with the pdb as an input if using a tool in say Phenix (mtz2map) as a reference. When you open the ccp4/map format map it should be aligned with the pdb Sent from Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Thursday, April 24, 2025 5:58:37 PM To: 1025049892@qq.com <1025049892@qq.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified? Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover> 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match?
Thank you for your attention. I'm looking forward to your reply.
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Thank you for your attention and suggestions. I have read the command, but when I attempted to display only the density maps for several amino acids, I was unable to make it happen. I earnestly look forward to your professional guidance and would be extremely grateful if you could spare the time to assist me. Thank you very much! ------------------ 原始邮件 ------------------ 发件人: "ChimeraX Users Help" <meng@cgl.ucsf.edu>; 发送时间: 2025年4月24日(星期四) 晚上11:58 收件人: "张馨丹 四川大学生物治疗国家重点实验室"<1025049892@qq.com>; 抄送: "chimerax-users"<chimerax-users@cgl.ucsf.edu>; 主题: Re: [chimerax-users] How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified? Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>; 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? > > Thank you for your attention. I'm looking forward to your reply.
Sorry, without knowing your specific data and what exactly you want, it is not possible for me to give you a specific answer. I thought you meant that the map was in a different place than your atoms, in which case you might need "volume cover" However, if you mean instead that you want to hide part of the map and only show the part near some atoms, you might need "volume zone": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> Elaine
On Apr 29, 2025, at 6:12 AM, 张馨丹 四川大学生物治疗国家重点实验室 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you for your attention and suggestions. I have read the command, but when I attempted to display only the density maps for several amino acids, I was unable to make it happen. I earnestly look forward to your professional guidance and would be extremely grateful if you could spare the time to assist me. Thank you very much!
------------------ 原始邮件 ------------------ 发件人: "ChimeraX Users Help" <meng@cgl.ucsf.edu>; 发送时间: 2025年4月24日(星期四) 晚上11:58 收件人: "张馨丹 四川大学生物治疗国家重点实验室"<1025049892@qq.com>; 抄送: "chimerax-users"<chimerax-users@cgl.ucsf.edu>; 主题: Re: [chimerax-users] How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need.
see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>
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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match?
Thank you for your attention. I'm looking forward to your reply.
Thank you for your attention. The problem has been solved very well. Thank you！ ------------------ 原始邮件 ------------------ 发件人: "ChimeraX Users Help" <meng@cgl.ucsf.edu>; 发送时间: 2025年4月29日(星期二) 晚上11:25 收件人: "张馨丹 四川大学生物治疗国家重点实验室"<1025049892@qq.com>; 抄送: "ChimeraX Users Help"<chimerax-users@cgl.ucsf.edu>; 主题: Re: [chimerax-users] How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified? Sorry, without knowing your specific data and what exactly you want, it is not possible for me to give you a specific answer. I thought you meant that the map was in a different place than your atoms, in which case you might need "volume cover" However, if you mean instead that you want to hide part of the map and only show the part near some atoms, you might need "volume zone": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>; Elaine > On Apr 29, 2025, at 6:12 AM, 张馨丹 四川大学生物治疗国家重点实验室 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > > Thank you for your attention and suggestions. I have read the command, but when I attempted to display only the density maps for several amino acids, I was unable to make it happen. > I earnestly look forward to your professional guidance and would be extremely grateful if you could spare the time to assist me. Thank you very much! > > ------------------ 原始邮件 ------------------ > 发件人: "ChimeraX Users Help" <meng@cgl.ucsf.edu>; > 发送时间: 2025年4月24日(星期四) 晚上11:58 > 收件人: "张馨丹 四川大学生物治疗国家重点实验室"<1025049892@qq.com>; > 抄送: "chimerax-users"<chimerax-users@cgl.ucsf.edu>; > 主题: Re: [chimerax-users] How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified? > > Without knowing your exact data, I can only guess that maybe the "volume cover" command is what you need. > > see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>; > > 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 Apr 24, 2025, at 2:26 AM, 1025049892--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > > > Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? > > > > Thank you for your attention. I'm looking forward to your reply. >
participants (4)
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1025049892＠qq.com -
Elaine Meng -
Kelvin Lau -
张馨丹 四川大学生物治疗国家重点实验室