Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
Hi Samuel, In general it is better to use ChimeraX as it is being developed and may get new features, whereas Chimera is no longer being developed. However, neither Chimera nor ChimeraX has the specific capability that you are asking about. However, please see this recent discussion on how to create composite maps when the parts are of different resolutions or quality -- some users suggested Phenix or TEMPyReFF: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 Jun 12, 2025, at 9:30 AM, Samuel Leite Guimaraes via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães
[heart] Samuel Leite Guimaraes reacted to your message: ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, June 12, 2025 8:49:09 PM To: Samuel Leite Guimaraes <samuel.guimaraes@lnbio.cnpem.br> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Composite map: select only voxels within a range of resolution? [Geralmente, você não obtém emails de meng@cgl.ucsf.edu. Saiba por que isso é importante em https://aka.ms/LearnAboutSenderIdentification ] Hi Samuel, In general it is better to use ChimeraX as it is being developed and may get new features, whereas Chimera is no longer being developed. However, neither Chimera nor ChimeraX has the specific capability that you are asking about. However, please see this recent discussion on how to create composite maps when the parts are of different resolutions or quality -- some users suggested Phenix or TEMPyReFF: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 Jun 12, 2025, at 9:30 AM, Samuel Leite Guimaraes via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães
Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
Thank you very much, Elaine! I´ll take a look! Samuel L. Guimarães ________________________________ De: Elaine Meng <meng@cgl.ucsf.edu> Enviado: quinta-feira, 12 de junho de 2025 17:49 Para: Samuel Leite Guimaraes <samuel.guimaraes@lnbio.cnpem.br> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Assunto: Re: [Chimera-users] Composite map: select only voxels within a range of resolution? [Geralmente, você não obtém emails de meng@cgl.ucsf.edu. Saiba por que isso é importante em https://aka.ms/LearnAboutSenderIdentification ] Hi Samuel, In general it is better to use ChimeraX as it is being developed and may get new features, whereas Chimera is no longer being developed. However, neither Chimera nor ChimeraX has the specific capability that you are asking about. However, please see this recent discussion on how to create composite maps when the parts are of different resolutions or quality -- some users suggested Phenix or TEMPyReFF: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 Jun 12, 2025, at 9:30 AM, Samuel Leite Guimaraes via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães
Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
participants (2)
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Elaine Meng -
Samuel Leite Guimaraes