Difficulty with Ribbon Visualization in Chimera Software
Dear Chimera Software Team, I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode. When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking. I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization. Thank you in advance for your time and support. I look forward to your prompt response. Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信
It's a data problem. The data is in a molecular format, but does not appear to be molecular data. All of the atoms in each residue have the same name. And the distances between the atoms are out of range for molecules. And there is no secondary structure information in the file. If you undisplay the ribbon representation and display the atoms and bonds, you'll see the strangely linear arrangement of atoms. In ChimeraX, our follow-on to Chimera, you won't get a ribbon representation at all because the data is so misformed. HTH, Greg On 5/15/2024 12:03 AM, 罗舒月 via Chimera-users wrote:
Dear Chimera Software Team, I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode. When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking. I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization. Thank you in advance for your time and support. I look forward to your prompt response. Best regards, Shuyue Luo the result of my file the effect I want ------------------------------------------------------------------------ 发自我的企业微信 <https://work.weixin.qq.com/wework_admin/user/h5/qqmail_user_card/vcdefb74f84825c935?from=myprofile>
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Yes, the file looks like the output of DAMMIF, <https://www.embl-hamburg.de/biosaxs/manuals/dammif.html> which is an array of "beads" instead of a molecular structure that you could show ribbons for. I would recommend these commands (Favorites→Command Line) to view your file: open noprefs path-to-damflit.pdb ~bond #0 repr sphere This will clearly show your bead array. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 15, 2024, at 12:33 AM, Greg Couch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
It's a data problem. The data is in a molecular format, but does not appear to be molecular data. All of the atoms in each residue have the same name. And the distances between the atoms are out of range for molecules. And there is no secondary structure information in the file. If you undisplay the ribbon representation and display the atoms and bonds, you'll see the strangely linear arrangement of atoms. In ChimeraX, our follow-on to Chimera, you won't get a ribbon representation at all because the data is so misformed.
HTH,
Greg
On 5/15/2024 12:03 AM, 罗舒月 via Chimera-users wrote:
Dear Chimera Software Team, I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode. When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking. I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization. Thank you in advance for your time and support. I look forward to your prompt response. Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信 <https://work.weixin.qq.com/wework_admin/user/h5/qqmail_user_card/vcdefb74f84825c935?from=myprofile>
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participants (3)
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Eric Pettersen -
Greg Couch -
罗舒月