- Chimera-users - RBVI Mailing Lists

Saving symmetry model in pdb format
by Kailash Singh Bisht 17 May '24

17 May '24

Hello ChimeraX team I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files -- With Regards Thanking You Kailash Singh Bisht Ph.D. Student

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Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 15 May '24

15 May '24

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

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Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 15 May '24

15 May '24

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

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Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Chimera scripting
by Flip Jansen 06 May '24

06 May '24

Hello Chimera dev team, I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? Any help is highly appreciated, I would also be happy to come by an talk in person. Best, Flip Jansen

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Issues installing chimera on linux
by Conor Bonal 02 May '24

02 May '24

Hello, I tried to follow the tutorial to install Chimera on Linux. I'm using a computer with Ubuntu 18.04.5 and it is 64-bit. I followed the tutorial word for word then substituted "chimera-installer.bin" with the file name "chimera-1.17.3-linux_x86_64.bin" and I continued to get the same error message telling me the file or directory does not exist, although I can clearly see it in my downloads folder. Can you provide any assistance with installing the software? Thank you! Conor Bonal

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Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Ligand has no chain ID after saving docked complex
by kalabamelisa＠yahoo.com 24 Apr '24

24 Apr '24

Hello. I want to use PRODIGY web server to predict the binding affinity of my docked complexes, and the server requires a single PDB file containing both the docked ligand and the protein. I open the .pdbqt file containing the docking results using ViewDock and then I open my receptor file in .pdb format. I combine the two (receptor and the best ligand) and then save the complex as a PDB file. The server requires the ligand's name and what chain it's on, but when I open the complex in Chimera the ligand has no chain ID, it just shows up as "het". How do I assign a chain ID to my ligand in this situation?

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Problem in Docking Output
by Mrs Kumud Pant 22 Apr '24

22 Apr '24

Dear Developers, I am facing problem of incomplete docking. The error statement is pasted below. Also attaching receptor and ligand file for your perusal. Since I am new to this software therefore, detailed explanation is requested in eliminating the problem. #0, chain A: prostaglandin G/H synthase 1 Model 0 (oxidoreductase.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: LEU 599.A Chain-final residues that are not actual C terminii: 595 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 No incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 Wrote C:\Users\GEU\Downloads\new dock\oxidoreductase.pdb #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713445280.81 1713445293.84 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Status file contents: 1639 1713445301.94 1713445303.83 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447116.49 1713447119.45 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447148.99 1713447151.35 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Thank you in advance Dr. Kumud Pant Associate Professor Department of Biotechnology Graphic Era (Deemed to be) University Dehradun

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