April 2024 - Chimera-users - RBVI Mailing Lists

Selecting chain via command line
by Ellen Shrock 19 Sep '24

19 Sep '24

Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen

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Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

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Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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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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i can´t installate chimera.
by Suilma Ivette Pérez Pineda 14 Apr '24

14 Apr '24

hi! i cannot installate chimera, when i acept "terms and conditions", the windows says tht "i dessagree", when im agree. Suilma Ivette Pérez Pineda

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AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 12 Apr '24

12 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

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AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 12 Apr '24

12 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

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Protein Modeling with Model/Refine Loops Tool
by Ecem Güngör 09 Apr '24

09 Apr '24

Hello all, I have encountered an issue while working with a protein in complex with ligands. There are some missing regions in the protein structure, and I attempted to model these regions using the "Model/Refine Loops" tool in UCSF Chimera (version 1.17.3). However, I observed that when I saved the modeled structures as PDB files, the ligands were not included in the file. Additionally, in some models, the modeled C-terminal extended into the binding pocket in an unusual manner. I am curious whether this tool takes into account the presence of ligands or molecules in the structure while modeling missing regions. How can I prevent such issues from occurring? How can I model the missing long C-terminal in Chimera while ensuring that the presence of other ligands or molecules is also considered? Thanks in advance. Ece.

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