- Chimera-users - RBVI Mailing Lists

Connecting ends of a peptide
by Marco Sette 04 Sep '26

04 Sep '26

Hi all, I'm following the procedure reported in a previous message to connect the ends of a peptide. In my case ~ribbon display delete :41@oxt bond :1@n: 41@c After, I run minimization, but I have the following message Charge model: AMBER ff14SB Total charge for #0: 0.810 The following residues had non-integral charges: SER 1.A 0.8102 1 model(s) had non-integral total charge Details in reply log Residue #0:1.A (SER/serine) is missing atom H_1 In my model SER1 has two hydrogens named H2 and H3. Now the nitrogen has four covalent bonds that is unusual. If, before connecting residues 1 and 41, I add hydrogens to the molecule I obtain SER1 with 3 hydrogens. After I remove H2 and H3 and repeat the procedure, in the minimization step I obtain the message that H3 is missing... Any suggestion? Thanks Marco -- Marco Sette, PhD Associate Professor of Molecular Biology Department of Chemical Sciences and Technology The University of Rome, "Tor Vergata" Via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Command line dock prep in Chimera
by Alexander Hung Lee 27 Jul '26

27 Jul '26

Hello, I've been using the energy minimization protocol in Chimera via commandline, nogui. Recently, I've needed to keep the solvent from crystal structure when minimizing but the integrated Dock Prep deletes it. Is there a way to prevent Dock Prep from deleting solvent in Chimera? I know in ChimeraX has the command line implementation of Dock Prep as "dockprep", but I didn't find a counterpart to it in the older Chimera program. Thank you, Alex Lee

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adding residues to N-terminal
by Dilara KARAMAN 27 Jul '26

27 Jul '26

Good days, I'm new user of Chimera therefore I need help using build structure option of program. I want to add MRAE residues to N-terminal of enzyme as an alpha helix structure but I can not use the directions of tutorial such as: addaa tyr,30 :29.a - add tyrosine in an extended conformation as residue 30, after residue 29 in chain A (the new residue will also be in chain A) Where can I write this command? I'm trying to add four residues to N terminal but I'm adding them to another point. I'm sending the screen image. Please help me. Best regards Dilara Karaman

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I need older version
by Dilara KARAMAN 21 Jul '26

21 Jul '26

Good days, Thank you for your usefull protein preparation options. I have a problem when setting the Chimera in my Windows 7, 64 bit computer. Because of this old version of Windows Chimera can not be established. Is there any older version of Chimera to set on Windows7? Before 10 years, I used chimera on Windows7 but now it is not available. Please help me. Best regards Dilara Karaman

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Query regarding saving protein–ligand complex from docking results in Chimera -Reg.
by k Gayathri 16 May '26

16 May '26

Dear Sir/Madam, I am a research scholar from Anna University, Chennai, India, and I have been using UCSF Chimera for my research for the past two years. Recently, I encountered an issue during the visualization and saving of protein–ligand interactions, which I have been unable to resolve. I performed docking simulations using AutoDock Vina and obtained the output in PDBQT format. Initially, I used the ViewDock module to visualize the docking poses and hydrogen-bond interactions. However, since the output file contained multiple poses, I was unable to correctly save only the favorable protein–ligand complex for further analysis. To address this, I used the vina_split utility to separate the individual poses from the docking output file. After splitting, I was able to open the single ligand pose in PDBQT format along with the protein and successfully visualize the hydrogen bonds. However, when I saved this selected protein–ligand complex in PDB format and reopened it, the hydrogen bonds were no longer visible in Chimera. As I require the final protein–ligand complex in PDB format for further molecular dynamics simulations, I would like to clarify the correct procedure for saving the selected docked pose together with the protein structure from the docking results. I would also like to confirm whether the saved PDB complex remains structurally reliable for subsequent MD studies, even though the hydrogen bonds are not displayed after reopening. I would be grateful if you could kindly guide me on the correct workflow for saving the protein–ligand complex from docking results and ensuring that the structure is suitable for further simulation studies. Thank you in advance for your support and guidance. -- *Thanks and Regards*, *K. Gayathri* Research Scholar Department of Physics Anna University Chennai-25

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help
by Claire Ellena 15 Apr '26

15 Apr '26

Hello, can you help me. I don’t know where the error is

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Unable to make a distance for a particular residue
by SHUBHRAJYOTI PANDA 06 Apr '26

06 Apr '26

Dear, This is Shubhrajyoti Panda, research scholar at Birla Institute of Technology, Hyderabad. I am using 6XG5 PDB ID for my work. But in this particular protein I want to show the distance between particular residues. But when I am going to show manually or through command it is showing the following error. Distance between PHE 31.A CA and GLY 15.A CA: 15.891 Distance between PHE 31.A CA and MET 16.A CA: 19.088 Distance between PHE 31.A CA and ALA 19.A CA: 15.571 Distance between PHE 31.A CA and ILE 14.A CA: 14.072 Error while sourcing chimera_distances.cmd, line 14: "distance :31.A@CA :45.A@CA" *Exactly two atoms/axes/planes must be selected. You selected 3.* But in the protein structure there is only one 45th number residue. But I could not understand why it is showing selected 3 repeatedly. Kindly help me. Thanks & Regards Shubhrajyoti Panda Phone: +91-7001855842 Email: panda.jyoti.shubhra(a)gmail.com

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Question about AlphaFold prediction in ChimeraX
by Ehsaneh Khodadadi 16 Mar '26

16 Mar '26

Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi

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how to increase the size of the metal spheres
by 吴林 12 Mar '26

12 Mar '26

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No command line on Apple silicon M1
by Marco Sette 12 Feb '26

12 Feb '26

Hi all, the command line is not working on apple silicon with the latest Chimera versions. Do you have suggestion how to solve the problem? Thanks for your help. Best regards Marco -- Marco Sette, PhD Associate Professor of Molecular Biology Department of Chemical Sciences and Technology The University of Rome, "Tor Vergata" Via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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