February 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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Dock problem selenium atom
by turgut şekerler 11 Feb '24

11 Feb '24

Dear Chimera Team, I hope this message finds you well. I am writing to inquire about an issue I encountered while attempting to perform docking with a selenium atom using the Dock Prep module in Chimera. My goal is docking selenium atom and my target protein. But ı always get a error message : cant prepare ligand. I have been utilizing Chimera's Dock Prep module to prepare ligands for docking with proteins, and it has been an effective tool thus far. However, I have encountered difficulties when attempting to prepare a ligand containing a selenium atom. It seems that the Dock Prep module is unable to handle the selenium atom properly, resulting in errors during ligand preparation. I have attempted to troubleshoot this issue by researching error codes and exploring potential solutions, but I have been unable to find a resolution. As such, I am reaching out to inquire if there are any specific recommendations or alternative approaches that could be used to successfully prepare a ligand containing a selenium atom for docking in Chimera. I understand that Chimera utilizes standard force field parameters for ligand preparation, but given the unique properties of selenium, it may be necessary to consider additional or specialized parameters to ensure accurate docking results. Any guidance or assistance you could provide on this matter would be greatly appreciated. I am eager to resolve this issue and continue utilizing Chimera for my docking studies. Thank you for your attention to this matter. I look forward to your response. Sincerely,

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Trouble in Creating Peptide bond
by Vignesh Nandhagopal 06 Feb '24

06 Feb '24

Dear Chimera Help Team, I want to create a peptide bond. I followed this manuscript which I have attached along with this mail. I followed the steps of the manual I have used and I have seen a slight change in build structure. Kindly help me with this I am getting an error in the unrecognized protein code. Kindly help me with the steps.

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polymer formation
by Kainaat Mahzaib 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

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polymer formation
by Kainaat Mahzaib John 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

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