November 2024 - Chimera-users - RBVI Mailing Lists

Issue with Display of Hydrogen Bonds in Find H Bond Tool in Chimera
by GABRIELE SANTOS CEPINHO 12 Nov '24

12 Nov '24

Dear Chimera Support Team, My name is Gabriele Cepinho, and I am using Chimera version 1.17.3 for molecular docking analysis in my research. Recently, I encountered an issue with the Find H Bond tool that I have been unable to resolve, and I hope you may be able to assist me. When I use the Find H Bond tool to display hydrogen bonds between molecules, the generated image also shows polar interactions along with the specific hydrogen bonds. However, in the tool’s output file, I can clearly identify which interactions are true hydrogen bonds. My goal is to display only the hydrogen bonds in the image, excluding the polar interactions, but I have not been able to adjust the tool to achieve this. I have tried modifying the distance and angle parameters to restrict the display, yet polar interactions still appear alongside the hydrogen bonds in the visualization. I appreciate any guidance or recommendations you can provide regarding this matter. If there is any additional option to filter these interactions directly in the image, or if there is an update or specific setting available for the Find H Bond tool, I would be grateful to know about it. Thank you in advance for your attention. Best regards, Gabriele Cepinho -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

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Write out SeqRes entry
by David Bhella 07 Nov '24

07 Nov '24

Dear Chimera/ChimeraX team, I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? Thanks D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [signature_1350623625] [Logo, company name Description automatically generated]

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Values at Atom Positions
by jp d 01 Nov '24

01 Nov '24

hi, sorry to bother you again, is it possible to run "Values at Atom Postions" from a script where i specify map,pdb and just the output attribute file ? thanks jpd

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