November 2021 - Chimera-users - RBVI Mailing Lists

Showbox
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 03 Nov '21

03 Nov '21

Hi, I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users... Maybe someone could help me here. I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation. I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure. Does anyone know it? Thanks and regards.

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Counting the number of water molecules
by Prathvi Singh 02 Nov '21

02 Nov '21

Hi, Is there a command in UCSF chimera to count the total no. of water molecules in a PDB file? Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Bug Report: Chimera exit abnormally: code 1073741819
by Jyoti Singh 01 Nov '21

01 Nov '21

Dear Sir, I have installed Chimera 1.15 successfully.When I try to open it, a window pops-up and gives an exit code: 1073741819 and it never opens for analysis. Below I have shared the start information and please find the attachment. *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* Kindly do needful. Regards. *Jyoti SinghPh.D. Scholar [UGC-SRF]"Molecular Biology and Biotechnology lab"CPMB DIVISION, GARDEN BLOCK.CSIR - National Botanical Research Institute, Lucknow [UP], 226001, 'INDIA'*

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