June 2019 - ChimeraX-users - RBVI Mailing Lists

ISOLDE 1.0b3 now released for ChimeraX 0.9
by Tristan Croll 17 Jun '19

17 Jun '19

Dear ChimeraX users, Just letting you know that I've released ISOLDE 1.0b3 on the ChimeraX Tool Shed for use with ChimeraX 0.9. If you're not familiar with ISOLDE, you can get an overview at https://isolde.cimr.cam.ac.uk/. In brief, ISOLDE is designed to allow the high-fidelity, interactive remodelling/refinement of atomic models into low-medium resolution cryo-EM or crystallographic electron density maps. In designing ISOLDE, I've always had two groups in mind. The first is, of course, the experimental structural biologists whose job it is to solve the structures of new macromolecules and their complexes. The second (and, to my mind, equally important) group is the downstream *users* of such models. Like every other human endeavour, macromolecular model building is an imperfect field, and (particularly in the worse-than-2-Angstrom resolution range targeted by ISOLDE) many deposited models contain serious errors that are eminently fixable with modern tools. My hope is that ISOLDE will become a useful tool allowing you to directly inspect your model of interest in the context of its original data, providing you with a feasible pathway towards fixing any issues you find (or, failing that, moving to a new target) prior to committing serious resources to its study. Please enjoy. Constructive feedback is always welcome. Best regards, Tristan

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Transparent background movie
by Norberto Escudero 14 Jun '19

14 Jun '19

Hi, I have succesfully created images with transparent background, but it seems is an impossible task for a movie. Is there any way around this? Thanks and regards, -- Dr Norberto Escudero Urquijo Prof. A. Warren's group Cambridge Institute for Medical Research (CIMR) Hills Road, Cambridge, CB2 0XY

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Saving stereo pairs
by Gyunghoon Kang 14 Jun '19

14 Jun '19

?Hi, apologies if this information is available somewhere but all my searches returned information for the original Chimera. Is there a way to generate stereo pairs either in the command line or GUI? Best, Gyunghoon Kang

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set silhouettes false for volume mesh only?
by Alexis Rohou 13 Jun '19

13 Jun '19

Hi there, Is there a way to set silhouettes false for volume meshes, but keep it true for other object types (ribbons, surfaces,...)? Cheers, Alexis

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SMILES Input With ChimeraX
by Victor Blaga 05 Jun '19

05 Jun '19

Hello, I am just wondering if there is a way to input a SMILES string with ChimeraX, as with Chimera? I can't seem to find it in the documentation so I just want to confirm this functionality has indeed been dropped? Thank you, Victor Blaga Research Assistant McMaster University Department of Biochemistry and Biomedical Sciences

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ChimeraX-users June 2019