the information icon is blue when one or more background tasks are running, a lighter blue when no tasks are running; clicking it brings up the Task Panel the magnifying glass icon is colored when something is selected ; mousing over it reports in a text balloon what is selected, and clicking it …

[chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax Elaine Meng meng at cgl.ucsf.edu Tue Feb 2 08:27:18 PST 2021. Previous message: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax

Previous message: [Chimera-users] color a small molecule in a .mol2 file by red to blue gradient of the partial charges. UCSF Chimera - I - Introduction [Chimera-users] color a residue Elaine Meng meng at cgl.ucsf.edu Tue Sep 5 10:02:48 PDT 2006. Previous message: [Chimera-users] color a residue Next message: [Chimera-users] PDB Coordinates Messages sorted by: This class is designed to help scientists, not artists, use UCSF Chimera to create images of their data. (If you collaborate with an artist, you often get better results.) Students are expected to have already used UCSF Chimera to view their own data. This class will cover the typical workflow for creating a publication-quality image. Learn the basic functionality of UCSF Chimera, such as loading PDB coordinates into the software, manipulating the structure in 3D, and saving your session.

Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Background white. Command set bg white * *as of Chimera 1.9, set bgcolor white; Silhouette edges. Tools / Viewing Controls / Effects Enable shadows. Background gradient.

UCSF Chimera - I - Introduction 3https://www.cgl.ucsf. edu/chimera/docs/ ContributedSoftware/ coulombic/coulombic. html 7Surface and electrostatics 7.1Learning objectives • Createamolecularsurface • Colorbyelectrostaticpotential(Coulombic) 7.2Show molecular surface TASK Showmolecularsurface. • Actions >Surface >Show

Chimera Introduction to Protein Structure Bioinformatics 2007 Vincent Zoete – 02/23/2007 1/21 User-Driven Analysis. Users can easily import structure-related data into Chimera in the form of attributes, or values associated with atoms, residues, or models.The data can be imported with Define Attribute and then represented visually with color ranges, atomic radii, or "worm" thickness. About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety How YouTube works Test new features Press Copyright Contact us Creators Se hela listan på identity.ucsf.edu Learn how to use some of the tools of UCSF Chimera to analyze and explore a protein structure.

> Cheers, > Christian > _____ > From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu >] On Behalf Of Francesco Pietra [chiendarret at gmail.com] > Sent: 12 October 2008 12:44 > To: chimera > Subject: [Chimera-users] Printing on white background > > When mapping protein residues around a ligand I would like to have a > printout of the enlarged binding site area, so

Then just save your image as usual and it should be on a white background. choose Actions→Color→all options to show the Color Actions dialog, and in that dialog: change the Coloring applies to (target) setting to surfaces; click light gray (keep the dialog open) Select just netropsin again, make just its surface red: Select→Residue→NT; in the Color Actions dialog: click red (keep the dialog open) Animating conformation change, Part 2 Color all options or any of the methods available for starting tools. It is a tool in the Depiction category. Color Actions provides access to all 60 colors and allows finer control than the menu over which types of items are colored. See also: coloring. Color Actions includes the same coloring choices as the Actions Color menu: [top 20 colors] - color all histidine residues in model 2 green, as well as any associated labels, ribbon segments, surface patches, etc.

The Column Element has the same options, with the Since Jalview 2.8.2, Chimera (http://www.cgl.ucsf.edu/chimera/) can be used for Colours each residue in the structure with the colour of its corresponding Stephanie Lewis' tutorial "AutoDock 4.0 and AutoDockTools 1.5.2 Tutorial." Things to know when working with UCSF Chimera.
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• Actions >Surface >Show High quality imaging for publication. Chimera Introduction to Protein Structure Bioinformatics 2007 Vincent Zoete – 02/23/2007 1/21 User-Driven Analysis. Users can easily import structure-related data into Chimera in the form of attributes, or values associated with atoms, residues, or models.The data can be imported with Define Attribute and then represented visually with color ranges, atomic radii, or "worm" thickness.

colon 5.3817. herki 8.5172 background 3.6268. stamped 6.1193 ucsf 7.8240.
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choose Actions→Color→all options to show the Color Actions dialog, and in that dialog: change the Coloring applies to (target) setting to surfaces; click light gray (keep the dialog open) Select just netropsin again, make just its surface red: Select→Residue→NT; in the Color Actions dialog: click red (keep the dialog open)

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Command: rangecolor kdHydrophobicity min dodger blue 0 white max orange red. This gives the same coloring as the “hydrophobicity surface” preset: from dodger blue for the most hydrophilic, to white, to orange red for the most hydrophobic. The IHP-binding pocket is primarily blue, indicating its hydrophilic character.

Fri Aug 3 09:38:49 PDT 2018. Previous message: [chimerax-users] Setting the bgColor transparent in ChimeraX.

Learn how to use some of the tools of UCSF Chimera to analyze and explore a protein structure.

These settings can also be adjusted (and saved for later uses of Chimera) with the Background preferences. the information icon is blue when one or more background tasks are running, a lighter blue when no tasks are running; clicking it brings up the Task Panel the magnifying glass icon is colored when something is selected ; mousing over it reports in a text balloon what is selected, and clicking it … On Monday, August 18, 2003, at 09:36 AM, Thomas Goddard wrote: > Hi Jakob, > > To change the background color in Chimera use Favorites/Preferences, > category Background, and click on the "Background color" button. That > will bring up the color chooser, and you can set the color to white > for printing.

Close the color editor. Click on Silhouettes. Click on Silhouettes to show outlines.