new Chimera snapshot release
Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu General changes --------------- The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs. Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured. Moved C3' off of ribbon backbone so that the sugar ring isn't distorted. New Tools --------- Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool. Tool Changes ------------ AddH improved to avoid steric clashes (and appears in model panel) Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise] Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame) Multalign Viewer can save a subset of an alignment to a file Multiscale Models includes the zone-selection options Near and Contacts PipesAndPlanks now connects the secondary structure elements with loops Web Data preference category renamed to Web Access and includes HTTP proxy options Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value) Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids ViewDock includes new interface for choosing compounds by descriptor values New Commands ------------ addaa: add amino acids to the C-terminus of a peptide/protein addh: add hydrogens (command implementation of AddH) bond/~bond: create and delete bonds chirality: report the R/S configuration of a chiral center (see User's Guide for caveats) defattr: define a new attribute and/or assign attribute values (command implementation of Define Attribute) rangecolor: color over a range according to attribute values rmsd: evaluate the RMSD between specified sets of atoms (without matching) Command Changes --------------- atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes] hbonds has "tilde version" (~hbonds) which removes the pseudobonds showing hydrogen bonds labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name) rainbow can color by model (previously only by residue or chain); likewise for Rainbow tool select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection
The release notes include: initial OpenGL Shading Language API support. Do you have any documentation on how you expose this functionality, or could you offer a brief explanation on how you see it being integrated? Thanks, Charlie On Fri, 2004-10-08 at 19:44, Eric Pettersen wrote:
Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html
Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu
General changes ---------------
The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs.
Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured.
Moved C3' off of ribbon backbone so that the sugar ring isn't distorted.
New Tools ---------
Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings
Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool.
Tool Changes ------------
AddH improved to avoid steric clashes (and appears in model panel)
Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise]
Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame)
Multalign Viewer can save a subset of an alignment to a file
Multiscale Models includes the zone-selection options Near and Contacts
PipesAndPlanks now connects the secondary structure elements with loops
Web Data preference category renamed to Web Access and includes HTTP proxy options
Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value)
Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids
ViewDock includes new interface for choosing compounds by descriptor values
New Commands ------------
addaa: add amino acids to the C-terminus of a peptide/protein
addh: add hydrogens (command implementation of AddH)
bond/~bond: create and delete bonds
chirality: report the R/S configuration of a chiral center (see User's Guide for caveats)
defattr: define a new attribute and/or assign attribute values (command implementation of Define Attribute)
rangecolor: color over a range according to attribute values
rmsd: evaluate the RMSD between specified sets of atoms (without matching)
Command Changes ---------------
atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes]
hbonds has "tilde version" (~hbonds) which removes the pseudobonds showing hydrogen bonds
labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name)
rainbow can color by model (previously only by residue or chain); likewise for Rainbow tool
select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection
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On Tue, 19 Oct 2004, Charles Moad wrote:
The release notes include: initial OpenGL Shading Language API support.
Do you have any documentation on how you expose this functionality, or could you offer a brief explanation on how you see it being integrated?
So everyone understands the power of the OpenGL Shading Language, OGLSL, the idea of using shaders is to provide interactive stylized images. Especially black and white images for publication, but possibly for other effects too. The attached image has a molecular surface covered with bricks using OGLSL, which has dubious scientific value, but as a proof of concept shows the power of shaders. The initial OGLSL support is exposed via chimera python scripts. Enclosed below is testshader.py which as used to produce the brick surface. Shaders fit in to the existing chimera internal dichotomy of ColorGroups amd Colors. Color groups are textures, materials, or shaders and colors are per vertex attributes for a particular color group. So for textures those attributes are texture coordinates, for materials the attributes are RGBA (the diffuse component), and for shaders the attributes are the OGLSL varying data. A shader is expected to be packaged as a directory with an XML file, shader.xml, giving meta-information about the shader and links to individual vertex and fragment shader files. Enclosed below is an example of the current version of the XML format. It may change as I learn more about OGLSL and XML. The current "shader color" is a place holder and does not set any per-vertex attributes so the shader program needs to figure out what to do from standard OpenGL pipeline data. Luckily, many of the book examples fall into this category, like the brick shader used in the attached image. Since shader programs are tightly integrated into applications, I will have to document what OpenGL state a shader may expect and should use. For example, the brick shader, that I tested with, takes a LightPosition parameter rather than use the current set of OpenGL lights. That makes for a simplier example, but effectively disables chimera's lighting interface. I would welcome alpha testers, so please speak up if you wish to participate in developing this feature. The more programming skill and OGLSL knowledge, the better initially as the work will be to write appropriate shaders and possibly modify chimera to provide computed data to shaders. And the user interface will need work too. :-) Hope this helps, Greg Couch UCSF Computer Graphics Lab gregc@cgl.ucsf.edu ------------- testshader.py ------------- import chimera import Midas Midas.open('1gcn') m = chimera.openModels.list()[0] Midas.surface('#', 'main') s = chimera.Shader_lookup('brick') sc = chimera.ShaderColor(s) m.surfaceColor = sc ----------------------------------- ~/.chimera/shaders/brick/shader.xml ----------------------------------- <?xml version="1.0" ?> <vertex_shader filename="brick.vert"/> <fragment_shader filename="brick.frag"/> <uniform name="BrickColor" type="vec3" metatype="color"> 1.0 0.3 0.2 </uniform> <uniform name="MortarColor" type="vec3" metatype="color"> 0.85 0.86 0.84 </uniform> <uniform name="BrickSize" type="vec2"> 0.30 0.15 <min> 0.0 0.0 </min> <max> 1.0 1.0 </max> </uniform> <uniform name="BrickPct" type="vec2"> 0.90 0.85 <min> 0.0 0.0 </min> <max> 1.0 1.0 </max> </uniform> <uniform name="LightPosition" type="vec3"> 0.0 0.0 4.0 <min> -10.0 -10.0 -10.0 </min> <max> 10.0 10.0 10.0 </max> </uniform>
participants (3)
-
Charles Moad -
Eric Pettersen -
Greg Couch