Changes between Version 1 and Version 2 of 2014-11-20


Ignore:
Timestamp:
Nov 20, 2014, 3:26:39 PM (11 years ago)
Author:
Scooter Morris
Comment:

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  • 2014-11-20

    v1 v2  
    1120 November 2014 meeting, 2:00 - 3:30
     2
    23Attendees
     4 Conrad, TomG, Sam, Eric, TomF, Greg, Elaine, Scooter
    35
    4 
    5 Agenda
    6 
     6'''Agenda'''
    77 1. Updates on progress
    88 1. Next API?
    99 1. Final look at [http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/frameatom_spec2.html atomspec] document
    1010
    11 Action Items
     11'''Next Meeting'''
     12 1. Work through details of implementation plan
    1213
    13 Results
     14'''Action Items'''
     15 1. Conrad to try using Anaconda to build chimera2
     16 1. Greg to finish startup implementation
     17
     18'''Results'''
     19 1. Updates
     20  * Conrad:
     21   * !ToolShed API: working on implementing it, but sidetracked by build problems.  He finally has a useful build on Yosemite.
     22   * !AtomSpec implementation: waiting for !ToolShed completion.
     23  * Eric:
     24   * Revised UI to call new Graphics API routines
     25   * Waiting for !ToolShed to implement command line
     26   * Working on translating SEQRES records into Sequences
     27   * Had to implement C++ logging methods to prepare for !PyLogger implementation.
     28  * Greg:
     29   * Have command line working with aliases
     30   * Need to commit MMCIF changes
     31   * Looking at chimera2 startup and putting in stubs
     32  * Tom:
     33   * Working on the Graphics API implementation
     34   * Looked at WebGL implementation for some of Dyche Mullins data
     35 1. Next API?
     36  * Logging - Eric (next meeting)
     37  * Triggers
     38  * Preferences
     39  * Python versions of main data objects (Molecules, etc.)
     40  * IO Module (File type registration)
     41 1. !AtomSpec
     42  * [http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/frameatom_spec2.html atomspec] document
     43  * Remaining issues:
     44   * In many commands where the specification is the last argument (e.g. color), a blank specification means “all.”
     45     * Still true
     46   * Would spaces on either side of a cluster of symbols like “ &~ ” be collapsed?
     47     * yes
     48   * Asterisks (*) in input atom names will be translated to prime symbols ('), but translated back if coordinates are later saved to a file. Prime symbols in input atom names are not translated on input or output.
     49     * For PDB files (only), we will translate for * to ' but we will not try to translate back.
     50   * Any residue in PDB HETATM records (or the mmCIF equivalent) that does not already have a chain ID is assigned to chain het, unless the residue is named WAT or HOH, in which case it is assigned to chain water; residue numbers are unchanged. (See also the residue attribute isHet.) Residue specifications with chain IDs omitted will match residues in chains with single-character IDs but not residues in these special chains.
     51     * No.  Leave it as we read it.
     52   * Support selection name via ''sel=selection_name''
     53     * No, get rid of it
     54   * custom amino acid categories that have been defined with ResProp
     55     * No need: already supported through selection term
     56   * need to decide on a priority order of built-in classifications vs. target aliases vs. named selections in case of conflict, or disallow name conflicts at time of creation
     57     * Can't override built-in classifications
     58     * target aliases can either be symbolic or based on data
     59     * aliases can override previously defined aliases (as long as they aren't built-in)
     60   * Attribute names are case-sensitive; attribute values, if any, are case-sensitive if specified with ==, but not if specified with =. Attribute values containing spaces (some color names, for example) must be enclosed in double quote marks.
     61     * Keep single = only, but we may need to add "==" and "~" at a later time
     62   * Within an attribute specification, ~ can be used in place of = to indicate that the subsequent string should be treated as a regular expression.
     63     * See above
     64   * When placed before an attribute name, the caret ^ indicates that the atoms, residues, or models have not been assigned any value for the attribute. For example, :/^kdHydrophobicity designates residues (such as water or nucleic acids) that lack a Kyte-Doolittle hydrophobicity assignment.
     65   * OK, keep it.
     66
     67'''Discussion'''
     68 * Discussion came up about how to go about getting the first graphics up on Chimera2 screen. Specifically how much of the Hydra code to pull in.
     69 * Will Chimera2 have triggers or not?
     70 * Proposal for getting things built on Windows.  Proposal is to use Anaconda.