Changes between Initial Version and Version 1 of Ticket #1009


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Timestamp:
Jan 18, 2018, 12:34:04 PM (8 years ago)
Author:
Elaine Meng
Comment:

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  • Ticket #1009

    • Property Cc chimera-programmers added; Eric Pettersen removed
    • Property Owner Tom Goddard removed
    • Property Summary surface command changes definition of ~protein? → molecular surface not included in command-line specifiers of corresponding atoms (protein, nucleic, many others)

  • Ticket #1009 – Description

    initial v1  
    1 This example structure 1ncc is antibody H and L chains, and N chain mostly protein but also some glycosylations.  The first ~protein in the commands below specifies what I expect, only the glycosylations, but the second one also colors the antibody chains.
     1For example, structure 1ncc is antibody H and L chains, and N chain mostly protein but also some glycosylations.  The first ~protein in the commands below specifies what I expect, only the glycosylations, but the second one also colors the antibody surfaces.
    22
    33open 1ncc
    … …  
    66surf /n enclose /n include ligand
    77color ~protein steel blue
     8
     9I'm thinking this affects all the command-line specifiers of sets of atoms (protein, nucleic, sidechain, ligand ...).  Yes, molecular surface models are not atoms, but I think this is wrong behavior.  The atomic patches of a molecular surface should be specified along with the corresponding atoms.
     10
     11I don't know to whom this should be assigned.