#36 cartoon misdraws ends of helices in pdbs

v1.6.0.0
closed-works-for-me
5
2013-03-29
2004-08-31
Cowbert
No

Somewhere between PyMol 0.90 and PyMol 0.95, cartoon
rendering changed somewhat and it no longer
automatically draws open ends of helices correctly.
This applies to PDBs with no secondary structure
information. In versions including and prior to 0.90,
the cartoon does a better job of drawing helical ends
without requiring secondary structure assignment. I
have to change a bunch of scripts now to explicitly
assign secondary structure, whereas I did not have to
before. I have tested the behavior on 0.90, 0.95, and
0.97 on both Linux, FreeBSD, and IRIX.

See the figure where on the left is a render using 0.90
and on the right using 0.95. The script just sets
'smooth_loops, 0' calls 'cartoon oval' and 'show
cartoon'. On the right in the red circles, the ends are
rendered incorrectly.

Discussion

  • Cowbert

    Cowbert - 2004-08-31

    pymol rendering differences

     
  • Warren L. DeLano

    • labels: --> Scientific Correctness
    • assigned_to: nobody --> wdelano
     
  • Warren L. DeLano

    Does this problem still occur with PyMOL 1.2?

     
  • Thomas Holder

    Thomas Holder - 2013-03-29

    Works for me, I tested a couple of versions from 1.0r2 to 1.6-alpha with this code snipplet:

    set cartoon_smooth_loops, 0
    fetch 4dkk, async=0
    remove not resi 409-418
    as cartoon
    orient
    
     
    Last edit: Thomas Holder 2013-03-29
  • Thomas Holder

    Thomas Holder - 2013-03-29
    • status: open --> closed-works-for-me
    • milestone: --> v1.6.0.0
     

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