Control helix curvature

[susan.lea@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-07)
Description
when we redefine the secondary structure elements using setattr res ss_type the dialogue says they are redefined for the sensible number of items but the cartoon drawn is still broken in the middle of where we want a continuos helix. 
Secondly - how can we reduce the level of curvature along the helix if we ask for the helix to be approximated as a cylinder?

Log:
UCSF ChimeraX version: 0.91 (2019-09-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /processing/MotAB/cspor/13may/cspor_best_model_rebuild3_jcd-coot-0.pdb

Summary of feedback from opening
/processing/MotAB/cspor/13may/cspor_best_model_rebuild3_jcd-coot-0.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.009 0.105 10367  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.245 14.284 13978  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.067 0.376 1616  
  
16 messages similar to the above omitted  
  
Chain information for cspor_best_model_rebuild3_jcd-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D E G | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> color

> rainbow chains palette gray

> set bgColor white

> sequence chain #1/A

Alignment identifier is 1.A  

> select /C:8-259

1934 atoms, 1965 bonds, 1 model selected  

> sequence chain #1/B

Alignment identifier is 1.B  

> sequence chain #1/C#1/D#1/E#1/G

Alignment identifier is 1  

> select #1/C-G:11-20,40-50,52,162-172,188-198

1595 atoms, 1595 bonds, 1 model selected  

> color sel red

> select #1/C-F:13-14,16-18,20,40,43,46-48,50,163,167,170,197,193-194

560 atoms, 528 bonds, 1 model selected  

> color sel green

> show sel atoms

> select #1

10220 atoms, 10387 bonds, 1 model selected  

> ~select #1

Nothing selected  

> select #1/C-G:13-14,16-18,20,40,43,46-48,50,163,167,170,197,193-194

700 atoms, 660 bonds, 1 model selected  

> show sel atoms

> color sel green

> select #1/A-B:26-37

198 atoms, 200 bonds, 1 model selected  

> color sel red

> select #1/A-B:26,31,33-34,36-37

106 atoms, 102 bonds, 1 model selected  

> color sel green

> style sel sphere

Changed 106 atom styles  

> show sel atoms

> select #1

10220 atoms, 10387 bonds, 1 model selected  

> ~select #1

Nothing selected  

> select #1

10220 atoms, 10387 bonds, 1 model selected  

> ~select #1

Nothing selected  

Missing or invalid "target" argument: Expected a text string  

> info resattr

resattr atoms  
resattr atomspec  
resattr center  
resattr chain  
resattr chain_id  
resattr chi1  
resattr chi2  
resattr chi3  
resattr chi4  
resattr cpp_pointer  
resattr deleted  
resattr description  
resattr has_custom_attrs  
resattr insertion_code  
resattr is_helix  
resattr is_strand  
resattr mmcif_chain_id  
resattr name  
resattr neighbors  
resattr num_atoms  
resattr number  
resattr omega  
resattr phi  
resattr polymer_type  
resattr principal_atom  
resattr psi  
resattr ribbon_adjust  
resattr ribbon_color  
resattr ribbon_display  
resattr ribbon_hide_backbone  
resattr ring_color  
resattr ring_display  
resattr session  
resattr ss_id  
resattr ss_type  
resattr standard_aa_name  
resattr structure  
resattr sym_chi1  
resattr sym_chi2  
resattr sym_chi3  
resattr sym_chi4  
resattr thin_rings  

Expected a keyword  

Expected a keyword  

Unknown command: resattr #1:C, 40-100 is_helix  

> info resattr

resattr atoms  
resattr atomspec  
resattr center  
resattr chain  
resattr chain_id  
resattr chi1  
resattr chi2  
resattr chi3  
resattr chi4  
resattr cpp_pointer  
resattr deleted  
resattr description  
resattr has_custom_attrs  
resattr insertion_code  
resattr is_helix  
resattr is_strand  
resattr mmcif_chain_id  
resattr name  
resattr neighbors  
resattr num_atoms  
resattr number  
resattr omega  
resattr phi  
resattr polymer_type  
resattr principal_atom  
resattr psi  
resattr ribbon_adjust  
resattr ribbon_color  
resattr ribbon_display  
resattr ribbon_hide_backbone  
resattr ring_color  
resattr ring_display  
resattr session  
resattr ss_id  
resattr ss_type  
resattr standard_aa_name  
resattr structure  
resattr sym_chi1  
resattr sym_chi2  
resattr sym_chi3  
resattr sym_chi4  
resattr thin_rings  

Missing or invalid "attr_name" argument: Expected a text string  

Missing or invalid "attr_value" argument: Expected an integer, a number, true
or false, or a text string  

Missing or invalid "attr_value" argument: Expected an integer, a number, true
or false, or a text string  

Missing or invalid "attr_name" argument: Expected a text string  

Missing or invalid "attr_value" argument: Expected an integer, a number, true
or false, or a text string  

> setattr #1/C:1-200 ss_type state 1

Unknown attribute target: 'ss_type'  

> setattr #1/C:1-200 res ss_type 1

Assigning ss_type attribute to 193 items  

> setattr #1/C:1-200 res ss_type 0

Assigning ss_type attribute to 193 items  

> setattr #1/C:1-200 res ss_type 1

Assigning ss_type attribute to 193 items  

> cartoon

Unknown command: cartoonstyle  

Expected a keyword  

Expected an atom specifier or a keyword  

> cartoon style sides 20

Unknown command: cartoonstyle stub  

> preset stub

Changed 10220 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> cartoon style sides 20

> cartoon style radius 4

> cartoon style radius 2

Invalid "sides" argument: Must be less than 24or equal to  

> cartoon style sides 24

Invalid "sides" argument: Must be greater than 3or equal to  

Invalid "sides" argument: Expected an even integer  

> cartoon style sides 4

> cartoon style sides 24

> setattr #1/C:1-200 res ss_type 0

Assigning ss_type attribute to 193 items  

> setattr #1/C:1-200 res ss_type 1

Assigning ss_type attribute to 193 items  

> color

> color #1/C teal




OpenGL version: 4.1 ATI-1.68.22
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Hi Susan,

For a secondary structure element to be drawn in a continuous fashion, it must also have the same 'ss_id' attribute (an integer) throughout. If the ss_id changes in the middle, you will see a break in the secondary structure element there. ChimeraX automatically assigns (low) integer ss_ids to a structure as it is opened. Therefore you should also assign a uniform ss_id attribute to your helix, using high numbers (e.g. 1000+) to ensure to differentiate them from the automatically assigned ss_ids.
Right now there is no control over the amount of curvature of helices, just whether they are curved at all or depicted as straight. This recent post on the chimerax-users list discusses the issue and offers some possible workarounds: ​http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-October/000683.html

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Elaine Meng]

Actually there isn't an option to make the tubes straight either; that's ticket #1242.