[chimerax-users] Cuved helix tubes

[Elaine Meng]

Hi Ernesto,
I gave one way to break the helix, which was to change a residue in the middle to non-helix.

A second way to break the helix, but keep all residues defined as helix, is to change the residue attribute ss_id described here:
<http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>

You can use some high number like 1000, 1001, ... (unlikely to be used already since the automatically assigned ones start at 1) for a segment of helix that you want to separate, e.g. for my example of chain C in 5gmk:

setattr /c:532-587 res ss_id 1000

It is still breaking the cylinder, so might not be any better for you, but it makes the helices directly abutting instead of having one non-helix residue in between.
Best,
Elaine

> On Oct 2, 2019, at 1:10 AM, Ernesto Arias Palomo <earias at cib.csic.es> wrote:
> 
> Hi Elaine,
> 
> Thank you very much for your help. Since it’s a continuous helix I’d prefer not to break the cylinder, but I’ll try that approach and see how it looks.
> 
> Thanks again,
> Ernesto.
> 
> --
> Ernesto Arias Palomo, PhD
> Group Leader
> Biological Research Center (CIB-CSIC)
> Ramiro de Maeztu, 9.
> 28040. Madrid. Spain
> earias at cib.csic.es
> +34 91 837 31 12 ext 4446
> 
>> On Oct 1, 2019, at 5:39 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Ernesto,
>> Sorry, there is no option to make a helix tube fit the residues more closely; it just makes one smooth arc per helix (no “S” or “J” shapes, only “C”), with no user control over the radius of curvature.   I’ve also had these issues with certain structures.
>> 
>> However, these approaches might help:
>> 
>> (1) try breaking a long helix into two or more shorter helices.
>> (2) make tube radius fatter if the problem is certain sidechains far from tube
>> 
>> Details.  (1) For example, this is part of chain C in 5gmk, with a very long S-shaped helix:
>> 
>> <5gmkc.png>
>> 
>> Then if I put the mouse over the structure I can see that the middle of the S shape is approximately residue 532 in chain C.  I can break the helix by changing the type of that residue to non-helix, command:
>> setattr /c:532 res is_helix false
>> 
>> Then it fits better
>> <better.png><better2.png>
>> 
>> 
>> (2) Depending on the situation, however, the other approach of just making the tube fatter might work, e.g. command: cartoon style radius 4
>> 
>> <fatter.png>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Oct 1, 2019, at 2:50 AM, Ernesto Arias Palomo <earias at cib.csic.es> wrote:
>>> 
>>> Good morning,
>>> We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices?
>>> Thank you very much for your help.
>>> Kind regards,
>>> Ernesto.
> 
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