[chimerax-users] Cuved helix tubes

[Ernesto Arias Palomo]

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 <mailto: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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