[chimerax-users] Labelling w.r.t Secondary structure elements

[Eric Pettersen]

Hi Arun,
	Thanks for pointing this out.  I have fixed the problem in the script on the ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/> site.  Use that one.

--Eric

> On Nov 9, 2021, at 1:16 AM, Gupta, Arun <Arun.Gupta at warwick.ac.uk> wrote:
> 
> That' really great Eric. Also, Recently I have noticed that previous version of the script worked wonderfully for the proteins, which have both the secondary structural elements in the protein structure i.e α-helices and β-strands. However, when the protein has only one prominent type of structural elements, it failed to recognize the structural elements correctly and did mis-labelling of the secondary structural elements for e.g In the attached pic, the protein which I used for labelling purpose has all α-helices but the script has mis-labelled them as all β-strands. Please have a look into this issue. 
> 
> 
> 
> Thanks a lot! 
> 
> Arun 
> 
> 
> Arun Gupta PhD, MRSC
> Research Fellow
> Challis & Lewandowski Group
> Chemistry Department
> University of Warwick
> Gibbet Hill Road
> Coventry CV4 7AL
> United Kingdom
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Sent: Monday, November 8, 2021 10:28 PM
> To: Gupta, Arun <Arun.Gupta at warwick.ac.uk>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Labelling w.r.t Secondary structure elements
>  
> Hi Arun,
> Glad it's useful to you.  For the benefit of others, I have put a slightly improved version of the script on the ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/> site.  The improvement is that it will prefix the labels with the chain ID if there is more than one chain in the structure.
> 
> --Eric
> 
>> On Nov 4, 2021, at 2:10 AM, Gupta, Arun <Arun.Gupta at warwick.ac.uk <mailto:Arun.Gupta at warwick.ac.uk>> wrote:
>> 
>> Thanks a lot Eric. Script works pretty nicely.  It saves a lot of time.
>> 
>> Best wishes,
>> Arun
>> 
>> Arun Gupta PhD, MRSC
>> Research Fellow
>> Challis & Lewandowski Group
>> Chemistry Department
>> University of Warwick
>> Gibbet Hill Road
>> Coventry CV4 7AL
>> United Kingdom
>> From: Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
>> Sent: Thursday, November 4, 2021 12:11 AM
>> To: Gupta, Arun <Arun.Gupta at warwick.ac.uk <mailto:Arun.Gupta at warwick.ac.uk>>
>> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
>> Subject: Re: [chimerax-users] Labelling w.r.t Secondary structure elements
>>  
>> Hi Arun,
>> Elaine is correct that there is no easy command equivalent for this.  I wrote a short Python script to label the middle label of each secondary structure element with α/βN for helices/strands respectively.  Run the script simply by opening it with the open command.  You can adjust the initial height of the labels by editing the first line of the script, or afterward with the "label height N" command.  Keep in mind that secondary structure element numbering resets with each chain, so if you have a multi-chain structure then this script may not produce what you want.
>> 
>> --Eric
>> 
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> 
>> 
>>> On Nov 3, 2021, at 1:55 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>> Hi Arun,
>>> Not completely sure this is what you're asking, but I'm guessing something like how "label" shows residue labels, but instead showing a label like alpha1 or beta1 for each secondary structure element (SSE)?  There is nothing like that, sorry.  
>>> 
>>> Personally I would use 2D Labels before Powerpoint, but you undoubtedly have more Powerpoint skills than I do.  You can enter the text, colors, arrows, etc. in 2dlabels commands, and then drag them to the desired locations with the "move label" mouse mode.
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>>
>>> 
>>> The closest "automatic" thing I can think of is the following, but it doesn't look good enough for a figure, partly because every residue has a label.  I can't think of a simple way to only add one label per SSE. Example:
>>> 
>>> open 2gbp
>>> label (helix | strand) attribute ss_id height 1.2
>>> 
>>> ... that just gives an integer 1 for residues in first strand and first helix, 2 for second strand and second helix, and it doesn't say whether it's a strand or helix (0 for all coil).  You could also label by secondary structure type, but that attribute is also an integer, not the words or greek letters alpha and beta (ss_type 1 for helix, 2 for strand).
>>> 
>>> label delete
>>> label (helix | strand) text "{0.ss_type}:{0.ss_id}" height 1
>>> 
>>> see "label" options
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/label.html#options>>
>>> and attribute names
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html>>
>>> 
>>> Again, I'd use 2dlabels, but to assist with identifying which SSE is which, I might use the first label command example above (and delete those labels when I was done), or just rainbow the chain and go progressively from blue to red.
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Nov 3, 2021, at 1:10 PM, Gupta, Arun via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>> 
>>>> Hello,    
>>>> I was wondering is there a quick fix way around by which we can define in an automated fashion the numbering and further labelling of secondary structural elements labels, alongside the structure, based on “dssp” described symbol notation "for example starting from α1/β1-α10/β14 " for any protein instead of manually labelling later in Power point.  
>>>> Thanks a lot!   
>>>> Arun  
>>> 
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> <091121__Structure_1.png>

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