[Chimera-users] generate helical symmetry mates around an axis

Thu Sep 17 11:55:34 PDT 2020

Hi Tom and Elaine,

Thanks so much for the help. I have learnt some really cool tricks now.

Best,
Sadeem

> On Sep 10, 2020, at 6:29 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Here I colored the RNA yellow so you can more clearly see it.
> 
> 	Tom
> 
> <6g19_helix2.png>
> 
> 
>> On Sep 10, 2020, at 3:22 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Sadeem,
>> 
>>   As Elaine points out the trick is to get the helix axis in a form that the sym command can use.  Unfortunately the sym command does not know about axes made with "define axis".  But here is a pretty easy way to get the axis.  I open 2 copies of the RNA structure, align the second copy RNA to the first copy shifted by one nucleotide, then use the axis of rotation defined by that alignment:
>> 
>> 	open 6g19
>> 	open 6g19
>> 	match #0:2-14.X,1-13.Y at P #1:1-13.X,2-14.Y at P 
>> 	measure rotation #0 #1 
>> 	sym #0 group H,46,74,3 axis #2 center #2 
>> 
>> Below is what the result looks like.
>> 
>> 	Tom
>> 
>> <6g19_helix.png>
>> 
>>> On Sep 10, 2020, at 1:31 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Sadeem,
>>> If the axis defined from the RNA is what you really need, here are some thoughts on a few steps of how to convert it to something that could be used by "sym."
>>> 
>>> If there are two atoms that fall very close to the axis, you can just specify those as the axis value in the "sym" command.  You would probably want to make the axis with a small radius in the define command and show the nucleic acid as atoms so that you can evaluate this, e.g.
>>> 
>>> define axis radius 0.2 #0:.X,.Y
>>> ~nuc
>>> ~ribbon nucleic acid
>>> 
>>> Then specify those two atoms as the "sym" axis value, e.g. select them with ctrl-click, Shift-ctrl click, and then specify the in the command as "sel", e.g.
>>> 
>>> sym #0 group H,46,74,3 axis sel
>>> 
>>> I tried that on some other structure with a RNA double helix and the result didn't look very good.  It looks somewhat better if I also specify a center value, e.g. maybe in your case something like
>>> 
>>> sym #0 group H,46,74,3 axis sel center #0:.X,.Y
>>> 
>>> However, I don't know if that gives the appropriate center point for your system.  See the "sym" pages for possible ways to specify a center.
>>> 
>>> A longer way is to add new atoms at the axis-object endpoints:
>>> Use the "Save" button on the Axes/Planes/Centroids table to save the axis information to a text file.  Then calculate the endpoint coordinates of the axis according to the formulae given right next to the bottom of this page:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
>>> 
>>> Then use the Build Structure tool, Start Structure to add one atom at the coordinates of one end of the axis and then again to add another atom at the coordinates of the other end of the axis.
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
>>> 
>>> Then in the "sym" command you can specify the two atoms you just added as the axis value.  Maybe the axis center would be an appropriate point for the "sym" center value.
>>> 
>>> I hope this helps,
>>> Elaine
>>> 
>>>> On Sep 10, 2020, at 12:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi Sadeem,
>>>> Axis objects from the "define" command cannot be used as axis specifications for the sym command.
>>>> 
>>>> See the "sym" command documentation for how to specify axes:
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
>>>> 
>>>> "Specify axis of symmetry (default z), where the axis value can be:
>>>> 	• x - X-axis
>>>> 	• y - Y-axis
>>>> 	• z - Z-axis
>>>> 	• x,y,z (three values separated by commas only) - an arbitrary vector in the reference coordinate system    
>>>> 	• an atom-spec of exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the word selected, sel, or picked; any atoms also selected at the time will be ignored."
>>>> 
>>>> I hope this helps,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.                       
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>> 
>>>>> On Sep 10, 2020, at 12:18 PM, sadeem ahmad <sadeemahmad at gmail.com> wrote:
>>>>> 
>>>>> Hi all,
>>>>> I am trying to generate a helical trimer from the monomer pdb around a central double-stranded RNA. The rise and twist are 46 A and 74.0 deg respectively. I opened my monomer pdb in chimera (Screenshot-0) and used the following command to generate an axis around the central RNA double helix:
>>>>> 
>>>>> define axis #0:.X,.Y
>>>>> 
>>>>> where X and Y are the chain IDs for the 2 RNA strands
>>>>> 
>>>>> This command helped me generate an axis named a1 along the RNA duplex (Screenshot-1). Now I want to generate a helical trimer along the RNA duplex with rise=46A and twist=74deg. For this I used the command:
>>>>> 
>>>>> sym #0 group H,46,74,3 axis a1
>>>>> 
>>>>> However, it is not placing the symmetric copies around axis a1 but around a distant axis (Screenshot-2). I am not sure how to generate the helical trimer along the a1 axis. Any help in this regard would be appreciated. Thanks.
>>>>> 
>>>>> -Sadeem
>>>> 
>>>> 
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