that's neat - I have used chimera to build filaments from fibre
diffraction where you specify the rise and angle rather than symmops.
'Sym' command specifying 'group h' then rise and angle.
Martyn
On Fri, Dec 9, 2016 at 1:34 PM, Paul Emsley <[log in to unmask]> wrote:
>
> I would use the function new_molecule_by_symop
>
> e.g.
>
> # python
> imol = new_molecule_by_symop(0, "Y,-X+Y,Z+1/6", 0,0,0)
>
> then do this 5 more times selecting the other symmetry operators that
> generate the helix around the z axis..
>
> or the attached script (adjust as necessary)
>
> Paul.
>
>
> On 09/12/16 13:06, Martyn Symmons wrote:
>>
>> Yes I would do it that way by clicking on the ones I want to see -
>> then saving them and then reading them back in. You can change the
>> chainids so Coot makes them different colours which might help.
>> Things might be easier in PyMol if you want interactive control over
>> the colours for a picture say.
>> cheers
>> Martyn
>>
>> On Fri, Dec 9, 2016 at 12:59 PM, Smith Liu <[log in to unmask]> wrote:
>>>
>>> Dear All,
>>>
>>> I mean if the radius set in the Coot "Cell Symmetry" was too small, not
>>> enough monomers (less than 6) can be displayed to show the "continuous
>>> helix
>>> with a six-fold screw axis". If the radius was too large, as for the
>>> "continuous helix with a six-fold screw axis" can be regarded as a "rod",
>>> too large radius will lead to show several rods in one window. But with
>>> the
>>> Coot window, it cannot distinguish which monomer was from which rod. Thus
>>> I
>>> cannot identify 6 monomers forming the single rod, i.e., a "continuous
>>> helix with a six-fold screw axis".
>>>
>>> Can anyone explain in this situation how can I identify the 6 monomers in
>>> the Coot "Cell and SYmmetry" windows forming a single "continuous helix
>>> with
>>> a six-fold screw axis"?
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>> -------- Forwarding messages --------
>>> From: "Smith Lee" <[log in to unmask]>
>>> Date: 2016-12-09 18:12:20
>>> To: [log in to unmask]
>>> Subject: [ccp4bb] on Cell & Symmetry in coot
>>> Dear All,
>>>
>>> There is a pdb, once opended in coot, it was a monomer (space group P
>>> 65 2
>>> 2 ). But in the correspondence paper, it writes, "the subunits form a
>>> continuous helix with a six-fold screw axis".
>>>
>>> I have tried to view with Coot the "six-fold screw axis" formed by 6
>>> monomers. But in the "Cell & Symmetry" in Coot, if the radius is small, 6
>>> monomers cannot be shown. If I increase the radius, more than 6 monomers
>>> would occur in the window, and it can hardly distinguish the 6 monomers
>>> forming the "six-fold screw axis".
>>>
>>> In this situation, will you please let me know how to use Coot to
>>> identify
>>> the 6 monomers forming the "six-fold screw axis"? In addition, suppose 6
>>> monomers forming the "six-fold screw axis" have been identified in Coot,
>>> in
>>> order to save the pdb of each monomer, I need to click each monomer in
>>> mouse, then by "Save symmetry coordinates" to save the pdb of each
>>> monomer,
>>> right?
>>>
>>> I am looking forward to getting your reply.
>>>
>>> Smith
>>>
>>>
>>>
>
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