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Re: [PyMOL] cgo cylinders with flat ends? More details
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From: T.A.Wassenaar <T.A...@ru...> - 2005-05-11 11:12:17
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Hi Martin,
For me (Suse 9.0 Linux, Pymol 0.98b) this scripts seems to
do exactly what you want. After rendering that is. If the
scene is not rendered, the cylinder is an eight-sided
prism, which is due to the openGL implementation. Maybe it
would be nice if there would be a setting like cgo_quality
to enhance such a view without rendering.
But does your problem persist after rendering, and if so,
could you show an image illustrating that? Though I have
to add that I won't be the one to help from that point on,
as it'll be in the implementation.
Cheers,
Tsjerk
On Wed, 11 May 2005 11:45:36 +0100
Martyn Symmons <ma...@cr...> wrote:
> Dear Tsjerk and other pymolites
>
> To draw my cylinders I just modified Warren's example
>from the CGO
> demos in the examples/devel directory. I give this
>below. Maybe there is
> another way to do this? I would like cylindrical
>cylinders with sharp cut
> ends rather than rounded ends. I guess this is down to
>OPENGL not to
> pymol.
>
> I have another program that looks at the RNA atomic
>coordinate file and
> writes in the coordinates of the double-helical regions
>of the RNA.
> (currently this is based on a user going through the
>secondary structure
> by hand - I discussed with Luca Jovine a little about
>whether it could be
> done automatically but he has not time just now to spend
>on this).
>
> So below is an example of Warren's code after I hack in
>my coordinates,
>
> You get it into pymol by using the 'run' command.
>
> Thanks for any help with this.
> Best wishes and regards
> Martyn
> -------------------------------------------------------------------
>
>
>
> # this is a trivial example of creating a cgo object
>consisting of a
> # a single state
>
> # first we create a list of floats containing a GL
>rendering stream
> # obj is an empty list to begin with...
> obj = []
>
> obj.extend( [ CYLINDER,
> 13.839,-33.646,20.164,24.5685,-15.6645,16.6015, #hacked
>in from coords
> 10.0,
> # Radius
> 0.0, 0.0, 1.0, # RGB Color 1
> 0.0, 0.0, 1.0, # RGB Color
>2
> ] )
> # then we load it into PyMOL
>
> cmd.load_cgo(obj,'cgo013')
>
> # move the read clipping plane back a bit to that that
>is it brighter
>
> cmd.clip('far',-5)
>
> On Tue, 10 May 2005, T.A.Wassenaar wrote:
>
>> Date: Tue, 10 May 2005 21:37:33 +0200
>> From: T.A.Wassenaar <T.A...@ru...>
>> To: Martyn Symmons <ma...@cr...>
>> Subject: Re: [PyMOL] cgo cylinders with flat ends?
>>
>>
>> Hi Martyn,
>>
>> It sounds like you used the SAUSAGE keyword rather than
>> the CYLINDER keyword, the latter of which is a true
>> cylinder. But if this line of deduction is wrong, please
>> show what you tried and the result it gave.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Tue, 10 May 2005 18:22:10 +0100
>> Martyn Symmons <ma...@cr...> wrote:
>> > dear pymol-users
>> > I have used CGO to put down 20
>> >angstrom-wide cylinders on
>> > the helical bits of a large RNA molecule. They come
>>out
>> >with nice rounded
>> > ends but I would prefer flattened ends if possible. Is
>> >there any way I can
>> > do that?
>> > Thanks for any help/advice.
>> > cheerio for now,
>> > Martyn
>> > Martyn F. Symmons (Ph.D.)
>> > Research Associate
>> > Crystallography and Biocomputing Group
>> > Department of Biochemistry
>> > University of Cambridge
>> > Phone: 01223 766020
>> > -----------------------
>> > "Abair ach beagan agus abair gu math e"
>> > Seanfhacal Gaidhlig (Gaelic Proverb).
>> >
>> >
>> >
>> >
>> >
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>>
>
> Martyn F. Symmons (Ph.D.)
> Research Associate
> Crystallography and Biocomputing Group
> Department of Biochemistry
> University of Cambridge
> Phone: 01223 766020
> -----------------------
> "Abair ach beagan agus abair gu math e"
> Seanfhacal Gaidhlig (Gaelic Proverb).
>
>
>
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