On 10/26/2012 12:29 PM, Francois Berenger wrote:
> On 10/26/2012 12:16 PM, James Stroud wrote:
>> This sounds like something that a PDB file is not intended to do. I
>> think everyone has universally agreed to the PDB specification at the
>> RCSB, which makes no provisions for arbitrary objects, as cool as they
>> would be.
>>
>> But you could put your information into REMARK records, which are
>> free-form. Maybe you could then find some people to honor your
>> specification or build an implementation yourself...
>>
>> ================
>> 21st century solution
>> ================
>>
>> The simplest way, would be to write a "converter" that embeds a pymol
>> script into REMARK records and a preprocessor for pymol that extracts
>> them and feeds them into the pymol stream.
>
> That's an idea.
> I may have a look at Pymol's support for user-defined object indeed
> (specification and rendering).
I found this up to now:
Compiled Graphics Objects
http://pymol.sourceforge.net/newman/user/S0500cgo.html
http://www.pymolwiki.org/index.php/CGO_Text
and this for arrows at least:
http://www.pymolwiki.org/index.php/Modevectors
>> If you write the implementation then you have a de facto standard. It
>> would take a handful of lines of code. Write it in python and claim
>> the mantle of coolness and the disdain of python detractors everywhere!
>
> I was looking for something already existing, as I guess
> I'm not the first person to need this (for productivity reasons also).
>
>> You could set up a home page using wikispaces or even the pymol wiki,
>> pointing to your implementation that you keep on github.
>
> I do have a github page, and do open source what's worth it. ;)
>
> Thanks,
> F.
>
>> James
>>
>>
>> On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote:
>>
>>> Hello,
>>>
>>> For some new project, I'd like to be able to generate things
>>> and store them in PDB format.
>>>
>>> For example, a triangle, a line segment, a square,
>>> a cube, a sphere, an arrow, etc.
>>> Being able to change the color and "line width" would be nice.
>>>
>>> Is there some official recommended way of doing this?
>>>
>>> Is there some software able to read and display such
>>> graphical annotations of PDB files?
>>> I'll also need the format description in that case.
>>>
>>> I want to be able to process a PDB file and store the result
>>> of my processing in the same PDB file as some kind of annotation.
>>>
>>> My current way of doing this is to discretize my objects as H atoms
>>> in some other output PDB file, but that's just a temporary workaround.
>>>
>>> My current search got me this:
>>> http://www.cgl.ucsf.edu/eccc1/
>>> So, maybe there is some support for what I am looking for into
>>> Chimera.
>>>
>>> Thanks a lot for your suggestions,
>>> Francois.
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