Re: [PyMOL] new to list -- simple questions

[Tsjerk W. <ts...@gm...>]

Hi Bob,

I notice that this question has not yet been answered, unless you have
received private answers. To start with the second question, this list is
followed by those who are most involved in the code, and, AFAIK, there is
no specific developers list (I do care to know if there is :P). Also for
general how-to questions, this is the place to be.

As for the first question, I would say that it would be valuable to have a
way to communicate not only a static picture with caption, but also an
annotated, interactive view.

Finally, I don't think there's a repository of session files. Are there
specific things that you're missing in the set you have? I can probably
provide some examples with various classes of CGO objects.

Hope it helps,

Tsjerk



On Fri, May 24, 2013 at 9:59 PM, Robert Hanson <ha...@st...> wrote:

> Hello, PyMOL users!
>
> I'm new to this list. Some may recognize me as the current principal
> developer of Jmol. Until recently I hadn't explored PyMOL much, mostly
> because I'm not myself a biochemist. For about three months now, though,
> Jaime Prilusky (Weizmann Institute) and I have been working on a PSE file
> reader for Jmol, and I think we're just about ready to roll that out, at
> least in a preliminary version.
>
> A few questions:
>
> Q: Does the availability of a way to manipulate PyMOL models on the web
> using Java or just HTML5 interest this crowd? Or are people more focused
> specifically on journal image production or stand-alone PyMOL application
> use?
>
> Q: Are there people on this list who can answer fundamental PyMOL
> programming issues, or is that another list? I'm pretty much a autodidact,
> but there are some nuances that I don't understand. I don't want to waste
> this list's bytes if questions like "Is the second array in a scene color
> definition list always just a list of 1s?" are inappropriate.
>
> Q: I also have lots of questions relating to how you go about doing things
> in PyMOL. (Getting a list of all defined scenes, for example.) OK to ask
> those here?
>
> Q: Now that we have a pretty good handle on how PyMOL is organized and
> most of the basic data structures, and with all the *basic* modeling
> options reproducible in Jmol, we need more examples. More interesting CGOs
> than "Hello, World," examples of various specific objects such as Surface
> object, that sort of thing. I think I'm just about done with our current
> sample set of about 100 PSE files. Anyone interested in contributing PSE
> files to the Jmol project? Is there a repository somewhere of those?
>
>
> Thanks in advance,
>
> Bob Hanson
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.