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Dear Paul,

my email was meant to be provocative but neither insulting nor offensive
(having provoked quite a few responses when I last used the word
'offense' this email does not suffer from a subtle misinterpretation of
mine while not using my mothertongue. The German 'Provokation' is
something a scientist would welcome since it is critism expressed in a
rhetorically pleasing or intelectually amusing way, and criticism
drives science forward).

I am very grateful never to have met a non-helpful developer when I
addressed one with a request or suggestion and I fully agree with you.

I rather meant to point out that most developers are usually
overwhelmed with work, suggestions, or ideas for improvements, and for
that reason I think having formats that allow users to help themselves
or each other (while of course they still can suggest their ideas to
the developers) is a good thing, and having a format that only allows
access through some API (or help from a developer) is not.

I would also like to point out that my initial fear that we were
moving away from such a format with the replacement of PDB with mmCIF
has been soothened with this discussion and hence the content of my
previous paragraph is deprecated w.r.t this thread's context.

Regards,
Tim

On 08/08/2013 05:29 PM, Paul Adams wrote:
> Tim,
> 
> I'm sure your email was tongue-in-check, but it's provocative 
> nevertheless. I suspect that Nat's point was that scientific
> software developers (who are predominantly scientists of course)
> are helpful people who want to see their field of research be
> successful. If it is possible to spend an hour writing a tool that
> helps several thousand researchers to do their work that's probably
> a valuable use of time. An enlightened funding agency might even
> see the value! Sometimes it's a challenge to figure out exactly
> what would be of most help, hence Nat's plea for input. I don't
> know about other software development efforts, but we're very happy
> to get ideas and suggestions from researchers - just don't assume
> that we can implement them all (by tomorrow)!
> 
> Cheers, Paul
> 
> On Aug 8, 2013, at 12:17 AM, Tim Gruene <[log in to unmask]> 
> wrote:
> 
> 
> 
> On 08/07/2013 11:54 PM, Nat Echols wrote:
> 
>>>> PLEASE tell the developers what you need to get your job
>>>> done; we can't read minds.
>>>> 
>>>> -Nat
>>>> 
> 
> Dear Nat,
> 
> I have a student working for me until the end of the month. I asked
>  her to calculate the mean ratio of U(H)/U(X) where X is the atom
> the corresponding hydrogen is bound to. I would like her to group 
> together as follows:
> 
> 1) all N-H and O-H within that protein 2) all Calpha-Halpha 3) all 
> remaining C-H bonds 4) all O-H from the H2O and H3O in the 
> structure.
> 
> I am not sure whom to address this request to, so please forward
> it to the developer. If the could would actually work on a shelxl 
> res-file it would be brilliant. I shall not ask George for this 
> software because as a scientist he has much more important and
> much more general problems to work on than this.
> 
> At the moment the person is doing it by hand which might take a
> day. So if you could return the code by tomorrow that would be
> nice.
> 
> Out of the tens of thousands of crystallographers coming up with 
> funny ideas (because, yes, you cannot read minds) you might
> receive such requests several times a day. And you seriously think
> this is the way we should go? Bless your funding agencies.
> 
> Cheers, Tim
> 
> P.S.: I found this discussing about mmCIF  quite interesting, and 
> since I was reminded that mmCIF is still kind of line oriented, I
> am pretty relieved. I just don't think that a 'universal' API
> exists - the student I am talking about does not know any
> programming language at all, and the next student might require an
> API in scheme, ruby, java, C#++-3.141, fortran-123, ...
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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