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Dear all,
I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.
If I write now is because Martynn's e-mail have reminded me of something
I thought once, but forgot to ask for to the ccp4i developpers: perhaps
the GUI could have "two faces/modes", a basic one and an expert/advanced
one. I understand that they already exist, but the "expert" one is
hidden under the "Run&View Com File", while I'm thinking on a real
expert GUI-mode. Users should be able to choose one or the other in
their defaults, or switch from one to the other on-the-fly.
I don't have a particular problem in editing the scripts as it is done
now, but I have found that students tend to get a bit nervous about
doing it themselves ;-)
Cheers,
Miguel
Martyn Winn escribió:
> The level of detail in the GUI is a matter of constant debate. The
> underlying programs are far far richer, so the question is how much to
> expose in the GUI. We try to get a balance between ease-of-use and
> coverage, but it won't always work. BTW I don't think we ever claimed
> that ccp4i (or anything else in ccp4) is "finished" ;-)
>
> Having said that, we're always happy to hear about specific defects in
> the GUI. When reporting these to [log in to unmask] please give as much
> information as possible, in particular knowing the context is always
> helpful.
>
> Cheers
> Martyn
>
> On Thu, 2007-05-10 at 17:39 +0800, Charlie Bond wrote:
>> I would add that I have found the CCP4 development team very receptive
>> to being informed about specific improvements which could be made, and
>> even more so to fixes implemented by users themselves.
>>
>> Perhaps an explicit list of the many limitations which need attention
>> would be useful to the development team.
>>
>> Cheers,
>> Charlie
>>
>>
>> Flip Hoedemaeker wrote:
>>> Hi Simon,
>>>
>>> Well, X-ray crystallography nowadays often, but certainly not
>>> always, amounts to running a set of programs with default settings with
>>> a few mouse clicks in the GUI. The fun part is knowing when you have to
>>> deviate from default, leave the well travelled paths etc.
>>>
>>> The GUI is excellent with the straightforward stuff, if this fails you
>>> actually have the option of editing the generated scripts (run and view
>>> com file option), or leave the GUI altogether and go to old fashioned
>>> command mode or your own scripts. Think of the GUI as a welcome
>>> addition, but not as a panacea for all your crystallography problems,
>>> and certainly train new crystallographers in such away that they at
>>> least have an idea what is going on in the "black box"
>>>
>>> Flip
>>>
>>> ------------------------------------------------------------------------
>>> *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf Of
>>> *Kolstoe S.E.
>>> *Sent:* Thursday, May 10, 2007 11:09
>>> *To:* [log in to unmask]
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Thanks very much for the replies, and especially for the link to the
>>> previous thread on this topic (Eva).
>>>
>>> Just a comment about the ccp4i GUI in general - pretty much all the
>>> students in my department are slowly becoming dependant on the GUI
>>> because it is so much easier to use for those brought up using MS
>>> windows. However, is it really fair to be distributing the GUI as a
>>> "finished" product when it has so many limitations, and in this
>>> particular case is just plain misleading? Although I applaud the idea of
>>> making crystallography more user friendly, is it not just asking for
>>> trouble (and bad science) when software is written that gives the
>>> illusion that things are more straight forward than they actually are?
>>>
>>> Simon
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf Of
>>> *Eva Kirchner
>>> *Sent:* 09 May 2007 17:37
>>> *To:* [log in to unmask]
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Hi Simon,
>>>
>>> you can't stop it - I asked the same question (with some more questions)
>>> some weeks ago.
>>>
>>> You can find the original email and the tips I got for not-so-good
>>> resolution B-factor refinement here:
>>> [log in to unmask]" target="_blank">http:[log in to unmask]
>>>
>>> Good luck,
>>> Eva
>>>
>>>
>>> 2007/5/9, Kolstoe S.E. <[log in to unmask]
>>> <mailto:[log in to unmask]>>:
>>>
>>>
>>> Dear all,
>>>
>>> I have a structure at fairly low resolution that I am trying to refine
>>> with Refmac. I do not want to refine B factors so have arbitrarily set
>>> them all to 20 and then run refmac in the ccp4i GUI after deselecting
>>> the "refine temperature factors" box. However, when I look at the
>>> resulting pdb file my B factors vary from 2 to 90.
>>>
>>> Is Refmac just calculating my B factors or is it still refining them,
>>> and if the latter how can I stop it?
>>>
>>> Thanks,
>>>
>>> Simon
>>>
>>>
>
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [log in to unmask]
www: http://www.pangea.org/mol/spip.php?rubrique2
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Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie. (Raoul Vaneigem)
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