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
> >
> >
>
|