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 [EMAIL PROTECTED] 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:[EMAIL PROTECTED] *On Behalf Of > > *Kolstoe S.E. > > *Sent:* Thursday, May 10, 2007 11:09 > > *To:* [email protected] > > *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:[EMAIL PROTECTED] *On Behalf Of > > *Eva Kirchner > > *Sent:* 09 May 2007 17:37 > > *To:* [email protected] > > *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: > > http://www.mail-archive.com/[email protected]/msg01224.html > > > > Good luck, > > Eva > > > > > > 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>>: > > > > > > 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 > > > > >
