-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 [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:* CCP4BB@JISCMAIL.AC.UK >>> *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:* CCP4BB@JISCMAIL.AC.UK >>> *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/ccp4bb@jiscmail.ac.uk/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 >>> >>> > - -- 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: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGQvbPF6oOrDvhbQIRAu6xAJ9y+GZyEVbtkk7MqP5QL0ywMsaeGgCfWTQl dnm5yKadhfUfq8FkcH1jIP8= =i4fm -----END PGP SIGNATURE-----
