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Re: [ccp4bb] CCP4 GUI
 

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CCP4bb <-- 2007 <-- May 2007 <-- 10 May 2007
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Subject: Re: CCP4 GUI
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2007-05-10 		Next message:
Subject: Re: CCP4 GUI
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-10


Subject: Re: CCP4 GUI
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-05-10
... Forgot to say that Simon obviously is right in that the check box
before "refine B factors" should not be there.

Flip

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Charlie Bond
Sent: Thursday, May 10, 2007 11:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI

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:CCP4BB@JISCMAIL.AC.UK] *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:CCP4BB@JISCMAIL.AC.UK] *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.
> >:
>
>
> 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
>
>

--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
Charles.Bond@uwa.edu.au
+61 8 6488 4406
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