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CCP4BB  May 2007

CCP4BB May 2007

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Subject:

Re: CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)

From:

"Nave, C (Colin)" <[log in to unmask]>

Reply-To:

Nave, C (Colin)

Date:

Thu, 10 May 2007 10:38:13 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (72 lines)

Seems to be a general issue.
Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116.
"Under the microscope - The use of 'black box' techniques carries risks."
Colin
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]]On Behalf Of Flip Hoedemaeker
Sent: 10 May 2007 10:21
To: [log in to unmask]
Subject: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)


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]>: 

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

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