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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Refmac and B factors
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-05-10

Next message:
Subject: Re: Program to find the center of mass
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2007-05-10

Subject: CCP4 GUI (was:RE: Refmac and B factors)
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-05-10

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Refmac and B factors
From: "Kolstoe S {- dot -} E {- dot -} " S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-05-10

Next message:
Subject: Re: Program to find the center of mass
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2007-05-10