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
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406
