Re: [ccp4bb] NCS and manual building
Dear Olga,
I have also encountered the same problem. Find below a script which will
automate the superposition of one protomer onto the others.
Best wishes
Prakash
Superposition script :-
#!/usr/bin/tcsh -f
grep -v -E '^END' Aorig.pdb new.pdb
rm mat1.mat
foreach chain_name ( B C D E F G H I J )
# Superposition of A on chain_name
superpose Aorig.pdb tot.pdb -s ${chain_name} Aon${chain_name}.pdb | grep
-A 4 Rx mat1.mat
# Changing chain name to ${chain_name}
pdbset xyzin Aon${chain_name}.pdb xyzout ${chain_name}.pdb eof
CHAIN $chain_name
END
eof
grep -E ^ATOM${chain_name}.pdb new.pdb
rm Aon${chain_name}.pdb
end
Olga Boudker wrote:
Dear all,
I am working with a relatively low res. crystal structure with
multiple protomers in the asymmetric unit related by NCS. I am
currently running rounds manual model building in Coot and refinement
using Refmac5. Could anybody suggest a shortcut for the following
procedure: I start with an initial model containing all protomers;
generate NCS operators for A to B, A to C et c.; rebuild protomer A;
use the operators and the rebuilt A to generate all other protomers;
and combine them all in a single pdb file. Currently I do all that
manually using lsqkab and text edit and it is really painful. Is
there an available routine to do this? For various reasons I would
like to stick with Refmac5 rather then CNS, in which of course the
symmetry would have been easier to implement.
Many thanks,
Olga
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Re: [ccp4bb] RAxis fiber diffraction
Hello, You could try HELIX or FibreFix software, put crystalline DNA fibres into a capillary, no cryostream, shoot at full power for about an hour... from then it depends on the material. Regards, Mark _ Dr Mark Agacan Scientific Officer, Division of Biological Chemistry and Drug Discovery, Wellcome Trust Biocentre, College of Life Sciences, Dow St., University of Dundee, Dundee, DD1 5EH Tel: +44 1382 388751 Fax: +44 1382 345764 _ The University of Dundee is a registered Scottish charity, No: SC015096
Re: [ccp4bb] RAxis fiber diffraction
Sue, Louise Serpell at the University of Sussex, UK specialises on fibre diffraction and has some neat software that may be useful to your cause. You can contact her at [EMAIL PROTECTED] Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ - On 26 Nov 2008, at 03:08, Sue Roberts wrote: Hello Everyone Since I'm convinced that ccp4bb is the repository of all knowledge about all diffraction phenomena... A colleague would like to do some fiber diffraction studies. I have an RAxis - I know we can put the fiber in the beam and shoot it and get some pattern on the detector. Can anyone recommend some reading material or tutorials for me to learn more about what I've agreed to do? Assuming the material is actually crystalline enough to give a pattern on the detector, I can pick peaks and get d-spacings. What more sophisticated, readily available methods (software?) is out there for, perhaps, data reduction (if there is such a thing for fiber diffraction) or subsequent analysis. Thanks, Sue Sue Roberts Department of Biochemistry Molecular Biophysics University of Arizona [EMAIL PROTECTED]520 621-8171
Re: [ccp4bb] Reducing Agents and pH
TCEP is often sold as hydrochloride salt and therefore reacts highly acidic. We usually titrate the concentrated solution *before* we add it to our proteins. This can be done within small volumes by dropwise addition of a saturated TRIS solution, check pH by pipetting a drop on a pH test strip. Clemens Zitat von John A. Newitt [EMAIL PROTECTED]: At 5:04 PM -0600 11/25/08, Jacob Keller wrote: Sorry for this very prosaic question: does anybody have a reference describing the mechanisms of reducing agents (TCEP, DTT, BME, etc.), and in particular the effects of the reactions on pH? I think I can draw a convincing reaction mechanism for myself, but I am not sure theoretically why (or even whether) the pH drops in the presence of reducing agents (although I am pretty sure empirically that it does.) I have looked around a bit, but perhaps have not hit on the right google search terms... This doesn't directly address the question I think you are asking, but one obvious way that adding reducing agents could affect the pH is if they contain significant amounts of strong acids. One vendor of TCEP that we used in the past presumably had so much residual HCl in the solid reagent that even when TCEP was added at 1 mM it caused a significant decrease in pH of a buffered solution. It taught us to check the pH after adding reducing agents and also to find another vendor. - John
Re: [ccp4bb] RAxis fiber diffraction
Hi Sue, You said: Can anyone recommend some reading material or tutorials for me to learn more about what I've agreed to do? A nice tutorial on fiber diffraction is on Ken Holmes's website : http://www.mpimf-heidelberg.mpg.de/~holmes/ It might even work with other detectors ;-) ! Best wishes, Bram -- Bram Schierbeek Application Scientist Structural Biology Solutions Bruker AXS BV Oostsingel 209,P.O.Box 811 2600 AV Delft, the Netherlands T: +31 (0)152 152 508 F: +31 (0)152 152 599 E: [EMAIL PROTECTED] W: www.bruker-axs.com
[ccp4bb] Monitor
I am looking for a good CRT monitor for crystallography that supports stereo well. CRT monitors particularly large 20 inch viewable are harder to find these days. Any suggestions on the best monitor? Are any large LCDs capable of stereo support? Brian
[ccp4bb] Monitor
I am looking for a good CRT monitor for crystallography that supports stereo well. CRT monitors particularly large 20 inch viewable are harder to find these days. Any suggestions on the best monitor? Are any large LCDs capable of stereo support? Brian
Re: [ccp4bb] twin axis in p21
Dear Hua, Your problem sounds like a 'false origin' one, where due to the pseudotranslation the molecular replacement choses the wrong origin out of the two possible ones. Your space group is probably P212121. The best approach is to run Andrey Lebedev's program ZANUDA on YSBL server. http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Best wishes Misha Isupov From: CCP4 bulletin board [EMAIL PROTECTED] On Behalf Of Yuan, Hua [EMAIL PROTECTED] Sent: 26 November 2008 01:20 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] twin axis in p21 Dear Colleagues, I'd like to share with you with a twinning puzzle that's been troubling me for a while. I have a ~2.2 A data merged in p212121 space group with unit cell: 41.8300 117.4490 134.4840 90. 90. 90. Translational NCS was detected but structure solution was able to be obtained by phased molecular replacement as we have a Au derivative data set. Obtaining experimental phase or MR alone didn't work. However, with this model and data set, the refinement didn't work (with R-free ~40% or higher if with more cycles). Different twinning tests have been carried out and no sign of twinning. All possible p222 space groups have been tried but no luck or even worse. Considering that translational symmetry and perfect twinning may make things deceiving, the data was merged into p21 and a twin-refinement was performed in phenix.refine. After 3 cycles of rigid-body and group ADP, a R-free of ~30% was obtained and the output map looks OK. It looks like we got it. But then things get interesting when we tested other two axis as the p21 unique axis. With all the three choices plus corresponding twin-refinement, we could get a similar R-free (30%). Besides, the three maps all look OK except for one missing some side chains. Then the structure was solve in p1 and Xtriage was used with the hope that one axis would stand out. However, the RvsR for all three axis are almost the same. Did I miss anything here? Of course, we could pick up the one axis we like best and get the structure solved ^---^. However, this puzzle would eat me alive for a very long time. Best, Hua
Re: [ccp4bb] Resolve to CCP4...
Summary: A couple of people pointed out that refmac allows you to pick which Free set you use. Unfortunately, not all programs have this option, not all expose it via the GUI, and if you forget just once to change this from the default, you've messed up your free set. However, Tom Terwilliger email'ed to point out that since 2007, resolve has used the same convention as CCP4 - i.e. free sets numbered 0-19 with 0 being free by default. So the real answer is, if you have this problem, you should update you solve/resolve! For old files, it looks like sftools from the command line is the easiest method. sftools checks the Free-R flag and asks if you want to fix it. I did this: sftools read resolve.mtz Y write ccp4.mtz Kevin Cowtan wrote: Is there any way on the CCP4 GUI to covert the free-R flag from a resolve mtz file (where 95%=0, 5%=1) to a CCP4 style free-R flag (where 5%=0 and I don't care about the rest), while preserving the free-R set? I can do it a number of ways - e.g. using sftools from the command line, but it seems to me that this is a common enough task that there should be an easy way to do it. Kevin
