[ccp4bb] AMoRe

Hi, Has anyone tried the tutorial on the CCP4 website for AMoRe? http://www.ccp4.ac.uk/examples/tutorial/html/mr-tutorial-amore.html I am trying to learn how to use the package in CCP4 and it fails and I am wondering if the tutorial has become outdated? Thank you, George

Re: [ccp4bb] [phenixbb] So what is unique?

I think that 'observed' goes back to whether it was possible to see a reflection (and estimate its intensity by eye) on the photographic FILM. In small molecule crystallography it is usually understood to mean F>4sigma(F) (or I>2sigma(I)). George On 07/15/2014 07:02 PM, Edward A. Berry wrote

[ccp4bb] Postdoctoral Research Associate available - Structural biology-Computational modeling - University of Minnesota

Dear All, I would like to draw your attention to the postdoctoral vacancy in the research group of Prof. Larry Wackett at the University of Minnesota (USA): A postdoctoral position is available immediately at the University of Minnesota to conduct research with a team of biochemists and

[ccp4bb] Translational NCS and molecular replacement.

Dear Community, I have some doubts to clarify. In a way to solve a structure by Phaser-MR, I found phaser ended up with a potentially good MR solution (with good statistics, packing and electron density, and as we know the homolog structure so in a reasonable biological assembly also). However, th

Re: [ccp4bb] [phenixbb] So what is unique?

I don't think "observed" means all the reflections that were integrated, becasue one of the other parameters is the criterion for a reflection to be considered "observed", so that "observed" is a subset of "all". Here are some lines I saved from an adit2 session (some years back, but I believe it

Re: [ccp4bb] [phenixbb] So what is unique?

So on second thought, practically speaking I guess "observed" is all, since we never see the ones that are rejected by the -3 sigma "observed criterion" On 07/15/2014 12:44 PM, Edward A. Berry wrote: I don't think "observed" means all the reflections that were integrated, becasue one of the othe

[ccp4bb] LCP lipids

If you were going to start with 4 different LCP lipids what would they be? 9:9, 9:7 etc? why- channel size, temp range?

Re: [ccp4bb] AW: [ccp4bb] Weired Crystal packing

I suggest submitting your coordinates to the PDBe (EBI) web site to run PISA or using it via tthe CCP4I interface. This analysing contacts, and suggests the most favoured packing. It is not fool proof but worth checking. Eleanor On 15 July 2014 09:53, wrote: > Dear Appu, > > > > What is your

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

Hello Wei, is the modified base defined as DNA in the cif? (see below) Is the O3* or O3'? You need the latter. And check whether there are three hydrogens on the O3. You need to either remove one from the cif file manually, or name them according to a normal DNA base. (In the latter case, by ma

Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

You may need to 1) modify _chem_comp.group to be "DNA" in the cif-file 2) import the resulting cif-file in coot Cheers Sent on a Sprint Samsung Galaxy S® III Original message From: "Wang, Wei" Date:07/15/2014 5:14 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb]

[ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?

Hi, There is a problem about modified DNA refinement. I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. However I found the modified DNA could not be linked to the downstream DNA when I refined it in the COOT. Then I generated another CIF file using sketcher of CC

[ccp4bb] AW: [ccp4bb] Weired Crystal packing

Dear Appu, What is your problem? To me this crystal packing looks completely normal. If you look for tetramers in space groups with 422 symmetry I am sure you will find examples with a similar packing. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Appu k

[ccp4bb] AW: [ccp4bb] definitions of unique reflections

Dear Kenneth, You should be able to find the information you are looking for in the logfiles of your dataprocessing at the scaling/merging step. E.g. in the logfiles of scala you will find "Total number of observations" and "Total number unique". I am sure Scalepack will produce similar output.

[ccp4bb] remove

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