Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

Another cause of difficulty - nothing really to do with the spacegroup selection - is when one copy of the model has much higher B factors than others. Most MR searches assume that the copies contribute more or less equally to scattering. If you assign too high a symmetry this will make MR le

[ccp4bb] Can REFMAC5.2 use the library from REFMAC5.6?

Hi, For some reasons, I need to use REFMAC5.2. But this version doesn't include library for some ligand (eg NDG FUC MAN...). I don't have too much clue as to how to manually build the library, and I tried to copy the cif file from REFMAC5.6 into the current lib/data/monomers folder. However, it ju

Re: [ccp4bb] Low number of waters for a given resolution

You might want to take a look at the following paper: Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):479-83. How many water molecules can be detected by protein crystallography? Carugo O, Bordo D

[ccp4bb] Low number of waters for a given resolution

Hello all, Some crystal structures seem to contain a very low number of water molecules given their resolution (e.g 1 water for every 10 amino acid residues at 2.2Angstrom, whereas probably around 0.6 waters per residue is expected on average). I was wondering if anybody has any insights (or bet

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

The space group in which you do the RF makes no difference (assuming the model in each case is identical of course) because you're superposing the same amount of scattering matter: it has nothing to do with the fraction of the contents of the AU. In the high symmetry space group with say 1 instanc

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

In my experience, the success of molecular replacement depends primarily on the quality of the model. Thus if your model is good, even P1 will work. Two extreme cases that I encountered were searching with a monomer for what turned out to be 4 tetramers (thus first search only accounted for 1/16

Re: [ccp4bb] CNS and protein structure refinement

A quick PDB search reveals that 551 crystal structures were deposited in 2010 that were refined with CNS. On Wed, 2011-02-16 at 13:32 +, REX PALMER wrote: > Does anyone still use CNS ? > Do we expect Rfree from CNS for example to be different from the value > given by Refmac at the end of the

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

I think the question was not concerning right vs wrong space group, but right vs a lower symmetry superset space group - P4322 vs P43 for example. I would also be interested in the answer. At first glance it appears harder in the lower symmetry because with each monomer you would be searching for

Re: [ccp4bb] Liquid nitrogen resistant flooring

At ALS, we have a red epoxy-on-concrete floor, which is "lN2 resistant" but still cracks if abused. However, we have not repainted it for many years now. We found that one very good way to extend the life of the floor is to keep users from dumping their cryogens onto it. In Berkeley, it is e

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

Well P4 isnt a subgroup of P43212 - you would need P43 MR programs will often let you test several spacegroups. See Phaser MR or MOLREP - I would try that and choose the best Eleanor On 02/16/2011 02:48 PM, Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me

[ccp4bb] how can i cinfirm the ligand bindind

Dear CCP4 colleague I just wanted to ask a simple question that if the ligand has bind the molecules so how can i confirm it either my ligand has bind or not and which program should i used to visualize it??? Best Regards AFSHAN

[ccp4bb] MR problem in determining the number of identical molecules in ASU

Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in dete

Re: [ccp4bb] CNS and protein structure refinement

Dear Rex, Bernie and Fred, The following paper bears on the question of generally slight, but not always, R factor differences between published and recalculated Rfactors. [The paper is open access.] Greetings, John J. Appl. Cryst. (2010). 43, 669-676[ doi:10.1107/S0021889810015608 ] phenix.m

Re: [ccp4bb] Liquid nitrogen resistant flooring

Dear Nick, in the sample preparation areas of our beamlines we had the same problem. We have a new floor since mid 2009 and are so far happy with it. It was supplied by the IRL Industrial Flooring Group/Flowcrete UK (www.irlgroup.co.uk and www.flowcrete.com) The floor is Cat 3 compatible. Hope th

Re: [ccp4bb] CNS and protein structure refinement

Hi Rex, There will be small differences in particular due to the different ways of treating the solvent. How large of a difference are you talking about? Normally the difference should not be very large... And if this related to solvent effects, it will affect the low resolution reflections w

Re: [ccp4bb] CNS and protein structure refinement

Ditto. YES, still generally prefer CNS v1.3 to REFMAC, especially due to composite and simulated-annealing maps. Different set of flagged reflections, so it might very well be different. Also, the low-resolution solvent scaling is different between the two refinements. Bernie Santarsiero On W

Re: [ccp4bb] CNS and protein structure refinement

Yes X 2            Boaz - Original Message - From: REX PALMER Date: Wednesday, February 16, 2011 15:32 Subject: [ccp4bb] CNS and protein structure refinement To: CCP4BB@JISCMAIL.AC.UK > Does anyone still use CNS ? > Do we expect Rfree from CNS for example to be different from the > val

Re: [ccp4bb] Liquid nitrogen resistant flooring

Dear Nick, We start have the same sort of problem here at MPL. However, we have already a few solutions to put in practice. 1-The research complex at Harwell has a excellent floor on the Liquid Nitrogen Room. The name of the floor tiles are Matlocker and you can find it from this site www.jay

[ccp4bb] CNS and protein structure refinement

Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement?   Rex Palmer   Birkbeck College

Re: [ccp4bb] Liquid nitrogen resistant flooring

 We have linoleum floor in the x-ray room which of course cracks under LN2. We put wood panel under the large container of the Oxford Cryo to prevent this. We have tiled floor in the corridor outside the room and that's where we empty the containers used for freezing crystals and other container

Re: [ccp4bb] Liquid nitrogen resistant flooring

BS"D Dear Nicholas, Three possible solutions that I have seen: 1. A sheet of stainless steel under the filling area over concrete (I think I saw that at the ESRF). 2. A "throw-away" layer of linolium that you replace every few months. Sort of like an ablation layer on a heat shield

Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time

We use Google Calendar for booking our X-ray facility. Klaus === Klaus Fütterer, Ph.D. Reader in Structural Biology Undergraduate Admissions School of Biosciences

Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time

Hi Darren, Sunbird from mozilla is accessible in any computer running linux and windows connected to the home network (I guess it should be compatible with other OS systems as well) and it's free. The problem is that it's getting slow depending how many instruments you have for booking. To a

Re: [ccp4bb] Liquid nitrogen resistant flooring

We went through a building renovation and this has been a problem for us too. In the old days, our building was simply sealed concrete - and you could do anything with it with no issues. Now, it's an epoxy floor, but really what happens is the liquid nitrogen cools it down and breaks the seal

[ccp4bb] PhD studentship in enzyme engineering at University of Reading

3-year PhD studentship available from October 2011 Department of Food and Nutritional Sciences and School of Biological Sciences University of Reading Project title: Optimisation of prebiotic galactooligosaccharide production through enzyme engineering Project overview: Prebiotic oligosacc

Re: [ccp4bb] Liquid nitrogen resistant flooring

This has been a problem for us too. Sorry, I don't have a solution to offer except, recently, we have provided metal buckets filled with a layer of aquarium gravel at each station and encouraged users to dump their excess nitrogen there instead of on the floor. Richard On Feb 16, 2011, at 7:

[ccp4bb] Off Topic: Web or e-tools for booking instrument time

Hello, Since we are now part of the "Facebook Generation" (or at least 10% of the planet is), it seems there must be a better way of distributing time on our various Aktas to an institute of scientists than our current system which involves a race for the paper booking sheet every Thursday morning.

[ccp4bb] Liquid nitrogen resistant flooring

Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Prof Nicholas H. Keep Ex

Re: [ccp4bb] PDB deposition ADIT without frames?

Dear Dirk, Not a remedy, but how about iyour colleague trying a different browser or deposition site (e.g. www.pdbe.org)? Cheers, Tim On Tue, Feb 15, 2011 at 05:00:00PM +0100, Dirk Kostrewa wrote: > Dear CCP4ers, > > a colleague of mine is just going through the PDB deposition process > using t