Re: [ccp4bb] Crystallization buffer pH optimization

Hi Mike, check out the EZ screen builder from Emerald Bio, that is a really nice tool for this purpose: http://www.emeraldbiosystems.com/escreentoolkit/escreen.html Select your screen, your hit condition, then hit 'optimize' and you will have a screen that will vary the precipitant concentration

[ccp4bb] Crystallization buffer pH optimization

Hello, Shameful and sorry for asking this simple question, it looks like this when first starting a new setup in so-called structural biology. I remmeber a book of, probably, Hampton, in which there are tables of pH optimization for many buffers. For example for buffer TRIS, the table will l

[ccp4bb] Unit Cell of Ensemble must be orthogonal

Dear all, When I used PHASER to do a molecular replacement and define ensemble via map (mtz file), the program stoped very soon. The log file showed that "Unit Cell of Ensemble must be orthogonal". I tried many ways to generate the map file, but the results are the same. Can anyone help me to so

Re: [ccp4bb] how many metal sites

*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** I agree with Dale that your four metals are not in the density and also don't seem to make sense in terms of chemistry

Re: [ccp4bb] how many metal sites

On Wed, Jan 16, 2013 at 2:53 PM, Roger Rowlett wrote: > When you are a building a metalloenzyme model you should really have some > solid evidence that a metal ion is present by (1) inclusion in the > crystallization medium, (2) direct determination by an analytical technique, > (3) UV-visible spe

Re: [ccp4bb] how many metal sites

The geometry is difficult to see from a static image, but it looks like you possibly have a His(2)Glu(4) coordination environment around what looks like one likely metal ion, based on the difference density. Zn(II) is typcially (but not always) tetrahedral with Zn-O/N bond distances of approxim

Re: [ccp4bb] how many metal sites

Zn is a very electron rich atom so a 2.3 A resolution data set should be a fine experiment to determine the number of fully occupied metal sites. It is always hard to be sure about screen shots of density, but it looks to me that you only have evidence for one zinc here. In my opinion, it i

Re: [ccp4bb] protein degradation in crystal

Could you identify the cleavage sites by protein sequencing and design new constructs (truncated versions) accordingly? It might improve your crystal quality to get better resolution. Joe On Wed, Jan 16, 2013 at 9:22 AM, Tom Murray-Rust wrote: > Just to add to Herman's suggestions, if you are

Re: [ccp4bb] side question re crystal dehydration

Dear Enrico, I agree that in broad terms even bad weather (happens a lot here) could be considered a change in humidity. I'm not trying to claim that every time someone changes something in their drop dehydration is to be blamed. But it is a fact that by simply opening your drop you are causing

[ccp4bb] CCP4 package and update managers: relocating installations

Hi, I had exactly the same problem. I wanted to install ccp4 on a Mac Server & then export it to other devices. What I found was that the setup script needed to be edited to reflect the new location. (/Applications/Software/ccp4-6.3.0/ccp4.app/Contents/Resources/ccp4.sh) However ….. There do

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Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

Excellent. Thanks a lot for the clarifications. ciao, s On Jan 16, 2013, at 4:14 PM, Kay Diederichs wrote: > Sebastiano, > > CORRECT does scale the data. XSCALE is only needed for two or more datasets, > or if other requirements exist - you named one. > > The two varieties of FRIEDEL'S_LAW

Re: [ccp4bb] side question re crystal dehydration

I think one may need to distinguish between three different kinds of dehydration experiment, because of the different forces they will exert on a crystal to shrink the unit cell, creating new stabilizing crystal contacts or perhaps causing contacts to fail in a chaotic manner, disordering the cry

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Dear Colleagues, We announce a call for synchrotron beam time applications in biological small-angle scattering (SAXS) and macromolecular crystallography (MX). The beamtime will be available at the PETRA-III storage ring from *March, 1st, 2013 to September, 15th, 2013* (please note the end date c

Re: [ccp4bb] CCP4 package and update managers: relocating installations

Dear Chris, Indeed, you cannot use Package Manager on Mac OSX for installing CCP4 in custom location, which is due to petty technicalities and "pragmatism". However, CCP4 can be installed in non-standard locations with raw *.dmg's downloadable from our web site, which is supposed to be as easy

Re: [ccp4bb] CCP4 package and update managers: relocating installations

Hello Chris, > Is there any way to install the CCP4 suite in a non-standard location > under OS X and still use the package manager and update facilities? With > a large number of Macs it's much easier for me to have CCP4 living in a > single, network-mounted directory than on each machine. I us

[ccp4bb] CCP4 package and update managers: relocating installations

Dear CCP4, While we're talking about the package and update managers, I have a question. Is there any way to install the CCP4 suite in a non-standard location under OS X and still use the package manager and update facilities? With a large number of Macs it's much easier for me to have CCP4 li

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

Sebastiano, CORRECT does scale the data. XSCALE is only needed for two or more datasets, or if other requirements exist - you named one. The two varieties of FRIEDEL'S_LAW differ in their rejections! HTH, Kay Sebastiano Pasqualato schrieb: > >Thanks to Kay and Tim or the feedback. > >The

[ccp4bb] ccp4 update

Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing "update" :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers,

Re: [ccp4bb] ccp4 update

Ah, I see. This was part of update 10. Thank you. Andreas On 16/01/2013 2:51, Qixu Cai wrote: Dear Andreas Förster, You can use "ccp4um" (ccp4 update manage) to update CCP4 from command line. Best wishes, Q. Cai -- Andreas Förster, Research Associate Paul Freemont & X

Re: [ccp4bb] ccp4 update

Dear Andreas Förster, You can use "ccp4um" (ccp4 update manage) to update CCP4 from command line. Best wishes, Q. Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/1/14 Andreas Förster > Dear CCP4 maintainers, > > I've come to appreciate th

Re: [ccp4bb] protein degradation in crystal

Just to add to Herman's suggestions, if you are trying to crystallise a protease then you could also try using the S195A variant rather than an inhibitor. This would certainly be the case if you ever want to co-crystallise in a substrate, as PPACK (or the like) would occupy the active site cleft an

Re: [ccp4bb] protein degradation in crystal

Hi John, This is really an amazing wild west story: the man who crystallizes faster than his protease! I really must compliment you with how you successfully performed these experiments! Unfortunately, proteins usually do not crystallize that fast (at least not in my hands), so in these cases o

Re: [ccp4bb] protein degradation in crystal

Were the crystals which run different on gels from the same drop, or separate drops? Yes, it is possible that the protein is being cleaved in the crystal (self-cleavage?); but it may also be that it is being cleaved in the mother liquor, and that crystallization is enriching one form or anoth

Re: [ccp4bb] protein degradation in crystal

Were the crystals which run different on gels from the same drop, or separate drops? Yes, it is possible that the protein is being cleaved in the crystal (self-cleavage?); but it may also be that it is being cleaved in the mother liquor, and that crystallization is enriching one form or anoth

Re: [ccp4bb] crystal dehydration

Indeed! We have a short communication in Acta D that is under revision (no preprint yet, sorry!), going in the same direction than what Hagelueken et al have done (using saturated salt solutions in the reservoir and transferring your crystals in perfluoropolyether oil (see paper here that we ha

Re: [ccp4bb] side question re crystal dehydration

Juan, Humidity variation is what vapour diffusion crystallization achieves. In your list of all possible dehydration methods you would end up classifying all vapour diffusion experiments as a case of dehydration. After nucleation, crystals continue to grow and the drop continues to become mor

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Re: [ccp4bb] protein degradation in crystal

Hi Lisa, Speed is definitely a big factor here. With a protein I work with I can get large crystals in myriad conditions that only diffract to about 4-5 Ang. What I ended up doing was taking these crystals and seeding entire screens. I found that not only would crystals appear sooner but it rev

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

On Jan 16, 2013, at 2:19 PM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Sebastiano, > > if the output of GO.COM produces an mtz-file you can use for phasing > or refinement, I am very confident there is a scaling step involved. Sorry, my bad. I meant there's

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

The XDS CORRECT step will also (by default) do scaling - if I understand correctly the same scaling as in XSCALE, but for a single sweep and with no zero-dose. If what you want is merging statistics, I find it helpful to write out the data unmerged and then use pointless -c and aimless to merge th

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Sebastiano, if the output of GO.COM produces an mtz-file you can use for phasing or refinement, I am very confident there is a scaling step involved. This might also be an explanation for the discrepancy you point out: With FRIEDEL'S_LAW=TRUE the

[ccp4bb] side question re crystal dehydration

Dear all, From Leonid's reply earlier you can see a problem some of us have been having for a while now, when looking for literature regarding dehydration. Most of you that perform dehydration either don't consider it happening or don't report it in great detail in your publications. This is on

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

Thanks to Kay and Tim or the feedback. The reason I wanted to get statistics from the CORRECT step of XDS is that I have refined a structure using the mtz output by the GO.COM automatic reduction routine of SLS beamline PXIII, which does not involve a scaling step (I discovered recently). I wa

Re: [ccp4bb] crystal dehydration

Judith, If you can, try monitoring the diffraction during the dehydration experiment. There are plenty of ways of doing this. Perhaps the simplest is to shoot your crystals in-situ after swapping the precipitant for a more concentrated one. The is also the Free Mounting System. David Hargreaves

Re: [ccp4bb] advices

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mike, difficult to give specific advice without knowing the crystallisation conditions. - - at the beginning in the unmixed drop your protein is soluble - - after equilibration with the mother liquor there is a crystal. Think about what is happ

Re: [ccp4bb] protein degradation in crystal

Dear Lisa It is not uncommon to see breakdown products when you run crystals on gel. Espesially if they are older crystals, sometimes you even see higher molecular bands, these are probably due to intra molecular cross links formed over time. If you are worried about stability, try to increase

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Sebastiano, you could use xprep to get the statistics in user defined resolution shells. Out of curiosity: Would you mind sharing why you want to do this and why you don't want to use the XSCALE statistics instead? The statistics are probably mo

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[ccp4bb] protein degradation in crystal

Hi All, I have an 36KD protein which can be crystallize in two days. Most of the crystals are very big. But all cystals have poor resolution,lower than 3.8 A. I picked some crystals, washed them in the mother solution and then run SDS-PAGE. It is surprised to find that different cystals have differ

Re: [ccp4bb] changing resolution bins statistics in CORRECT.LP

Dear Sebastiano, sorry, it is not possible. Indeed, only XCSALE allows you to define the resolution ranges yourself. HTH, Kay On Tue, 15 Jan 2013 16:22:14 +0100, Sebastiano Pasqualato wrote: > >Hi all, >I was wondering if XDS allows to change the number of resolution bins >appearing in the