[ccp4bb] concentration of protein by TFF

Dear All, we use proflux M12 machine for concentrating our protein using two pellicon 2 casettes PLCC of 0.1 m2. We recently replaced these casettes with new one and now we are facing a problem of low flow rate. i.e earlier when we used to run at a particular pump speed and pressure the flow rate

Re: [ccp4bb] Sub-angstrom resolution

There are two sides to this qustion: the scientific one is actually easier to answer in generic terms - but I also would like to point out the very recent example of a mystery that required very high resoluton (and orthogonal techniques) to answer, namely the puzzle of the light atom in the center

Re: [ccp4bb] Always Modelling Anomalous Signal

On Tuesday, January 10, 2012 02:46:21 pm Ian Tickle wrote: > Jacob, > > Actually the R factors including the Bijvoet pairs would be higher, > because the uncertainties in F(+) and F(-) are higher than that of > F(mean) by a factor of about sqrt(2). R factors will always be higher > for unmerged d

Re: [ccp4bb] Always Modelling Anomalous Signal

Jacob, Actually the R factors including the Bijvoet pairs would be higher, because the uncertainties in F(+) and F(-) are higher than that of F(mean) by a factor of about sqrt(2). R factors will always be higher for unmerged data because averaging always reduces the uncertainty. This means that w

Re: [ccp4bb] Always Modelling Anomalous Signal

On Jan 10, 2012, at 22:00 , Jacob Keller wrote: > Dear Crystallographers, > > it seems to me that on a certain level we are always throwing away > (sort of) about half of our data when we merge Bijvoet pairs--why Who "We" ? > shouldn't we keep them separate, since we know that they should be

[ccp4bb] Always Modelling Anomalous Signal

Dear Crystallographers, it seems to me that on a certain level we are always throwing away (sort of) about half of our data when we merge Bijvoet pairs--why shouldn't we keep them separate, since we know that they should be a little bit different, especially in light of the higher multiplicities w

Re: [ccp4bb] Sub-angstrom resolution

One more to add to Ed's list: highly accurate ultra-high resolution structures may allow calculation of electrostatic potential around protein ligand binding site. There are plenty of reference... Pavel On Tue, Jan 10, 2012 at 11:04 AM, Ed Pozharski wrote: > On Tue, 2012-01-10 at 18:30 +, T

Re: [ccp4bb] Sub-angstrom resolution

On Tue, 2012-01-10 at 18:30 +, Theresa H. Hsu wrote: > Thank you for the interesting replies so far. > > Please let me ask a related question - at what resolution should we stop > efforts to get better diffracting crystals? Are there *biological* questions > that a model with 1.8-2.0 A resol

Re: [ccp4bb] Sub-angstrom resolution

Thank you for the interesting replies so far. Please let me ask a related question - at what resolution should we stop efforts to get better diffracting crystals? Are there *biological* questions that a model with 1.8-2.0 A resolution (with combination of complementary methods like spectroscopy

Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

Yep, phenix.refine also always creates one reflection file that contains map coefficients. In fact, it contains all together: - original Iobs (or Fobs - whatever the user specified); - Fobs used in refinement; - Fmodel (the total model structure factor including all scales, bulk-solvent etc), so on

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

I think what Jacob is looking for is something akin to the transition between slides 20 and 21 in this PowerPoint: http://bl831.als.lbl.gov/~jamesh/nearBragg/nearBragg.ppt But, if you're looking for something with a more complex molecule, this movie might be what you want: http://bl831.als.lbl

Re: [ccp4bb] Sub-angstrom resolution

Ed The crystal size form factor will change the intensity of each spot so that instead of being a sharp maximum it will have a sinx/x behaviour. This will occur for each spot independently of resolution. There is a very good illustration of this in the paper referred to by Ethan where the sin(x)

Re: [ccp4bb] Sub-angstrom resolution

I think once you start getting down to such small crystals, the spots are not really important, as the pattern starts getting continuous. Interestingly enough, I guess for single-molecule diffraction, resolution is limited only by radiation damage, and not by any sort of lattice disorder (or even b

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Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

Including the final map coefficients as part of the structure factor file deposited and then archived by the PDB provides a means to directly see the actual map as interpreted by the crystallographer. EDS is useful in providing a "third party view" but the actual map is really better. We think

Re: [ccp4bb] reliable/unreliable maps?

On Tue, 2012-01-10 at 13:25 +, Luca Pellegrini wrote: > "This is not a reliable map." There are many reasons why one could get the gap in R-values. As the proud author of an "unreliable" map myself (3pht), I found that what did it was that the TLS-refined model was deposited with the full B-f

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Re: [ccp4bb] Sub-angstrom resolution

On Tue, 2012-01-10 at 09:04 +, Colin Nave wrote: > Yes, I think Ed's analysis is a bit misleading. I apologize if I misled anyone. Re-reading my post, I can see that it lacked precision. Indeed, in a perfect monocrystal all the molecules are lined up perfectly, so I should have emphasized ra

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Re: [ccp4bb] reliable/unreliable maps?

Hi Frank, EDS already does that. Even so, reproducing the R-factor does not prove that the map is reliable. See for instance 3frk for which the deposited dataset is much smaller and less complete than the one used for refinement. The map from EDS is therefore completely model biased. I only recen

Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

Dear Stephen, The thought that using the CSD via Mogul for generating good refinement dictionaries in the first place was THE way to go, rather than relying on the PDB to use the same information later to try and catch errors at the time of deposition, has been the driving force in the develo

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Re: [ccp4bb] reliable/unreliable maps?

> > Or just print both Rfactors...? This is what phenix.model_vs_data does, leaving for you to decide if the difference is "significant": http://phenix-online.org/documentation/model_vs_data.htm Pavel

Re: [ccp4bb] reliable/unreliable maps?

Or just print both Rfactors...? On 10/01/2012 15:21, Luca Pellegrini wrote: Hi Paul, What would you rather it say, I'm happy to change the message. "The EDS does not think that this is a reliable map, in that it is or may be inconsistent with what the authors were looking at during deposit

Re: [ccp4bb] reliable/unreliable maps?

Hi Paul, > What would you rather it say, I'm happy to change the message. "The EDS does > not think that this is a reliable map, in that it is or may be inconsistent > with what the authors were looking at during deposition"? How about "Warning: the R-factor calculated for this map differs sig

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

The diffraction pattern we see results from the convolution of the crystal lattice with the fourier transform of the electron density, as I understand it. I guess I am interested in seeing the unconvoluted transform of the electron density, just to get a feeling for what the characteristics of thos

Re: [ccp4bb] reliable/unreliable maps?

There can be many different reasons why EDS calculates an R-value that is different from the one reported by the authors - some of these are listed here: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS Back in the "dark ages" (actually, the late 90s) we arbitrarily decided to use a tolerance o

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

Thanks Colin! I was also going to mention the Chemical Database Service, available to UK academics. Their website is http://cds.dl.ac.uk/ In fact, the very nice and friendly CDS guys are just across the corridor from me, so please let me know if you have problems/questions. Cheers Martyn On Tue,

Re: [ccp4bb] reliable/unreliable maps?

By "calculated" do you mean Fc maps? I thought the maps were 2mFo-DFc of mFo-DFc (at least that's the prompt you get when you ask for a map). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone:

Re: [ccp4bb] reliable/unreliable maps?

On 10/01/12 13:25, Luca Pellegrini wrote: Dear all, A minor point but worth mentioning, I think... The EDS server does not produce a density map for PDB entries for which it cannot calculate R-factors within 5 percentage points of the published values. I believe that the maps are not availab

[ccp4bb] reliable/unreliable maps?

Dear all, A minor point but worth mentioning, I think... The EDS server does not produce a density map for PDB entries for which it cannot calculate R-factors within 5 percentage points of the published values. I understand that the server was set up in the dark ages of crystallographic refine

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

I'm sad to think that scientists may not 'bother' to use the CSD system 'just' to check the geometry of small molecule ligands, as they may, of course, be the main focus of the study, or the focus of subsequent researchers who use the structures. Moreover, comparison of small molecule and protei

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Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

"...available to anyone who has access to the Cambridge Structural Database System" How many academic labs will bother / can afford to buy a CCSD license just to check the geometry of small molecule ligands, especially when they need to do so them only once every blue moon? The ability for the PD

[ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

On 9 January 2012 06:13, Shveta Bisht wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I used > JME editor to draw the molecule and ran PRODRG online with the > options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the > attachments for the molecu

Re: [ccp4bb] Sub-angstrom resolution

Yes, I think Ed's analysis is a bit misleading. If, as an extreme case, you have just two unit cells (in each dimension) with 300A cell dimensions, the interference function could still manifest itself out to 1A resolution. Play around with some of James Holton's simulation programs to find out

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jacob, what do you mean by 'molecular transform'? Would you like to visualise the summed structure factors from the atoms inside the unit cell? - - What pattern are you talking about/ what pattern do you expect? - - What benefit do you expect fro