Re: [ccp4bb] twin refinement

Hi Teresa, As Eleanor has mentioned, you should probably check out other space groups. Xtriage gives a lot of great information and many plots to inspect. But, if you do not know what the plots mean and just look at the results that say the twin fraction is 0.48 you can get into some troub

Re: [ccp4bb] Harmful effect of X-ray

Is this a joke or are you serious??? Hopefully you haven't actually started shooting people with highly focused X-rays... Jon On 07/12/2013 10:14 AM, diptimayee mishra wrote: Dear All, Can anyone please tell me regarding the harmful effects of X-ray , we are using for protein crystallograph

Re: [ccp4bb] HKL2000 24IDE beam center.

Niu, Could you give me some information about when you came to NE-CAT and I will tell you the beam center. We can do this off the CCP4BB. My email is schue...@anl.gov Thanks, Jon On 01/17/2013 03:19 PM, Niu Tou wrote: Hi colleagues, We have collected several datasets at APS with det

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

I forgot to mention... there are two ways of calculating the phases in Phenix, try both ways because the maps can look very different. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue A

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Phenix does this (http://www.phenix-online.org/documentation/autosol.htm#anch125) Phaser-EP (http://www.phaser.cimr.cam.ac.uk/index.php/Experimental_Phasing#Combined_MR_and_SAD_Phasing) and SHELX using an experimental version you have to get from George Sheldrick. Jon -- Jonathan P. Schue

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

I have used and worked on both the Bio-Rad and Akta systems. It is really a matter of opinion, but they both get the job done. Exterior: The Akta systems look nice with metal exteriors while the Bio-Rads look a little cheap being plastic. Both are really heavy, though. Interior: Once you take

[ccp4bb] what is this called?

I am sure this has happened many many times before but I cannot find a reference. I have a protein/DNA complex structure where the protein has P212121 symmetry, but the DNA only has P21 symmetry. I know its pseudosymmetry caused by the NCS. Has anyone seen this with protein/DNA or have a refere

Re: [ccp4bb] Database access failure during program execution

If I'm not mistaken it is caused by /tmp/'username' not existing or being writable... Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (6

Re: [ccp4bb] Low resolution refinement

Dear Joane, Bert's recommendations are very good, but I'd like to add a little caution. If just part of the molecule has bad density then it is not unusual, but if the whole chain does not look very good (missing side-chains or backbone) you may have a couple of things going on. First, I w

Re: [ccp4bb] possible pseudo-merohedral twin?

Without seeing your NZ or L-test plots, but looking at the logs, your data does not appear to be twinned. It will not be R32 because the R-merge is too high. The probable space group is C2. The listed twin fractions will approach 0.5 if your data has perfect twinning or you processed in too low

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

According to the paper, the data was refined in REFMAC in 'twin mode' which, I believe, calculates the R-factor using a non-conventional R-factor equation which usually lower than the conventional R-factor. I believe this is dependent on the twin fraction which wasn't mentioned in the paper (o

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

Just to add to Phil and Eleanor's response... I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better. Its probably not C-centered (as Eleanor mentions) and you should try t

Re: [ccp4bb] Is the Rmerge invalidate by twinned data?

Fulvio, We need more info to give advice. First, when you say Rsym is 0.18, are you talking about in the high res bin or overall? Second, how did you determine you have twinning? In what space group did you scale your data? If your data is actually twinned with a high twin fraction, and yo

Re: [ccp4bb] difficult P1 crystal

cell and try to solve it that way without the pseudo-centering, especially if the off-origin Patterson peak is large (>50% of origin peak). Jon Schuermann -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 So

[ccp4bb]

Vandana, Roger gives some good advice and I agree with Fred about not knowing the number of mols in the AU. I routinely see solvent content in the 75% range for many different crystals, although they tend to diffract rather poorly. In addition, you may have to convert your search model to

Re: [ccp4bb] Merohedral twining for P212121.

Yang, There are not any merohedral twin laws, but there are several pseudomerohedral twinning possibilities. The most common would be a monoclinic cell with a beta ~90, so it appears orthorhombic. Going the other way, you could have an orthorhombic cell look tetragonal if A and B are close

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

Hari, What twin tests have you run? Results? If your data really is P43212 and you drop to P212121 you will still have the additional two-fold operator in your data. An operator is a mathematical operator, which could be crystallographic or twin. I never refine a structure with twin

Re: [ccp4bb] Calculation of electron density map for a twinned dataset

Mariah, Although your data may be perfectly twinned, more likely your data 'shows about 50 % twinning' because you are not in the correct space group. How are you determining your twin fraction and in what space group? Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Buil

Re: [ccp4bb] Expression of a protein of 43KDa

ld be although it's supposed to be 29kDa it runs funny and appears larger in the SDS gel, in that case it would be OK. If we only had some confirmation that the 43kDa band is the right one e.g. via Western Blot & Anti-His ... Jürgen On Feb 18, 2010, at 4:01 PM, Jon Schuermann wrote:

Re: [ccp4bb] Expression of a protein of 43KDa

Maybe I am not getting it, but I don't see your problem or question? What I understand from your message is that you have a protein that overexpresses, purifies, and crystallizes... where's the problem? We all wish we had that problem... Jon On 02/18/2010 11:49 AM, Armando Albert de la Cr

Re: [ccp4bb] Help request: Failed MR using the same molecule as model

Actually, another thing could be going on as well. You show a large off-origin peak in the Patterson in I422 so you may have pseudotranslation going on and you processed in the supercell. You could probably try to reindex choosing fewer spots and get your P422 cell. I am sure there is some law

Re: [ccp4bb] Help request: Failed MR using the same molecule as model

find the correct SG. Peter or Andrey will probably chime in here if this is your problem. HTH, Jon Schuermann -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email

Re: [ccp4bb] Supplementary density

Fabien, The extra density may be from a his-tag or cloning artifacts left over at the beginning or end of your protein sequence. You may be seeing the residues coming from a neighboring molecule. I have seen parts of a C-terminal his-tag ordered in the electron density before. Jon

Re: [ccp4bb] Question about merging of data from different crystals

tionality rules) which can introduce model bias, so your model should be pretty close to the end product. I recommend refining your structure as well as you can without inputting the twin law until the very end. Jon Schuermann -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Buildin