Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

No love for RNA!? Ouch ! I was in the similar problem ten years ago when I was solving riboswitch RNAs as a graduate student. B12 riboswitch,stuck at 5-6A for derivatives, but had pretty reasonable native data. It was a combination of experimental phasing using clusters at low resolution and

Re: [ccp4bb] Semet derivative dying almost immediately in beam

Ah, low resolution experimental phasing. Fun stuff, seems like a lost art these days. Are the crystals large ? Is it possible to do a (continuous helical data) collection? (Manually or if your beamline permits you to). Granted this is anomalous, is it possible to then merge enough partial da

Re: [ccp4bb] 3D

I’m crossing my fingers, or should I say my eyes, that they don’t! > On Mar 11, 2019, at 9:22 AM, David Schiller wrote: > > https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/ > > NVIDIA will stop supporting 3D glasses in April > > > > -- > ===

Re: [ccp4bb] ice build up during collection using 4 axis goniometer

I've had this problem with the four circle goniometers. I imagine your setup looks similar to https://www.med.upenn.edu/biocbiop/jf/bsbcore/images/X-ray_Rigaku_MicroMax-007.jpg ? At high chi values, I would also observe a 'tail' of ice off my pins. As you mentioned in the manual, it's because

Re: [ccp4bb] Rmergicide Through Programming

I find the lack of reporting statistics of the low resolution bins unfortunate! Most statistics in Table 1 report the average across all resolutions or just the high resolution reflection shell. With respect to Rmerge, the agreement between the most intense (low resolution) symmetry related

Re: [ccp4bb] Rcrane error, update

I'm thinking a nomenclature issue. H5 ? Should be H5' no? Have you run your structure through a pdb remediator? http://kinemage.biochem.duke.edu/software/remediator.php is my favorite. You will want to play around with the flags to get the right output. I think rCrane likes old style nomen

Re: [ccp4bb] mystery feature near a PLP substrate

Fidget spinner? https://en.m.wikipedia.org/wiki/Fidget_spinner F > On May 24, 2017, at 10:16 AM, Eleanor Dodson > wrote: > > Any ideas? >

Re: [ccp4bb] Estimating the amount of missing electron density for a model

This is a good point, the difference between Fo and Fc can be great if Fc is actually missing (an 'incomplete' structure). And of course this wreaks havok in defining the maskf for bulk solvent, and refinement, etc. Incomplete can be missing whole parts of the protein (say in model building) or

[ccp4bb] SHELXL refinement with TYR on special position

Hi all I'm trying to refine a structure with a tyrosine sitting on a special position , or maybe it's some disorder.. or Suggestions? https://i.imgsafe.org/7cfbf83a38.jpg Using just FLAT, CHIV,DFIX, and DANG from shelxpro doesn't work. Thanks, Francis

Re: [ccp4bb] pukka puckers within coot

Sounds like your refinement is failing probably because of the low data:parameter ratio at this resolution and/or the composition of your asymmetric unit, poor initial phase information (probably a molecular replacement solution which is close, but still far from the truth either in sequence co

[ccp4bb] collection strategy to collect the intersection with a reference set.

Hi all, I'm on the lookout for a prediction program that'll tell me the best collection angles that match the reflections of a reference set, as opposed to the the reflections that'll complete a reference set. It seems that mosflm and XDS prescribe the angles for completion rather than the in

Re: [ccp4bb] Sharp: Solomon density modification step

Also, check the quality of the map going into density modification (by either solomon or DM) and whether the output solvent mask is consistent with your structure. Depending on the quality of the experimental phases, you can generally see the outline of the molecule and see NCS in your experimen

[ccp4bb] Looking for supplier for 'Q' crystallization plates.

Hi all, This plate used to be the "Q" plate (HR3-124) from hampton research, but I cannot find them there anymore. Does anyone know where these plates can be bought from? Schematic of the plate and its wells is here : http://www.google.com/patents/US5419278. Thanks, F

Re: [ccp4bb] PyMol and Schrodinger

On Apr 23, 2014, at 11:43 AM, Cygler, Miroslaw wrote: > They do not offer the option of purchasing the software and using the > obtained version without time limitation. This policy is very different from > many other software packages, which one can use without continuing licensing > fees and

[ccp4bb] ipmosflm not connecting to XQuartz on Mac.

Hi all, Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a hang when running go just when I expect the old GUI to load. Thanks, F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder ---

Re: [ccp4bb] jiffy for analyzing spot.xds?

probably do the job... >> It would certainly be possible to write a jiffy that would read a >> SPOT.XDS and write it in Mosflm .spt format, which could then be read >> directly into iMosflm. >> On 15 Apr 2014, at 02:24, Francis Reyes wrote: >>> Hi all, >>>

[ccp4bb] jiffy for analyzing spot.xds?

Hi all, I'm trying to diagnose a tricky indexing issue and I suspect the spot picking is poor. Any jiffy's for analyzing the spot.xds file (prior to running IDXREF) ? (like an overlay onto the actual image)? Thanks, F - Francis E. Reyes PhD 215 U

[ccp4bb] rotating a map with maprot.

Hi all, I'm having a difficult time rotating a map from crystal A to crystal B. I obtained the transformation matrices from lsqkab. Specifically, the Crowther (Euler) Alpha beta gamma angles and the orthogonal A translation vector from superpose I supplied directly to maprot. However, the r

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

> > I'm guessing the low completeness of the 1.65 angstrom dataset has to do with > obstacles the processing software encountered on a sizable wedge of frames > (there were swaths of in red in HKL2000). I'm not sure why this dataset in > particular was less complete than the others. This is b

Re: [ccp4bb] Symmetry problem

I thought I saw this problem before. Though I wouldn't try it if you had solutions from different space groups. http://www.phenix-online.org/documentation/find_alt_orig_sym_mate.htm F On Feb 20, 2014, at 6:09 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear

Re: [ccp4bb] How to find the unfound part of a big protein

On Feb 13, 2014, at 4:53 PM, Sun Bingfa wrote: > Now we have dataset to ~4.2 Angstrom and using extracellular homolog > structure we can find a solution for this part(~45% of the whole molecule MW) > through molecular replacement, and the molecules are packed as layers, and > the other part ar

Re: [ccp4bb] Sister CCPs

Hi Tim Yes it is web-based. (Their iOS app works pretty well). Is it slow ? Well it depends. If you consider the situation where a ccp4bb poster has a specific question... "How do I determine the resolution of my data..." On the CCP4BB you get a number of posts of the following types in res

Re: [ccp4bb] Sister CCPs

The CCP4bb is great.. it truly is. The access to experts and their experience (probably the most valuable) is unparalleled. However, mailing lists to organize discussions and disseminate new ideas is just so ... 90s. Wikis? maybe you've just crossed into the new millenium. These days, if

[ccp4bb] off-topic Electron density map rendering..

Anyone know the program used to render the electron density maps for the fungal FAS in Figure 3c-3h from the paper "Mueller, M., Jenni, S. & Ban, N. Strategies for crystallization and structure determination of very large macromolecular assemblies. Curr Opin Struct Biol 17, 572–579 (2007).". T

Re: [ccp4bb] Phasing with Many Monomers/AU

Chris, > On Jan 19, 2014, at 11:30 AM, Chris Fage wrote: > > Thank you all for your responses. I already have a few ideas about how to > approach the problem. > > One of my concerns with so monomers per asymmetric unit at lower resolution > was the failure of MR software. Neither PHENIX nor P

Re: [ccp4bb] Phasing with Many Monomers/AU

You sure about this space group? 24 monomers in P1 is unusual (at least to me) F > On Jan 18, 2014, at 9:14 AM, Chris Fage wrote: > > Hello Everyone, > > I am currently trying to phase a structure with an asymmetric unit predicted > to contain 20-24 monomers (space group P1). The native cryst

[ccp4bb] Proper format for buccaneer heavy atom file?

Hi all, Is there a special format (residue naming, atom naming, etc) for the heavy atom file to assist buccaneer with sequence assignment? The one I have now seems to be returning structures that do not have SeMet at these locations. Thanks F - F

[ccp4bb] I want to dock/align an EM envelope (MRC) into a DM averaging and/or solvent envelope (MSK).

Is there a single tool or suite of tools that addresses this? Or a CCP4 workflow if need be. Thanks! F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] few questions about resolving new structure through MR

Do you expect more than one molecule in the asymmetric unit? Determined from the Matthews Coefficient (poor), size exclusion column (better), or self RF (best) ? On Nov 7, 2013, at 8:36 AM, Zhihong Yu wrote: > Hi, all > > I'm a rookie in resolving a brand new structure. I have some question

Re: [ccp4bb] MacBook Pro graphics card options - what about Mavericks?

I'm currently using CCP4/COOT (from the official installer) and autoPROC on Mavericks without any problems. I imagine the rest of the global phasing tools will work nicely. I had issues with fink, you have to use a branch from github as well as manually install and update the Command Line To