Re: [ccp4bb] Off-topic: NMR and crystallography

Well, if you do NMR you avoid the possible bottlenecks of having to obtain well-diffracting crystals, and having to phase the protein (i.e. obtain SeMet protein crystals or suitable heavy atom derivatives; or a suitable MR model). But instead, you'll need to prepare labelled protein (15N and/or

Re: [ccp4bb] Data processing - twinned xtals

doesn't necessarily looked twinned to me. Rather it looks like you have a trigonal or hexagonal cell with a long c-axis. On image 2 it seems you may have systematic absences along l, although it is hard to tell the order. Perhaps P31, P32, P62, P64 or spacegroups with these symmetries plus

Re: [ccp4bb] Data processing - twinned xtals

PS For future data collections, try to get the long c-axis roughly along the crystal rotation axis if possible. On 16 Aug 2013, at 16:38, Mahesh Lingaraju wrote: Hi CCP4 folks I have a data set which is looks twinned ( see the image-1 - I zoomed on to the image so that one can spot the

Re: [ccp4bb] Stuck rfree - possible non merohedral twinning ?

Dear Mahesh, from the images you showed a few days ago I am not convinced the issue is twinning, just overlaps due to the long c-axis. But of course, I do not have have as much info as you, just those images. Unless you are really convinced you have twinning, if you can see what you want to

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

Even if you remove the authors it is often easy to ascertain who they are by reading the paper and reference list. Marco Lolicato chimbio...@gmail.com wrote: Hi scientists, this interesting topic brought back to my mind a similar discussion I had with a colleague of mine and now I want to

Re: [ccp4bb] [phenixbb] Appropriate number of reflections for FreeR

at it). Mark van Raaij mjvanra...@cnb.csic.es 11/01/13 7:39 PM the limit of 2000 reflections I guess is just because it would be a waste to throw away more reflections for refinement, once the statistical minima for calculating a reliable Rfree have been met. I.e. if you have 100.000

Re: [ccp4bb] A question on protein microheterogenity for crystalization

Dear Brett, We have seen this behaviour several times for different adenovirus fibre head proteins and don't really have an explanation for it. We have always set the peaks up separately when we had enough protein. For this purification, as you don't have enough protein to pool them

Re: [ccp4bb] structural homologs as cross seeds

the differences are likely to be on the protein surface, and these would make the crystal contacts, i.e. it would be unlikely the protein could crystallise in the same crystal habit. Never say never in crystallisation (i.e. try anything), but I would go for other things first like additives,

Re: [ccp4bb] skin on crystal

Usually the skin is precipitated protein when it comes into contact with air. In this case, avoiding contact with air may be the only way to avoid the skin, i.e. crystallise using a technique that is not vapour diffusion, but for instance microbatch, microdialysis or free interface diffusion.

Re: [ccp4bb] resubmission of pdb

Well, like Folmer says, you don't have to withdraw the entry, you could just let it be released before the paper is accepted. While in some projects there may be a legitimate fear that other scientists use your unpublished entry for things you don't want them to, in many projects this doesn't

[ccp4bb] Check waters for possibly being sodium ions and similar

In the past I remember using a simple program or webserver to check whether modelled water molecules might be metal ions, especially sodium, magnesium etc. as they do not differ much in density to waters. Based on coordination. However, I can't remember the name and can't find it in google or

Re: [ccp4bb] Check waters for possibly being sodium ions and similar

turns out some people indeed have better memory than me: WASP inside STAN server http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl thanks! On 14 Feb 2014, at 12:49, Mark van Raaij wrote: In the past I remember using a simple program or webserver to check whether modelled water molecules

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

As the excellent tips that you got indicate, lower R-factors can be obtained by getting better data (better crystals, better data collection, better data processing) or better fitting, i.e. refinement. In this respect, I am impressed by the automatic data processing protocols now being

Re: [ccp4bb] CCP4-6.4.0 Update 018

same happened to me yesterday evening, but when I retried this morning, the update installed fine. Did not change anything in between. On 14 Jun 2014, at 11:21, Felix Frolow wrote: CCP4BB list, Today I tried to install update 018, however I have lost the ability to do it from the GUI. Menu

Re: [ccp4bb] gelification of a pure protein

reminds me of structure 1NEU, although here the gelation was reversible, see ref and abstract below - the paper has a photo of a tube of soluble protein and gelled protein we have also had a couple of cold-sensitive proteins in our hands, that precipitated at 4 degrees when concentrated, but

Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit

and 2VAK...average Bs for the twelve, sequence identical, chains vary from 28 to 53. On 29 Apr 2013, at 22:09, David Schuller wrote: On 04/29/13 12:26, Roger Rowlett wrote: FYI, I do know of one example of a solved structure where some of the molecules in the ASU are poorly defined. In

Re: [ccp4bb] Why the name aimless

i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the

Re: [ccp4bb] Phaser MR problem

Or perhaps there is only 1 copy and more solvent than you expect? This is not that uncommon. On 20 Sep 2014 12:09, Randy Read rj...@cam.ac.uk wrote: Just to add to what Herman said: The statistics are good for placing the domain represented by ensemble 1 (TFZ=14.3) and the first copy of

Re: [ccp4bb] Absence of contact between layers in a crystal

In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something similar, I suspect the domain that makes the crystal contacts is three-fold disordered, leading to layers of nothing. In our paper in JMB 314, 1137 (doi 10.1006/jmbi.2000.5204) we tried to explain it a bit, and describe what

Re: [ccp4bb] Assess anomalous signal?

sure, whether the structure can be solved is a good criterion. but often, when trying different heavy atoms, the structure can NOT be solved, and then some criterion to judge whether to continue to try and solve it with that data, or whether to focus on other datasets, other derivatives, another

Re: [ccp4bb] P3212--1's in Space Group Names?

the same as the 1 in P1 ;-) seriously, if you look at space group names: 143 P3 144 P31 145 P32 149 P312 151 P3112 153 P3212 150 P321 152 P3121 154 P3221 the 1s in 149 to 154 are necessary to differentiate them all. On 18 Feb 2015, at 04:51, Keller, Jacob wrote: Dear

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

Hi Ivan, Being in the same boat, I have investigated a bit. It seems to be a straight trade-off between more processing power, more RAM and less partability Macbook, Macbook Air, 13" Macbook Pro, 15" Macbook Pro. For running Rosetta I think you will be thankful for the faster processors and

Re: [ccp4bb] ccp4 release 7.0 update 023

Same here on El Capitan 10.11.6. Mutate & Auto Fit still works though, but Simple Mutate crashes. Mark J van Raaij CNB-CSIC www.cnb.csic.es/~mjvanraaijOn 23 Nov 2016 16:57, Julian Nomme wrote: > > Same here on masOS Sierra... > Julian > > Le 11/23/16 4:55 PM, Isupov,