Hello Tony, I think CueMol gives you the screw rotation and translation when you fit domains. Jon CooperOn 8 Jul 2020 18:53, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:Well - I use standard software.Use GESANT or some such program to fit Structure 2 A to Structure ! A only
I did crystallise a protein expressed in M. smegmatis a while ago (early 90's)! The cloning was done by Ying Zhang:https://www.jhsph.edu/faculty/directory/profile/786/ying-zhangIt might be worth dropping him a line. That's all I can suggest, sorry!!Good luck.Jon CooperOn 7 Jul 2020 10:07, Matthew S
I think it is quite an interesting question in principle for Laue crystallography (now probably only relevant in the neutron world?) since, for example, if one had a crystal in the 432 point group, you could collect an essentially complete dataset with one 'image'. Given that each image can take se
Hello JohnDoes the IUCr dictionary list 'degeneracy'?Jon CooperOn 30 Jun 2020 17:11, Gerard Bricogne wrote:Dear Bernhard,
That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones (
With wget you can pretend to be somewhere else with the: --referer "http://www../"option. You could even put in the heidelberg url and then the server thinks your request comes from there ;-0Might help ;-?Jon CooperOn 29 Jun 2020 02:17, Murpholino Peligro wrote:Dear Kay, I can download anythin
Hello, it downloaded to my phone from the link on this page:http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.htmlIt looks alright: http://u.cubeupload.com/jbcooper/20200628034613.jpgJon CooperOn 28 Jun 2020 01:39, Murpholino Peligro wrote:```~/Downloads$ aria2c ftp://ftp.mpimf-heidelberg.mp
Phil Jefferey was right about the point group (432), which looks like it represents about 0.7 % of the PDB! I tested the completeness with MOSFLM strategy for various sporadic missetting angles and 11 degrees of data does give you around 90 % completeness or more with redundancy close to 2, assumin
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From: CCP4 bulletin board on behalf of 0c2488af9525-dmarc-request@JISCMAIL.AC.UK <0c2488af9525-dmarc-request@JISCMAIL.AC.UK>
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Someone told me there is a cubic space group where you can get away with something like 11 degrees of data. It would be interesting if that's correct. These minimum ranges for data collection rely on the crystal being pre-oriented, which is unheard-of these days, although they can help if someone i
Robert, it would be very interesting to know your cell dimensions and corresponding N. mol. per AU to see if it's trying to be another space group. How long did the crystals take to grow? You could also try Contaminer and Simbad ;-)Jon CooperOn 18 Jun 2020 14:38, "Schreuder, Herman /DE" wrote:
De
Re: "it turns out to be very very easy to exceed the count rate where the detector electronics can keep up."Sorry if this is obvious, but I take it you mean "_can't_" keep up?Jon CooperOn 4 Jun 2020 13:06, "Winter, Graeme (DLSLtd,RAL,LSCI)" wrote:
Dear All,
A small word of caution regarding chem
I don't know about LCP but it sounds like a case for Contaminer or Simbad.Jon CooperOn 22 May 2020 11:08, "Demou, Maria" wrote:
Dear all,
I have a question that may have a straight forward answer, and was wondering if this is a common issue. We have a protein crystallised in I222 space group
Hello, you certainly could normalise maps (i.e. have a map of (density minus average)/rms) with mapman in the Uppsala suite and you can ask Phenix to make the electron electron density normalised when it generates a map (set "map scaling" to "sigma"). The web suggests you can do it with XDLmapman,
Re: injecting disinfect[ing]ant[?] through the USB cable [port?].Dear TimI am intrigued, seriously.Best wishes.Jon CooperOn 29 Apr 2020 19:53, Tim Gruene wrote:Dear all,
can you make suggestions for how to disinfect computer keyboards, and
instrument panels?
Our facility is going to reboot
Hello, it depends a bit on the resolution. With d<1.2 A you can, of course, do some quite complicated modelling of alternate confirmations, group occupancies, etc - actually you can do this very meaningfully at worse resolutions, too. My favourite subject - if your resolution is better than ~1.4 to
I take it that you have 2 molecules in the asymmetric unit. If so, you could try some sort of NCS averaging of the map or just NCS-refinement might help. Not much more here than has been expertly suggested already. Can you give us an idea of the resolution? How many RMS have you contoured the map a
There is CueMol which runs on iPhone. NDKmol/ESmol for Android. It's a few years since I used them, but they were good for teaching purposes. As suggested though, a web-based viewer is probably the way to go. Jon CooperOn 17 Apr 2020 15:43, "careinaedgo...@yahoo.com" <02531c126adf-dmarc-requ...
I had similar thing with linux (not Windows) and the cure was (from memory) to install the Truetype font. Absolutely no idea if this is relevant in your case!!Jon CooperOn 2 Apr 2020 14:51, "Horrell, Sam (DLSLtd,RAL,LSCI)" wrote:
Hi Huw,
Thanks for the advice, but I’m afraid my display sca
Well, as no one else has come back to you, I wouldn't say 10 % difference between R and R-free is 'bad' and it's certainly not super-bad! It's a bit high, but if you look at the papers by Ian Tickle from the late 90's and others I think you can be reasonably happy with it. I've been told that A N o
I was going to say there's no harm in depositing hydrogen atom positions! However, some structures of similar resolution that we refined with shelx using riding H's and anisotropic B's, somewhat embarrassingly, do not seem to have them! These were deposited about 20 years ago so my memory is vague.
... and don't say you're travelling with heavy water!Jon CooperOn 19 Feb 2020 17:12, "Azadmanesh, Jahaun" wrote:
Hello,
I have traveled to a neutron beamline ~6 times over the past several years.
I have had awful luck shipping crystals, so I decided to hand-carry and I found this best.
I was wondering why you believe it is a lattice defect rather than NCS. How well does the structure refine and does it have NCS? Do the twinning tests suggest anything?Jon CooperOn 11 Feb 2020 21:31, Daniele de Sanctis wrote:Hi all,I'm currently dealing with what I think it is a case of LTD (off-o
Hello, if you mean theoretical docking, here is an old list of links:https://zlab.umassmed.edu/zdock/dockingsites.shtmlSome of these will still be maintained.Jon CooperOn 10 Feb 2020 16:50, Sarah Bowman wrote:
Hi Careina,
There’s a program called FRODOCK that generates predictions of how tw
e name is
just that, and identifier.
Best,
Tim
On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
request@JISCMAIL.AC.UK wrote:
> Remembered earlier that if the "CL" is not shifted one place to the left,
> Shelx and probably most other programs treat it as car
is
just that, and identifier.
Best,
Tim
On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
request@JISCMAIL.AC.UK wrote:
> Remembered earlier that if the "CL" is not shifted one place to the left,
> Shelx and probably most other programs treat it as carbon
Thanks, sorry, shelx is wonderful! I was thinking back to shelxpro days when your hetero-atoms could acquire the wrong scattering factors if they were not positioned right in the pdb file. The classic, which I saw several times, was calcium (CA) being treated as an alpha-carbon (CA), and I think re
Remembered earlier that if the "CL" is not shifted one place to the left, Shelx and probably most other programs treat it as carbon, i.e. its assumed to have 6 rather than 17 electrons. Trust occupancies OK, too ;-?Jon CooperOn 3 Feb 2020 18:26, "Barone, Matthias" wrote:
Hi Pavel
glad you wr
Hello, sorry if this is a really obvious question, but have you used the ANIS option? I remember it is good at cleaning-up difference density around halogen atoms that sort of resolution.Jon CooperOn 3 Feb 2020 11:08, "Barone, Matthias" wrote:
Dear ccp4 community
Im having some problems solvin
Can you possibly expand a bit on exactly what you are asking?Jon CooperOn 2 Feb 2020 09:28, Rajnandani Kashyap wrote:Dear AllI am curious to know about the promiscuous activity of a protein based on their fold. Can a protein having same fold also have same function (say not 100% but some activity)
Hello, have you tried eluting from nickel-NTA straight into glycerol buffer so the protein has absolutely minimal time on it's own? Also, 10 mg/ml is quite a high concentration in my book. What is in your purification buffer? Just interested. Hope your competitors aren't reading all this! Best wish
It looks pretty metallic. It would be good to know the max peak height in rms for the difference map and also some of the distances between the His and Cys side chains. Are your sulphur occupancies alright ;-?On 21 Jan 2020 17:55, Chris Fage wrote:Dear CCP4BB Users,I've recently solved the ~2.2 an
I think Blend runs Pointless so that way you will get the best of both worlds.On 15 Jan 2020 14:08, Firdous Tarique wrote:Hi.I have collected multiple datasets for my crystals and now want to merge them. Iwanted to know that between Blend and pointless, which programme is better to merge two or mo
Hello, the statistics all look good apart from the R-merge and R-meas. It might be worth looking at the processing again in case it can be improved. I assume you mean rms rather than A when you say the difference density only disappears at 6 A and, if so, it must be a strong feature. Does the fragm
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