Re: [ccp4bb] off-topic: binding site comparison

Dear Daisuke, Thank you for your answer. I was looking at the 3D-SURFER server, it looks great. I'm only trying to compare pairs (or sometimes triplets) of proteins though. Is there a way to use 3D-SURFER for that purpose? And would it give me a 3D structural alignment of the binding sites? Thank

Re: [ccp4bb] proton scattering by X-rays

Hi Colin, you can add f' for every atom type in SHELXL yourself, so in that sense, it has been incorporated in SHELX. Bear in mind that the nucleus is point-like to X-rays at ordinary wavelengths so that it should not have a form factor like the electron cloud but a constant scattering length - ju

Re: [ccp4bb] proton scattering by X-rays

But, how with x-rays can one experimentally tell the difference between a hydrogen and a filled orbital (say of N)? I will grant that the electron density for a bound H should extend farther from the heavy atom but I believe you would need resolution better than 0.89 Ang to see this difference.

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

Andre, I agree with Adam. Rigid body modelling with the crystal structure or homology models using CORAL is the best way to proceed. Remember to model all of your molecule, even the missing bits. CORAL will use a chain of beads for missing N- and C- termini or short linkers. For missing domains

[ccp4bb] update to iMosflm/Mosflm

Hi folks We are pleased to announce the release of iMosflm/Mosflm 7.1.2; this version will be included in the next update of CCP4, so if you are prepared to wait a few days there is no need to download from our website, just use the "Manage updates" button in ccp4i (you will need to have versio

Re: [ccp4bb] CCP4 for twinned crystals?

Dear Jacob, For the molecular replacement part, twinning is not a great barrier. We've generally found that, as long as you get the space group right (which can be an issue with twinned crystals), the signal in the MR search is not that badly degraded. You could easily set up a search using d

[ccp4bb] CCP4 for twinned crystals?

Dear Crystallographers, Is there any software in CCP4 which can solve twinned structures? I have several datasets which appear to be tetartohedrally twinned, with possible spacegroup of p31/p32 masquerading as p6222/p6422. I think this is approximately equivalent to 1/8-fold NCS? The data qual

Re: [ccp4bb] adding a Cobalt atom within Coot

Thanks a lot Roger, that made it! Best, Almu.- 2015-02-02 16:16 GMT+01:00 Roger Rowlett : > This is a known bug in Coot 0.7.x. You can add the metal ion correctly > using the Get Monomer dialog and selecting "CO" as the monomer. This is > fixed in Coot 0.8.1. > > ___

Re: [ccp4bb] adding a Cobalt atom within Coot

This is a known bug in Coot 0.7.x. You can add the metal ion correctly using the Get Monomer dialog and selecting "CO" as the monomer. This is fixed in Coot 0.8.1. ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate Universit

Re: [ccp4bb] adding a Cobalt atom within Coot

Hi Julia, indeed it was crashing! I did not think it was because of this. My version is 0.7.2! Thanks a lot for the information. I will try to upgrade it as soon as possible. Best, Almudena. 2015-02-02 16:02 GMT+01:00 Julia Griese : > Hi Almudena, > > Which version of Coot are you using? The

Re: [ccp4bb] proton scattering by X-rays

“As you say the proton itself is invisible to X-rays.” Not quite! The ratio of scattering between electrons and protons should go as the inverse square of the masses. Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but doubtless it has been incorporated in to SHELX. Colin

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

Andre, some suggestions: 1. First be sure that shape reconstructions as an approach to interpreting your data is justified – the shape reconstruction approach can be quite misleading in some circumstances: i. Does

[ccp4bb] adding a Cobalt atom within Coot

Hi, this sounds weird but I am adding a Cobalt atom within Coot, with the option "place atom at pointer", then I select "other" and type in the textbox "CO". It adds an Atom that it calls "A", why does this happen? Any ideas? Thanks in advance. Best wishes, Almudena -- Almudena Ponce-Salvati

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

Dear Andre, In the past I had some good fitting results with SITUS (it was a case where the matched the crystal structure). Best, D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Adam Round [aro...@embl.fr] Sent: 02 February 2015 11:13 To

Re: [ccp4bb] proton scattering by X-rays

Thank you all for explaining, I'm glad it was my pedantic lack of ability to get over the description and think of the chemistry that was the problem. Of course the positive charge would not be localised just on the hydrogen, it is not really just a proton and so it will have some electron density

Re: [ccp4bb] proton scattering by X-rays

Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, it must have at least some partial electron around it for the (possibly partial) covalent bond, enough to diffract X-rays anyway. As you say the proton itself is invisible to X-rays. Cheers -- Ian On 2 February 2015 at

Re: [ccp4bb] proton scattering by X-rays

Hi Peter, I don't have access to the paper from here, but the abstract implies that the H+ is attached to a cysteine sulphur. In that case it have the shared electrons to scatter X-rays. The text "a proton (H+) attached to the sulphur of a cysteine ligand" is not very pretty. I would call it a

[ccp4bb] proton scattering by X-rays

Dear BB I have (again) realised how limited by understanding of our subject is. In Nature’s online site http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129 there is a paper describing an X-ray structure determined with sub-atomic data (nice!). The

Re: [ccp4bb] Young scientist travel awards for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology"

2-Feb-2015 Dear Colleagues, We are pleased to announce the availability of young scientist travel fellowships to the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot,

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

SUPCOMB will only give useful results if the shape of the SAXS envelope matches that in the Crystal structure. In this case with multiple subunits, fitting the chosen numbers of monomers to the SAXS data with SASREF (also from the ATSAS package) would be more appropriate. the resulting model

Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope

I supposed could be done by supcomb program at ATSAS package -- On 02/02/2015 11:52, Andre Godoy wrote: Dear users I'm having some troubles to fit my x-ray model in my SAXS envelope.. more about: 1) I have a SAXS model with enough room for 6 monomers. 2) I have the crystallographic structure,

[ccp4bb] [off topic] Fitting unknown model in SAXS envelope

Dear usersI'm having some troubles to fit my x-ray model in my SAXS envelope..more about: 1) I have a SAXS model with enough room for 6 monomers. 2) I have the crystallographic structure, but AU or any generate symmetry related doesn't appears to be the biological unit (I mean, crystal packing is

[ccp4bb] OPPF-UK Practical Course on High Throughput Protein Expression Screening

Hi, Inviting applicants for the Practical Course on HTP Protein Expression Screening. Details in the attached file. Regards Narayanan Krishnan OPPF - UK University of Oxford Research Complex at Harwell R92 Rutherford Appleton Laboratory Harwell Oxford OX11 0FA UK Tel: +44(0)1235-567729 Email: n