Re: [ccp4bb] atomic scattering factors in REFMAC

On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin wrote: > Does that mean, that with Bf>10 we cannot distinguish Mg and water by > electron density peak profile? Even if oxygen in water has twice as much > bigger radius than Mg2+? Yup. Pretty much. An "Mg+2" with B=10 is almost exactly the same d

Re: [ccp4bb] ions in REFMAC refinament

You do not have to change dictionary. You can specify charges on atoms using element columns in the pdb file. For example: ATOM139 O HOH A 35 13.139 -4.487 5.983 1.00 31.43 AA1 O ATOM140 CL CL A 35 13.139 -7.487 5.983 1.00 31.43 AA1 CL-1 Regards Garib

[ccp4bb] ions in REFMAC refinament

Dear Refmac users, Im a bit confused how Refmac treats ions. In the monomers library I can find Cl.cif: CL . 'chlorine' non-polymer 1 1 . # data_comp_CL # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_

Re: [ccp4bb] atomic scattering factors in REFMAC

Thanks everybody for the profound answers! As a summary, I can list the following reasons for the negative density defects at Se atoms: 1) the default scattering factors for Se are incorrect for wavelengths that are not close to CuKA, even though it may be not the major source of errors. Also,

Re: [ccp4bb] Off topic: Kendrew Model

Hi Andreas, It is much larger and looks slightly less like Chthulu cut himself shaving (I'm going to crystallographer hell for that comment). For those interested I've put the picture on Photobucket so as to not trash people's inbox. http://s1085.photobucket.com/albums/j422/KatherineSippel/?action

[ccp4bb] REFMAC number of reflections

I am absolutely sure this has been discussed before, and I have just re-convinced myself that refmac reports the number of reflections in just the working set, and not the total number of reflections. So my question is Is there a reason why the PDB ADIT tool imports the Nwork from the refmac pdb

[ccp4bb] PDBe deposition

For reasons I cannot explain even to myself I chose to use the PDBe to deposit the next structure (instead of RCSB). Curiosity may be one. This is a protein-DNA complex refined with latest refmac/coot and it uses (I presume) the modern naming convention (i.e. DA/DT/DG/DC for nucleotide names). D

Re: [ccp4bb] Archiving Images for PDB Depositions

On general scientific principles the reasons for archiving "raw data" all boil down to one thing: there was a systematic error, and you hope to one day account for it. After all, a "systematic error" is just something you haven't modeled yet. Is it worth modelling? That depends... There are

Re: [ccp4bb] Convert Bruker X8 sfrm to Mosflm format

Dear Stephen, Unfortunately you will find that the MOSFLM tab is not very helpful. The "Flip" part of the operation generates images that are not readable by MOSFLM - I think it may have been needed for older versions of the Bruker image format. Fortunately, it is perfectly possible to generate i

Re: [ccp4bb] Best route from x-files to scala

I'm not sure about the HKL2000 options, but you can convert .x files using the CCP4 program Combat. Note that Scala is not really suitable for scaling .x files, since they lack important geometrical information needed for the scaling model Phil On 1 Nov 2011, at 16:34, Jacob Keller wrote: > D

[ccp4bb] Best route from x-files to scala

Dear Crystallographers, I would like to transfer data from x-files (HKL2000) into scala, and think that the best way to do it is to tell HKL "no merge original index." Is that right, or is "no merge include partials" better? Jacob -- *** Jacob Pearson Kel

Re: [ccp4bb] atomic scattering factors in REFMAC

James, this may be one of those physics-vs-math arguments again. Surely the occupancy can be used to account for everything, but it makes it a fudge factor. I'd say the right way is to use the adjusted scattering factors first (after all, that is something we do know about the experiment), and i

Re: [ccp4bb] atomic scattering factors in REFMAC

Collecting "close to the edge" where the cross section of Se is higher does indeed increase the absorbed dose per scattered photon (Muray et al. JSR, 2005), but wavelength has absolutely no impact on the relative "rate" of Se-C bond breakage (Holton JSR 2007). The number of Se-C bonds broken i

Re: [ccp4bb] Off topic: Kendrew Model

Is it like this one: http://www.sciencemuseum.org.uk/images/I053/10321094.aspx Not sure I would want to put it into the dining room... Andreas On 01/11/2011 2:34, Katherine Sippel wrote: Hi all, I'm going to interject into the middle of this rousing though protracted debate to pick your b

Re: [ccp4bb] Archiving Images for PDB Depositions

Dear Gerard Isolating your main points: but there would have been no PDB-REDO because the data for running it would simply not have been available! ;-) . Or do you think the parallel does not apply? ... have thought, some value. From the perspective of your message, then, why are the bene

Re: [ccp4bb] Archiving Images for PDB Depositions

Gerard Bricogne wrote: . . . . the view, expressed by many and just now supported by George, that developers could perfectly well do their job on the basis of relatively small collections of test datasets that they could assemble through their own connections or initiative. I mostly agree with t

[ccp4bb] Sr. Scientist Membrane Protein Chemist opening at Takeda Pharmaceutical (San Diego)

Hello everyone. Sorry for the mass email but I wanted to post a position opening we have at Takeda Pharmaceutical in our San Diego office. I have pasted the position below. Candidates can apply online at our careers page: www.takedajobs.com job number- 1100408. Th

Re: [ccp4bb] Off topic: Kendrew Model

Maybe one of the PDB centers has room for it in the hall of their expensive buildings where the data are stored? Herman PS: I am very curious to see with what kind of robot the PDB redo people will come up to redo all the screws in the model. From: CC

Re: [ccp4bb] Off topic: Kendrew Model

Yeah, maybe if he got down to 1.0 Angstrom he could get it in the front door. Scott On Tue, Nov 1, 2011 at 8:39 AM, Jacob Keller wrote: > Maybe you could refine it using our new-fangled methods to improve the > model? (Couldn't resist such irony!) > > Jacob > > On Tue, Nov 1, 2011 at 9:34 AM, K

Re: [ccp4bb] Off topic: Kendrew Model

Maybe you could refine it using our new-fangled methods to improve the model? (Couldn't resist such irony!) Jacob On Tue, Nov 1, 2011 at 9:34 AM, Katherine Sippel wrote: > Hi all, > > I'm going to interject into the middle of this rousing though protracted > debate to pick your brains. I am in p

[ccp4bb] Off topic: Kendrew Model

Hi all, I'm going to interject into the middle of this rousing though protracted debate to pick your brains. I am in possession of a rather large and intact brass scale Kendrew model (sans mirrors). Due to facility restructuring we no longer have room for it. I have approached the local health sci

Re: [ccp4bb] Archiving Images for PDB Depositions

Dear Tassos, If you apologise for a long e-mail in a long chain of them, I don't know with what oratory precautions I should preface mine ... . I will instead skip the disclaimers and try to remain brief. It seems to me that there is a slight paradox, or inconsistency, in your position.

Re: [ccp4bb] atomic scattering factors in REFMAC

On Mon, 2011-10-31 at 15:57 +, Ivan Shabalin wrote: > As a result, red peeks around Se are significantly lower, Se B-factors are a > bit smaller (like 25.6 and 23.1), and Rf is lowered by a bit more than 0.1% > with the same input files. Hope others will comment to clarify my confusion: It

Re: [ccp4bb] Archiving Images for PDB Depositions

Speaking as a part-time methods developer, I agree with Tassos that a couple of hundred suitably chosen and documented datasets would be adequate for most purposes. I find that it is always revealing to be able to compare a new algorithm with existing attempts to solve the same problem, and this

Re: [ccp4bb] Archiving Images for PDB Depositions

To avoid misunderstandings, since I received a couple of emails already: Is it important to make such a resource available to developers? Absolutely? ? was a typo. I meant Absolutely! I think such data are essential for development of better processing software, and I find the development

Re: [ccp4bb] atomic scattering factors in REFMAC

That is correct. We saw this in every selenomethionyl protein structure that was determined at CESG. There are two reasons for the negative density defects at Se atoms. As you note, the default scattering factors for Se are incorrect for these experiments, as f' is large in Se SAD experiment

Re: [ccp4bb] atomic scattering factors in REFMAC

Hi, personally I didn't find that changing scattering factors for Se, Br, I etc made a big difference to the maps. The more likely explanation seems to be site occupancy disorder due to radiation-induced breaking of covalent bonds, in which case you need to refine the occupancy. But maybe it's a

Re: [ccp4bb] Archiving Images for PDB Depositions

Dear all, Apologies for a lengthy email in a lengthy chain of emails. I think Jacob did here a good job refocusing the question. I will try to answer it in a rather simplistic manner, but from the view point of somebody who might only have relatively little time in the field, but has enjoyed

[ccp4bb] Staff scientist and post-doctoral positions at the Institute of Cancer Research, London, UK

[Please note: I am posting this to ccp4bb on behalf of Prof. Dale Wigley and all communication should be directed to him.] Staff Scientist and Post-doctoral positions in Structural Biology and Biochemistry/Enzymology Following the award of a Wellcome Trust Senior Investigator Award to Professor

Re: [ccp4bb] Convert Bruker X8 sfrm to Mosflm format

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;7dda3e7c.0705