Re: [ccp4bb] peroxy-glutamate?

I would think the first goal is to model the observed data correctly, and then afterwards an accurate "before" model could be inferred. It seems that it would be extremely helpful to this end to add another column to the .pdb format: a "time constant" for radiation damage for each atom. When

Re: [ccp4bb] peroxy-glutamate?

Hmm... this is a bit of a philosophical pickle in my mind. Do we want to model the structure as what it looks like after radiation damage has had its way with it, or what it must have looked like *before* the damage? I can see arguments both ways (and can sympathise with the former if you want

Re: [ccp4bb] peroxy-glutamate?

In line with this, there are a number of pictures in the literature of the mitochondrial electron transport chain, with the complexes lined up in a row embedded in a membrane, and with yeast complex III still having the Fv fragments it was crystallized with, attached. Only obvious if you are

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Re: [ccp4bb] peroxy-glutamate?

Hi Tristan I'm not so sure. The co-ordinates are the result of the experiment. How other people choose to interpret those results is their affair. Taking it to its logical conclusion suppose that we 'damage' the protein by mutating/deleting some residues or adding tags purely for the purpose

Re: [ccp4bb] peroxy-glutamate?

Hmm... this is a bit of a philosophical pickle in my mind. I agree. Right now I want as accurate a model as possible to improve the phases for interpretation of a few remaining bits. I haven't decided what to deposit- maybe three separate structures: 1. Conservatively modeled: Everything that

Re: [ccp4bb] peroxy-glutamate?

A slightly different wrinkle on the perennial "do we model unresolved sidechains" debate, I guess. I would argue that in the case of mutations, tags etc. those are things you know were there before you started firing x-rays at your sample. In the case of the sidechain decarboxylation we know

Re: [ccp4bb] peroxy-glutamate?

Actually this is taken care of in the BIOMOLECULE definition. If the artist had used the principle biomolecule, it excludes the Fv fragments. On 05/09/2017 01:08 PM, Edward A. Berry wrote: In line with this, there are a number of pictures in the literature of the mitochondrial electron

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Re: [ccp4bb] how to run shelx C/D/E using CCP4 GUI on windows

Just to confirm what Eleanor said: all SHELX programs prefer to be given intensities but can accept F if the intensities have been lost. Converting intensities to F (e.g. with ctruncate) and back again degrades the statistics for the weak reflections and is discouraged. The same applies to

Re: [ccp4bb] convert hkl data to mtz

You can do this in the data reduction task in ccp4i2, which runs Pointless, Aimless and Ctruncate Phil > On 7 May 2017, at 23:10, Careina Edgooms > <02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > I have not been in the game of solving structures for years. In the past I >

Re: [ccp4bb] Problem with installation in Fedora 25

I guess it was a problem with the directories name. (Changed the locale when downloading... Did it all over again and it works). 2017-05-09 16:21 GMT-05:00 Murpholino Peligro : > The installation process remains here > ...(attached image) > > Is it doing something? > Is

[ccp4bb] SUMMARY: looking for paper describing optimisation of crystals using a screen kit as additive

Dear all, as usual the bulletin board nails it. The paper I was vaguely remembering was indeed the following: Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):646-50 Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy.

Re: [ccp4bb] peroxy-glutamate?

Hi Andrew We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So it's indeed very tempting to say that the CO2 is still there,

[ccp4bb] prepare stock solution of hampton heavy atom screen kits

Hello everyone! I want to prepare heavy atom stock solution to soaking my crystal, what should i use to soluble the heavy atom Pt, Hg and other hampton heavy atom screen kits, as i know someone not good soluble in water? can anyone give me some ideas! sincerely Liuqing chen

[ccp4bb] postdoctoral position available

Dear Board Readers, For anyone who might be interested, or know of interested persons, there is a postdoctoral position available at CSIRO: https://career10.successfactors.com/sfcareer/jobreqcareer?jobId=39270=CSIRO Best regards, tom

Re: [ccp4bb] peroxy-glutamate?

Wouldn’t the not-bonded CO2 have a new steric clash with the CG, though? And what happened to the radical that was presumably generated? Also, I would think solvent-exposed side chains would be more prone to diffusion than buried ones. JPK From: CCP4 bulletin board

Re: [ccp4bb] peroxy-glutamate?

Hi Jacob On 9 May 2017 at 14:03, Keller, Jacob wrote: > Wouldn’t the not-bonded CO2 have a new steric clash with the CG, though? > I think the CG can easily swing out of the way, since it's now only attached to the CB. > And what happened to the radical that was

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Re: [ccp4bb] BSA as additive

Dear H.Sin, These references may help you: Meireles, M., Aimar, P., and Sanchez, V. (2004) Albumin denaturation during ultrafiltration: effects of operating conditions and consequences on membrane fouling, Biotech. Bioeng. 38, 528-534. Schratter, P., (2004) Purification and concentration by

Re: [ccp4bb] peroxy-glutamate?

On 05/09/2017 06:18 AM, Ian Tickle wrote: We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So it's indeed very tempting to