Re: [ccp4bb] delete subject

2013-03-27 Thread VAN RAAIJ , MARK JOHAN
Dear Tom, don't feel too bad about it - everyone can make a mistake. Some of the replies give crystallographic tips that may be useful to other beginning and not-so-beginning crystallographers. Although I agree the attachments to the first mail would perhaps better be deleted from the

Re: [ccp4bb] Strange density

2012-11-28 Thread VAN RAAIJ , MARK JOHAN
could it be a PEG molecule? Quoting Read, Jon: Anyone see anything like this before? The data is 1.7Angstrom data with good statistics. The picture shows the solid FoFc density contoured at 3 Sigma in light brown and -3 Sigma in purple. The density is odd as it appears to be bound to a peptide

Re: [ccp4bb] ccp4mg question

2012-11-15 Thread VAN RAAIJ , MARK JOHAN
possible ugly workaround: renumber the pdb file so where ccp4mg thinks the N and C-termini are is hidden in the image you are making (if possible) if you want to make different views you may need to make differently renumbered pdb files. (but probably other people have a smarter way) as an

Re: [ccp4bb] side chain density

2012-11-10 Thread VAN RAAIJ , MARK JOHAN
before modelling a long side-chain in non-existing or dubious density, also make sure it is really there in the protein by sequencing your expression plasmid. Your arginine (for example) may in fact be a serine or glycine...databases are not 100% accurate and neither is PCR if it was used

Re: [ccp4bb] protein cleavage

2012-11-04 Thread VAN RAAIJ , MARK JOHAN
We once had a more-or-less MBP-sized fragment before cleavage, but this turned to be a spontaneous mutation. This expression experiment had been started from a glycerol stock with an unknown number of growth cycles prior to expression. Starting from a fresh transformation with the purified

Re: [ccp4bb] Plate crystals

2012-10-16 Thread VAN RAAIJ , MARK JOHAN
apart from optimising the crystallisation conditions, it might be worth optimising the protein preparation or do some limited proteolysis - or even express short N-terminal and/or C-terminal deletions. Mark Quoting Patrick Shaw Stewart: Jahan It sounds as though the protein crystallizes

Re: [ccp4bb] how to interpret DALI search results

2012-06-12 Thread VAN RAAIJ , MARK JOHAN
if this is the first (or second, or third) time you do a DALI search, take the list output from DALI, start from the top and superpose each structure with yours and look at the superpositions with your favourite superposition software. This is very educational and the only way you get a

Re: [ccp4bb] how to interpret DALI search results

2012-06-12 Thread VAN RAAIJ , MARK JOHAN
...I meant visualisation software of course... Quoting VAN RAAIJ , MARK JOHAN: if this is the first (or second, or third) time you do a DALI search, take the list output from DALI, start from the top and superpose each structure with yours and look at the superpositions with your

Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files

2012-04-27 Thread VAN RAAIJ , MARK JOHAN
so perhaps the problem indeed is sending different wavelengths as one file...in our case there is only one crystal, one wavelength, i.e. one loop, while I clearly submitted all three wavelengths. Quoting Miller, Mitchell D.: We (JCSG) too have been depositing multiple data sets

Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

2012-04-04 Thread VAN RAAIJ , MARK JOHAN
apart from radation damage it could be a combination of: - too tight restraints on the B-factors - 9 sigma not being that much on a the e/A3 scale, i.e. your difference map is very flat (which is good) and the few peaks that remain stand out a lot, even if their absolute height is low...

[ccp4bb] PEG MME 2000 in powder form?

2012-04-04 Thread VAN RAAIJ , MARK JOHAN
Dear All, is PEG MME 2000 still available in powder form? I think Fluka used to sell it, but Fluka is no more and Sigma-Aldrich don't sell it. Hampton Research and Molecular Dimensions (and perhaps others) do sell 50% (w/v) solutions. Mark Mark J van Raaij Laboratorio M-4 Dpto de

Re: [ccp4bb] PEG MME 2000 in powder form?

2012-04-04 Thread VAN RAAIJ , MARK JOHAN
ok, I stand corrected, Sigma DOES sell it, but under a slightly different name: 81321 FLUKA Poly(ethylene glycol) methyl ether average Mw 2,000 81321-250G, 23.60 euros 81321-1KG, 71.80 euros (prices given for Spain) thanks! Quoting VAN RAAIJ , MARK JOHAN: Dear All, is PEG MME

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-01 Thread VAN RAAIJ , MARK JOHAN
another singular/plural grump: Recently we can read: phage are. Phage is singular, the plural is phages (and this does not have that much to do with latin or greek). more reading: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109450/ Quoting Paul Emsley: The PDBe page for 3k78 says: The

Re: [ccp4bb] one datum many data?

2012-04-01 Thread VAN RAAIJ , MARK JOHAN
and using dice for the singular die Quoting Robert Blessing: How can spectrum and spectra have been overlooked in this thread? Síocháin! Sláinte! In Irish: Peace! Health! Pronounced roughly Shee'-kahn, Slawn'-tche. Bob Robert H. Blessing, Ph.D. Senior Research Scientist

Re: [ccp4bb] How to reduce no. of overlaps

2012-03-06 Thread VAN RAAIJ , MARK JOHAN
typo correction, you'll want the long axis parallel to the rotation axis, not to the beam. Mark Quoting Frank von Delft: You probably have to tilt your crystal, so that the long axis is parallel to the beam. We do this routinely: cut a plastic pipette tip to have a sharp point, then

Re: [ccp4bb] pH optimisation for crystallisation

2012-02-07 Thread VAN RAAIJ , MARK JOHAN
Dear Sreetama, First of all, there are no hard-and-fast rules for successful crystallisation, try changing as many different variables as possible and go with what works. Having said that, yes, next I would go for a grid optimisation varying the pH in 0.2 or 0.5 units over as wide a range

Re: [ccp4bb] symmetry for ages 6 and up

2011-12-13 Thread VAN RAAIJ , MARK JOHAN
reminds me of these symmetric 2D P3 lizards: http://www.worldofescher.com/store/Z51.html I bought the RGB-coloured set/puzzle after visiting an Escher exhibition and sometimes use them in crystallography/symmetry teaching. Nice to make the students assemble them and then decide on the

Re: [ccp4bb] symmetry for ages 6 and up

2011-12-13 Thread VAN RAAIJ , MARK JOHAN
(oops, previous mail got sent before I wanted) the turtles would be really nice to extend things into 3D. great find, Mark Quoting Phoebe Rice: Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups.

Re: [ccp4bb] SeMET inconsistency

2011-10-22 Thread VAN RAAIJ , MARK JOHAN
Dear Kavya, I don't think it is likely you have five MSE and one MET. Rather, I would guess the side-chain has some disorder, i.e. one or more alternative conformations. If you don't see density for alternative conformations, the best way to model the disorder might be partial occupancy of the

Re: [ccp4bb] Complex seeding

2011-09-22 Thread VAN RAAIJ , MARK JOHAN
agree, any crystallisation idea is worth pursuing, given you have or can make enough sample to try it with. having said that, wouldn't you tend to select for the same crystals as the seed, i.e. crystals of the component on its own? have you tried limited proteolysis of your sample, incl. a bit

Re: [ccp4bb] Complex seeding

2011-09-21 Thread VAN RAAIJ , MARK JOHAN
agree, any crystallisation idea is worth pursuing, given you have or can make enough sample to try it with. having said that, wouldn't you tend to select for the same crystals as the seed, i.e. crystals of the component on its own? have you tried limited proteolysis of your sample, incl. a

Re: [ccp4bb] Data from old tapes

2011-07-19 Thread VAN RAAIJ , MARK JOHAN
did you try looking if there is a company offering data recovery services from these kind of tapes? if there is, there may not be a need to buy a tape drive yourself.Mark Quoting Min, Xiaoshan: Dear CCP4 community, We have a few datasets that reside in tapes (Sony QG-112M 8 mm tape and

Re: [ccp4bb] Off topic question. NACCESS

2011-06-19 Thread VAN RAAIJ , MARK JOHAN
Dear Armando, don't know about NACCESS, but I guess it is superseded by AREAIMOL in CCP4 (also in CCP4i); it outputs the accessible volume per atom in the pdb file and per residue and per chain and some other statistics in the log-file. Mark Quoting Armando Albert: Does anyone has got some

Re: [ccp4bb] how to quantitate protein which dont have ne aromatic residue

2011-04-09 Thread VAN RAAIJ , MARK JOHAN
you can do amino acid analysis on your pure protein, using a commercial or academic service - I hope these are still around. You should only need to do this once, then relate the result to your A220, BCA and Bradford assays. Mark Quoting Arpit Mishra: hello everybody i am working on the

Re: [ccp4bb] OT: PCR instrument

2011-04-03 Thread VAN RAAIJ , MARK JOHAN
if the PCR machine is just to be used for standard sub-cloning (amplifying fragments from other plasmids, cloned cDNA etc.), I would go for the cheapest one I could find. I guess there are few crystallography projects were the first PCR step turned out to be the most difficult. For more

Re: [ccp4bb] what to do with disordered side chains

2011-03-30 Thread VAN RAAIJ , MARK JOHAN
yet, apart from (and additionally to) modelling two conformations of the side-chain, the B-factor is the only tool we have (now). Quoting Pavel Afonine: Hi Quyen, (...) And if B-factor is an estimate of thermo-motion (or static disorder), then would it not be reasonable to accept that

Re: [ccp4bb] off-topic: 2 peaks on Cation

2011-02-18 Thread VAN RAAIJ , MARK JOHAN
I observed 3-5 peaks for a baculovirus expressed protein once, and could only get good crystals if the peaks were crystallised separately, see: Virology 262, 333-343 (1999) Virology 262, 333–343 (1999) Mark Quoting Ulli Hain: Thanks for the suggestions/ideas. The protein is

Re: [ccp4bb] Problems with auto-indexing

2010-11-29 Thread VAN RAAIJ , MARK JOHAN
Dear Chen, It looks like you have a unit cell with two relatively short axes and one long one - and some disorder. I have experienced a few examples of this with virus fibre proteins (adenovirus fibre and T4 short tail fibre). For the short tail fibre we also obtained images in which some

Re: [ccp4bb] Editorial policies (was Citations in supplementary material)

2010-11-19 Thread VAN RAAIJ , MARK JOHAN
Regarding editorial decisions, I actually welcome editors making more rejection decisions, i.e. reading the paper before sending it to referees, so I waste less time, waiting as author, or as referee reading and commenting on papers for which it would have been clear beforehand that they are

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread VAN RAAIJ , MARK JOHAN
Hi Sebastiano, I don't see how the k-off would influence this, given the timescale of growing crystals. An explanation in terms of high Kd and relative lack of crystal contacts for the component with higher temperature factors would sound more convincing to me. Mark Quoting Vellieux

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

2010-10-27 Thread VAN RAAIJ , MARK JOHAN
perhaps we should campaign for it to be obligatory to provide the pdb and structure factor file to the journal, and thus referees, upon submission? Then he can look for himself to see that building and refinement have been performed satisfactorily. Mark Surely the best model is the one that