Re: [ccp4bb] pointless problem

Dear Ping, You need the unmerged data for this - for instance the output from Mosflm or the XDS INTEGRATE step. Pointless works by comparing potentially symmetry related measurements. Best wishes, Graeme 2011/11/17 Ping Wang : > Dear all, > I have a dataset with spacegroup undetermined. When I

[ccp4bb] pointless problem

Dear all, I have a dataset with spacegroup undetermined. When I use POINTLESS to determine laue group, the program gave the fatal error: HKLIN is merged and no HKLREF is defined, SPACEGROUP or REINDEX. In the protocol of POINTLESS for the determination of LAUE group, HKLREF can be not specified.

[ccp4bb] how to skip map calculation in refmac

Is there some way to make refmac *not* to produce the output mtz file, i.e. skip the whole FWT/DELFWT calculation altogether? -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

Re: [ccp4bb] Distinguish NH4 from Na?

Dear JPK, I think the coordination geometry of Na is a key, normally it adopts octahedral geometry with Na---O distances of 2.1-2.2 ang, whereas water molecule is h-bonded with H-acceptor or H-donor with the distances between 2.6-3.3 ang. I am not sure it is correct, as i used to be small-molecule

[ccp4bb] Oops-a-daisy! [Re: In the mood for some LEGO DNA to celebrate PDB40?]

Hi again, It turns out that, due to copyright restrictions, our German friends cannot view the Lego-DNA clip on YouTube (no, it was not in retalliation for your football team beating the Dutch last night!). Especially for them, the author of the clip has put an MP4 version on his website:

Re: [ccp4bb] Distinguish NH4 from Na?

Bond valence sum Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A) R On 16 Nov 2011, at 18:20, Jacob Keller wrote: > Dear Crystallographers, > > I have crystals containing 666mM NH4 and 540mM Na, and there appears > to be a "water" which is only about

[ccp4bb] Distinguish NH4 from Na?

Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a "water" which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Yes you can with the LABOUT command even in the GUI :-) Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Could DANO/SIGDANO be included to REFMAC output mtz automatically? I find it very useful on the various stages of refinement to observe anomalous map. Last time I was trying, I failed, probably due to GUI'sh addiction and abandonning line editor. Dr Felix Frolow Professor of Structural Biolog

[ccp4bb] Faculty position in X-ray crystallography at NC State University

Dear all, The link is: http://biochem.ncsu.edu/ad.php "The Department of Molecular and Structural Biochemistryat North Carolina State University invites applications for a tenure-track faculty position in X-ray crystallography, with preference given to candidates at the

[ccp4bb] Clontech's beads

Dear CCP4bb users, can anybody provide me a feedback on Clontech's Ni and GST beads. We need to buy the new resins. How is the binding capacity? And the most important, how stable are those resins, how many times can they be regenerated and keep the reasonable binding capacity. How is protein puri

[ccp4bb] CCP4 Study Weekend, Diamond MX User Meeting programme

Dear All, the programme of the CCP4 Study Weekend satellite Diamond MX User Meeting is now available on the following webpage: http://www.cse.scitech.ac.uk/events/CCP4_2012/UserMeeting.html We look forward to seeing you there. James Nicholson, Ralf Flaig Dimond Light Source

[ccp4bb] sftools bug

Hi, if you change crystal infro (SG P2 --> P21) and column labels at the same time F col label (like FP) cant be changed to anything else at the same time for whatever reason... at least i had this prob. ccp4 vs 6.2 tommi

Re: [ccp4bb] Crystallizing protein sitting in PBS

On Wed, 2011-11-16 at 09:26 +, Tom Murray-Rust wrote: > That way you should be able to > quickly identify any hits that are due to salt, and which are likely > to be your protein. Just a footnote to Tom's excellent comment: It is possible to have actual protein crystals to grow alongside sal

Re: [ccp4bb] Crystallizing protein sitting in PBS

A thing we frequently forget is that phosphate can be a precipitating agent try a phosphate grid screen, just like you would with ammonium sulfate. If your protein likes PBS, it may want to crystallize with phosphate See Enrico Stura's footprint screen for example On Tue, Nov 15, 2011 at 5:25 PM,

Re: [ccp4bb] Superpose tool in CCP4_some residues missing in RMS output list

By default it only gives those with rms > mean. There is an option to ask for all to be output to a separate file.. E On 11/16/2011 11:48 AM, WENHE ZHONG wrote: Dear all, I am using the Molecular Suporpose tool under Coordinate Utilities list in CCP4 to superpose two similar structures. I tick

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Yes - one solution is to use the MR phases to do a anom diff map to position the Se sites. You need to a) run CAD to combine the DANO/ SIGDANO columns from your data with the refmac output b) use the fft utility to do a DANO map with PHIC and FOM and run a peak search. Ideally you should f

[ccp4bb] Superpose tool in CCP4_some residues missing in RMS output list

Dear all, I am using the Molecular Suporpose tool under Coordinate Utilities list in CCP4 to superpose two similar structures. I ticked the "Output all distances to a file" option, selected "Superpose specified atoms/residues", fit "CA atoms of Residues" to the other one. I wanted to see the RMS n

Re: [ccp4bb] Bug in XIA2 0.3.3.3 Build 3479

Dear Tony, Many thanks for your additional help off list. The error is due to a corner case relating to setting the spacegroup on the command line. The fix is a one liner: in $XIA2_ROOT/Modules/Scaler/CCP4ScalerR.py at line 451 please add reindex_op = 'h,k,l' to give something like:

Re: [ccp4bb] Crystallizing protein sitting in PBS

Of course PBS should not be a first choice for screning crystal. But I will try all kinds of buffer until I got the structure. Nobady can tell you that you can't get crystal in the PBS buffer. and I will shot everything I have if I have enough beam time. Good luck.

Re: [ccp4bb] Crystallizing protein sitting in PBS

Hi JK, As mentioned, phosphate salts are the main disadvantage - you can get round this by setting up two drops per well: one with your protein in PBS, and the other with PBS only. That way you should be able to quickly identify any hits that are due to salt, and which are likely to be your protei

Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?

Hi Feng, If your native and selenomet data are isomorphous, I would use your native data, your selenomet data and your (partially correct) MR solution and your heavy atoms altogether in refmac. At the moment, the refmac gui does not support SIRAS refinement, but you can do it via script - Pav

Re: [ccp4bb] Crystallizing protein sitting in PBS

Dear JK, In principle, there is nothing against screening in phosphate buffer. The only reason it is not popular with crystallographers is that phosphate likes to form all kinds of salt crystals, e.g. with calcium. So if you screen, you should be prepared to see salt crystals as well. However, if