Re: [ccp4bb] Expanding p4212 coordinates to p1

I am confused by the discussion on this message. Although it says plane group I assume it really is a normal 3D tetragonal space group, P42(1)2 So Eleanor's suggestion should work and sftools expand command will do the job as well. Bart On

Re: [ccp4bb] Philosophical question

Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Bart Hazes Associate Professor Dept. of Medical Microbiology Immunology University of Alberta

Re: [ccp4bb] Philosophical question

*** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Bart Hazes Associate Professor Dept. of Medical Microbiology

Re: advice

I'd like to add that the value of a molecular replacement solution tends to be inversely correlated with the effort needed to find the solution. In other words, the harder you have to work to find the MR solution the less informative the phase information you tend to get. When you have very

Re: [ccp4bb] relation between wavelength and inter-atomic distances

of wavelengths in the 1 to 1.5 Angstrom range. Bart == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7

Re: [ccp4bb] practical limits of MR?

== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] A bit of history: John W Backus obit

A -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] Generate Random phase set.

to do the job. - Douglas Adams -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780

Re: [ccp4bb] Highest shell standards

really reject papers for that reason, but there appears to be a conservative epidemic when it comes to restricting the resolution of the data set. Bart -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology

[ccp4bb] Chi-by-Eye[ Highest shell standards]

James Holton wrote: I generally cut off integration at the shell wheree I/sigI 0.5 and then cut off merged data where MnI/sd(I) ~ 1.5. It is always easier to to cut off data later than to re-integrate it. I never look at the Rmerge, Rsym, Rpim or Rwhatever in the highest resolution shell.

Re: [ccp4bb] Strange behavior in R32

-- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

[ccp4bb] website back up

address (http://eagle.mmid.med.ualberta.ca/). Cheers, Bart == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7

Re: [ccp4bb] DANO from PDB

...this was a while ago), which didn't result in a good fit for our data. Pete Pete Meyer Fu Lab BMCB grad student Cornell University -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology

Re: [ccp4bb] Survey on computer usage in crystallography

currently available, let alone what I wish were available. -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta

Re: [ccp4bb] Survey on computer usage in crystallography

is for crystallographers. I personally think its a wonderful teaching tool which is currently under-utilized. Paul From: Bart Hazes [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 09:28

Re: [ccp4bb] difference density ripples around Hg atoms

-- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] Strange diffraction images

] *** -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622

thank suggestions, point to similar cases, etc... In fact, currently I wondered why refinement programs take B-factor to such low values Many thanks, Jorge -- == Bart Hazes (Assistant Professor) Dept. of Medical

Re: [ccp4bb] R-sleep

Bioquímica Estructural Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- == Bart Hazes (Assistant

Re: [ccp4bb] carving up maps (was re: pymol help)

indicate in the legend what map and carve settings were used. Bart -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta

Re: [ccp4bb] counting constraints?

becomes relevant when considering e.g. VDW restraints which normally only become active when the distance becomes less than a threshold. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bart Hazes Sent: 14 February 2008 15:53 To: Meyer, Peter Cc

Re: [ccp4bb] counting constraints?

on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- == Bart

Re: [ccp4bb] question about processing data

to) and no problems leading to systematic errors or outliers. Bart == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7

Re: [ccp4bb] twinned?

or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information. -- == Bart Hazes

Re: [ccp4bb] twinned?

/cgi-bin/paper?S0907444903007947S They suggest using neighbouring reflections pairs to test . This can often overcome the problem associated with pseudo-translation. However it is quite sensitive to data quality. See http://nihserver.mbi.ucla.edu/pystats/ Eleanor Bart Hazes wrote: Hi Qiang

Re: [ccp4bb] twinned?

/pubmed/10476961?ordinalpos=6itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Nature. 1999 Aug 26;400(6747):841-7. On 03/04/2008, at 17.48, Bart Hazes wrote: I just realized

Re: [ccp4bb] crystallisation robot

be trivial to set up.. -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax

Re: [ccp4bb] Negative density around C of COO-

rumors that mechanisms are known when in reality they are not. Just my little rant. -James Holton MAD Scientist -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1

Re: [ccp4bb] mutation to cysteines

== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] Using multiple crystals for structure solution in P1 using MAD/SAS/SAD

in different areas. HTH, Kay -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492

Re: [ccp4bb] truncate ignorance

for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences

Re: [ccp4bb] Fobs - Fobs

Hi Rana, You probably have multiple options suggested to you. One is sftools using the CALC command. If the subtraction includes a phase then sftools can also do the calculation on the full structure factor. Plain subtraction of amplitudes ensuring the result is = 0 READ yourfile.mtz CALC

Re: [ccp4bb] protein folds

Must be even smaller than Daresbury then. They don't even have a synchrotron! Bart James Holton wrote: Paul Emsley wrote: Here's an experiment: Find a blindfold and put it on. Oh, but before you do that, take a map of England and place it on a dartboard. Now take 56066 darts and throw

Re: [ccp4bb] .phs file conversion

SFTOOLS should read the phs file and allow you to write it out in a number of different formats, including MTZ. From the command line type: sftools read yourfile.phs write yourfile.mtz quit The program will ask a bunch of questions to get space group, unit cell etc. Bart John Bruning wrote:

Re: [ccp4bb] Calculation of angle between two helix of different subunits

Leiman Petr wrote: Every other week this question comes up! This is Geometry 101 or beginner's geometry!!! http://www.euclideanspace.com/maths/algebra/vectors/angleBetween/index.htm I am not sure if it possible to understand _anything_ in crystallography if it is not clear how to calculate an

Re: [ccp4bb] H3 to 2.0A but low observations:parameter ratio

Hi Francis, The asymmetric unit volume is approximately proportional to the number of atoms in your model, the basis for Vm, with some variation due to solvent content. In turn the number of unique observations at a given resolution is proportional to asymmetric unit volume. So twice the

Re: [ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?

-- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521

Re: [ccp4bb] Sftools can not handle non-standard settings?

-- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521

Re: [ccp4bb] How to automatically answer NO to SFTOOLS reading in a shell script?

Regards, Hailiang -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Bart Hazes (Associate Professor) Dept. of Medical

Re: [ccp4bb] [QUAR] Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

nd f' or f" will be much less noticeable for anomalous scatters with high B-values where the latter dominates the 3D distribution of the electrons. Bart ======== Bart Hazes (Associate Professor) Dept. of Medical Microbiol

Re: [ccp4bb] quantum diffraction

) they should be considered independent events. So the photon rate can probably be 5 to 6 orders of magnitude higher while still doing single photon diffraction experiments. Bart -- Bart Hazes (Associate Professor

Re: [ccp4bb] quantum diffraction

fractions lead to interference on most angles the results cancel out when they are not on a common wavelength you get loud distraction there is no single outcome until the polls measure something Bart -- Bart Hazes

Re: [ccp4bb] Against Method (R)

er Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- =

Re: [ccp4bb] Against Method (R)

I/sigma by attenuating the beam and collect another data set--same situation? JPK - Original Message - From: Bart Hazes To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, October 28, 2010 4:13 PM Subject: Re: [ccp4bb] Against Method (R

Re: [ccp4bb] Against Method (R)

to density surrounding that residue will suddenly disappear as well. The benefit of high resolution is that it is much easier to pick up and fix such errors (or not make them in the first place) Bart -- Bart Hazes

Re: [ccp4bb] Against Method (R)

The benefit of high resolution is that it is much easier to pick up and fix such errors (or not make them in the first place) Bart -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology Unive

Re: [ccp4bb] Strange spots

. Bart On 10-10-29 10:08 AM, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- Bart Hazes (Associate Professor) Dept. of Medical

Re: [ccp4bb] I/sigmaI of 3.0 rule

-- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521

Re: [ccp4bb] ssDNA self-aneal

est wishes. -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521

Re: [ccp4bb] program to calculate electron density at x,y,z

electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Thanks in advance, Ed. -- Bart Hazes (Associate Professor) Dept. of Medical

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

that converts a pdb file into a list of point statements. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Bart Hazes (Associate Professor

Re: [ccp4bb] writing scripts-off topic

On 12-01-23 09:59 PM, Ethan Merritt wrote: On Monday, 23 January 2012, Yuri Pompeu wrote: Hello Everyone, I want to play around with some coding/programming. Just simple calculations from an input PDB file, B factors averages, occupancies, molecular weight, so forth... What should I use

Re: [ccp4bb] Crystallization robot and trypsin

On 12-01-24 08:39 AM, Regina Kettering wrote: We have a Honeybee system but do not usually use proteases. The biggest problem we have found is that if anything precipitates in the tips they have to be washed very well, usually

Re: [ccp4bb] writing scripts-off topic

On 12-01-24 09:36 AM, Ian Tickle wrote: On 24 January 2012 14:19, David Schullerdj...@cornell.edu wrote: On 01/24/12 00:41, Bart Hazes wrote: www.cs.siue.edu/~astefik/papers/StefikPlateau2011.pdf An Empirical Comparison of the Accuracy Rates of Novices using the Quorum, Perl, and Randomo

Re: [ccp4bb] quasispecies

On 12-01-24 11:20 AM, Jacob Keller wrote: Inspired by the recent post about quasispecies: I have been bothered recently by the following problem: why do species of genetic uniformity exist at all (or do they?)? This first came up when I saw a Nature paper describing live bacteria extracted from

Re: [ccp4bb] sftools expand

On 12-02-06 08:37 AM, wtempel wrote: Hello, here is a question about the EXPAND command in SFTOOLS, specifically its effect on a free reflection flag. Do the flag values get copied to newly generated reflections based on symmetry, for example in the case of a P622 - P6 expansion? many thanks,

Re: [ccp4bb] choice of wavelength

Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy, so doubling the wavelength gives 8 times

Re: [ccp4bb] Disulfide bonds

many messages I got after the server relocation. SSBOND will soon get some competition for most used service as I am about to release some bioinformatics services. Bart On 12-03-04 02:36 AM, Frederic VELLIEUX wrote: I'd google for Bart Hazes and SSBOND myself. There is (or was) a server

Re: [ccp4bb] how to improve Rfree?

-factor is lower than the R-factor. I expect that future referees will not view that kindly. A number of people have suggested to use different approaches to get rid of this reciprocal space binding effect. One of these people (Bart Hazes I think, correct me if I'm wrong) suggests to take

Re: [ccp4bb] R-sym and R-merge

--- --- * total : 5601631.39% 30.88% 20.91% 24.72% 16.90% 13.95% 17.97% -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta

Re: [ccp4bb] Why Do Phases Dominate?

*** -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780

Re: [ccp4bb] odd request: add phase error linearly with resolution

- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- Bart Hazes (Associate

Re: [ccp4bb] Why Do Phases Dominate?

* * * === -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7

Re: [ccp4bb] some questions

-- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521

Re: [ccp4bb] sftools and batch mode

... Thanks for any pointers or alternatives! Seth -- Bart Hazes Associate Professor Dept. of Medical Microbiology Immunology University of Alberta