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 python,

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 wit

Re: [ccp4bb] writing scripts-off topic

On 12-01-24 09:36 AM, Ian Tickle wrote: On 24 January 2012 14:19, David Schuller 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 Programming Languages

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 fro

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, W

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 diffract

Re: [ccp4bb] choice of wavelength

a sets the wavelength sweet spot with a pilatus detector may be a bit longer then what used to be optimal for a given beamline on a previous generation detector. Bart On 12-02-16 02:09 AM, A Leslie wrote: On 15 Feb 2012, at 23:55, Bart Hazes wrote: Diffracted intensity goes up by the cube of the

Re: [ccp4bb] Modified Cys by TCEP?

On 12-02-21 10:11 AM, Björn Kauppi wrote: Hi all, I recently encountered a modified surface cysteine residue in one of my structures. The protein is expressed in E.coli and my data is to 1.7Å so I am positive of the number of extra atoms. It really look like one of the tails (the Propanoic a

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. T

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 12-04-12

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

mafft and muscle are both faster than clustalw and on average more accurate. You can also use different options for mafft to push for speed or accuracy depending on your needs and patience. Tcoffee has a flavour that includes structural information if available to assist alignment. Another flav

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

4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836 *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.918

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

ing factors for f0 and 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) De

Re: [ccp4bb] quantum diffraction

N THE CRYSTAL at once. A minor point: the interaction is not really "at once," is it? The photon does have to move through the crystal over a finite time. JPK -- ======== Bart Hazes (Associate Professor) Dept.

Re: [ccp4bb] quantum diffraction

Bernard's post) 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 -- ======

Re: [ccp4bb] quantum diffraction

r diffrent 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 -- ====

Re: [ccp4bb] refining structures with engineered disulfide bonds

the last time we needed it) and it does not refine occupancy. Bart On 10-10-20 03:34 PM, Frederic VELLIEUX wrote: Bart Hazes wrote a program (and published as well, Hazes & Dijkstra perhaps) called SSBOND I think. I cannot remember exactly what the computer program does, but it certainly h

Re: [ccp4bb] Against Method (R)

; > > for the R?  Isn't Rmerge a poorly defined measure itself that >> > > deteriorates at least in some circumstances (e.g. increased redundancy)? >> > > Specifically, shouldn't "ideal" R approximate 0.5*/? >> > > >> > > Cheers, >> > > >> > > Ed. >>

Re: [ccp4bb] Against Method (R)

mas? Or let's say I experimentally decrease 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: [ccp

Re: [ccp4bb] Against Method (R)

on-ideal fit 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 -- =====

Re: [ccp4bb] Against Method (R)

peptide > flips, 120 degree changes in side chain dihedrals, etc. If you can find > and fix one of those errors a lot of the stereochemical distortions and > non-ideal fit to density surrounding that residue will suddenly > disappear as well. > > The benefit of high resolution is t

Re: [ccp4bb] Strange spots

tion is not in the cards. 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 Pr

Re: [ccp4bb] I/sigmaI of >3.0 rule

7 fax. +39.049.8275239 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it -- ========

Re: [ccp4bb] I/sigmaI of >3.0 rule

ova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it -- ==== 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

  best wishes. -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edm

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

point 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 Me

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

can definitely come up with a script 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 -- =====

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

.72 55.0777.06 52.10 57.35 56.51 - --- --- --- --- --- --- --- * total : 5601631.39% 30.88% 20.91% 24.72% 16.90% 13.95% 17.97% --

Re: [ccp4bb] Why Do Phases Dominate?

il: j-kell...@northwestern.edu *** -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton,

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

n be done? Thanks FR - 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 -- ==== B

Re: [ccp4bb] Why Do Phases Dominate?

idt >>> Asst. Professor >>> University of Wisconsin-Milwaukee >>> Department of Physics Room 454 >>> 1900 E. Kenwood Blvd. >>> Milwaukee, WI 53211 >>> >>> phone: +1-414-229-4338 >>> email: m-schm...@uwm.edu >>> http://users.physik.tu-muenchen.de/marius/ >> Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/ -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- 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] some questions

static. Bart -- ======== 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] 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] Disulfide Designer Program

: 773.608.9185 email: j-kell...@northwestern.edu *** -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology& Immunology University of Alberta 1-15 Medical Scie

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

reuder -- 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?

hell script. Thanks! Best Regards, Hailiang -- ==== Bart Hazes (Associate Professor) Dept. of Medical Microbiology& Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 ph

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 hig

Re: advice

ecessarily the case if the search is hard because your search models individually constitute only a small part of the asymmetric unit. Say that 80% of the AU consists of multiple different proteins with known structure; the phase information would be very high if you find the solutions. Filip On 1/2

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

shorter than that. Hence the predominant use 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 B

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

apeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tamp

Re: [ccp4bb] practical limits of MR?

found, is going to be. Bart ====== 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

ermalink Pete 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.

ng themselves made President should on no account be allowed to do the job. - Douglas Adams -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical

[ccp4bb] [Fwd: Re: [ccp4bb] question about redundancy]

-- == 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-

Re: [ccp4bb] Highest shell standards

;t let the crystals diffract to their full potential. You can't 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 -- ======

Re: [ccp4bb] Highest shell standards

Don't you get a false sense of details when the missing reflections are filled in with DFc when computing a 2MFo-DFc map? P -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immuno

[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

hology. Thanks in advance, Dan -- ====== 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

Re: [ccp4bb] B-factor & Space gr questions!

he message from your computer and network. -- ====== 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

quares fit (following a reference I don't have in front of me...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 -- ===

Re: [ccp4bb] Survey on computer usage in crystallography

as a Virtual Reality headset)?" That does not cover all the choices currently available, let alone what I wish were available. -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Imm

Re: [ccp4bb] Survey on computer usage in crystallography

graphics 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: W

Re: [ccp4bb] difference density ripples around Hg atoms

e to get rid of the "ripples". best, Kay -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==

Re: [ccp4bb] difference density ripples around Hg atoms

xplanation of the convolution theorem on this particular case is very useful as a reminder of this important concept. Bart Kay Diederichs wrote: Bart Hazes schrieb: ... W.r.t. Kay's reply I think the argument does not hold since it depends on how badly the data is truncated. E.g. tru

Re: [ccp4bb] centrosymm structure

happening. - -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Albert

Re: [ccp4bb] Strange diffraction images

Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] *** -- == 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

P6, P312 and P321, all of course suggest twinning. I would 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 -- =======

Re: [ccp4bb] R-sleep

and too pessimistic? Mark J. van Raaij Unidad de 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/ -- ====

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

h me as long as you 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 Bui

Re: [ccp4bb] an over refined structure

imum likelihood refinement or to make general refinement strategy choices. Bart ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmon

Re: [ccp4bb] an over refined structure

Dale Tronrud wrote: Bart Hazes wrote: Dale Tronrud wrote: [EMAIL PROTECTED] wrote: > Rotational near-crystallographic ncs is easy to handle this way, but > what about translational pseudo-symmetry (or should that be > pseudo-translational symmetry)? In such cases one whole set

Re: [ccp4bb] counting constraints?

n't have a clear explanation for why, and of course I could be wrong on this. Thanks, Pete * Rough translation - I'm about to ask another stupid question. Not like it's the first time. -- ========

Re: [ccp4bb] counting constraints?

tive* restraint is counted. The question of inactive restraints 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

Re: [ccp4bb] counting constraints?

eption, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails 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 nu

Re: [ccp4bb] question about processing data

who you talk 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 E

Re: [ccp4bb] twinned?

983 and properly dispose of this information. -- == 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] twinned?

pts.iucr.org/cgi-bin/paper?S0907444903007947>S 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 Ha

Re: [ccp4bb] twinned?

i.nlm.nih.gov/pubmed/10476961?ordinalpos=6&itool=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 wro

Re: [ccp4bb] which concentrated salt has lowest vapour pressure?

nsight, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz -- ===

Re: [ccp4bb] crystallisation robot

e (2) slows up the robotics a little, but both should be trivial to set up.. -- ====== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Buildi

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

mical reaction is a "free radical" reaction (since they involve the movement of electrons). I think it best that we try to call the chemistry what it is and try to stamp out rumors that mechanisms are known when in reality they are not. Just my little rant. -James Holton MA

Re: [ccp4bb] mutation to cysteines

ll. Bart ====== 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

strengths 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 pho

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

0 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ******* - Original Message - From: "Bart Hazes" <[EMAIL PROTECTED]> To: Sent: Wednesday, July 23, 2008 10:05 AM Subject: Re: [ccp4bb] Using

Re: [ccp4bb] truncate ignorance

email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England

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 them

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 a

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 numb

Re: [ccp4bb] Software for predicting potential disulfide cross-linking sites?

contacting residues which I can then mutate to CYS in order to introduce an intermolecular disulfide bond to stabilize the biological assembly? Your input is greatly appreciated! Jie Liu -- Bart Hazes

Re: [ccp4bb] how to improve Rfree?

asymmetric unit. The free R-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 i

Re: [ccp4bb] sftools and batch mode

t Rfree?" "is it CV?" "is it bigger than a breadbox?" type >> stuff. >> >> Again, I know the sftools documentation is clear that the design goal was >> for interactive use and humans have little trouble with such questions, but >> when there might be several thousand of them... >> >> Thanks for any pointers or alternatives! >> >> Seth >> >> >> > -- Bart Hazes Associate Professor Dept. of Medical Microbiology & Immunology University of Alberta

Re: [ccp4bb] Philosophical question

7;t >> initiation occur also at methionines in the middle of proteins? I'm >> guessing it has to do with 5' untranslated region and ribosome binding >> sites. So could the start codon actually be anything you want, provided >> there is a strong ribosome binding site there? >> >> Just be

Re: [ccp4bb] Philosophical question

ason you invoke cannot be applied to other > features of this LUCA which are indeed seen to be variable. > > JPK > > > *** > > Jacob Pearson Keller, PhD > > Looger Lab/HHMI Janelia Farms Research Campus > > 19700 Helix Dr, As