Re: [ccp4bb] A crystallographer on Mars

Hi Ethan, The crystallographer is the next generation crystallographer: a robot. If there was a job interview (which I doubt) I guess he was asked about its power consumption, generated heat etc. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] cryo condition

Hi, Paraton oil worked nicely for me for these conditions. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] Off-topic: NMR and crystallography

Just to add on that, regarding membrane proteins: I noticed some recent publications on solid-state NMR for membrane proteins, not sure about solution NMR for this class. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail

Re: [ccp4bb] Off-topic: NMR and crystallography

/residue is equivalent to ~2A resolution structure. Maybe. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 On 06/09/2013 08:12 PM

Re: [ccp4bb] Concerns about statistics

geometry and e.d. for the co-factor upon adding (somewhat) higher resolution shells. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647

Re: [ccp4bb] ctruncate bug?

Hi Douglas, So will you and/or other participants in this fascinating and informative thread pick up the glove and implement the suggestions made here? At least we'll know if it makes a change to our data. In any case I doubt that it can harm.  Cheers,           Boaz Boaz Shaanan, Ph.D

Re: [ccp4bb] Refinement against frames

Pandora box. My 2p thoughts. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] Refinement against frames

. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] which dimer?

that it's a dimer? If the monomer is elongated and has MW of 15kD, running as 24kD is not unheard of. Analyzing SEC results can often be tricky when it comes to determining MW and size. My 2p late night thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University

Re: [ccp4bb] mmCIF as working format?

imagine how they'll cope with the cryptic mmCIF format. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From

Re: [ccp4bb] mmCIF as working format?

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: Nat Echols [nathaniel.ech...@gmail.com] Sent: Monday

Re: [ccp4bb] Fo simulators?

Isn't one of the tools/simulators that James Holton developed what you're looking for? They're accessible to the public as far as I know (if that's what you mean by 'open source'). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

Re: [ccp4bb] tNCS: indexing and EP problems

Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva

Re: [ccp4bb] tNCS: indexing and EP problems

In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. The new XDS gui can also serve for that these days, I guess. Boaz

[ccp4bb] השב: Re: [ccp4bb] tNCS: indexing and EP problems

Hi Nicolas, You may want to make sure that all other parameters in XDS are the same as in mosflm and particularly the origin. Otherwise, how does the xds indexing/integration look? Perhaps pointless will give a clue about the relation between the xds and mosflm cells/spacegroup? Cheers, Boaz

[ccp4bb] השב: Re: [ccp4bb] expanding reflections from C2221 to P21

Just wondering: what's the justification for this exercise? Aren't the two lattices sampling the molecular transform differently even though there is a transformation relating them? Wouldn't it be more correct to select a different R free set for the p21 cell? Boaz הודעה מקורית

[ccp4bb] השב: [ccp4bb] Why nobody comments about the Nobel committee decision?

Good point. Now since you mentioned contributions of the recent Nobel laureates to crystallography Mike Levitt also had a significant contribution through the by now forgotten Jack-Levitt refinement which to the best of my knowledge was the first time that x-ray term was added to the energy

[ccp4bb] השב: Re: [ccp4bb] largest protein crystal ever grown?

Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size

[ccp4bb] השב: [ccp4bb] LSQKAB with trajectory files

Hi Charlie, one possible way of doing this is through UCSF-Chimera. It'll read each of the models into a different slot, then you can apply the transformation you choose to each of the models. I think I'm right. The Chimera support team may help you figure out how to do this in one go. Best

Re: [ccp4bb] Spam:Re: [ccp4bb] Align linux version

that do the job. In fact, I myself don't use align these days, nor am I sure that the version I have will handle the v3 pdb's properly. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E

Re: [ccp4bb] unexplained density

Hi, You probably tried it but what happens if you fit in PMSF and refine? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8

Re: [ccp4bb] off-topic Electron density map rendering..

You're absolutely right Tim, but unfortunately that's very common these days not to mention the rendering program and ignore the efforts of those who developed it. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

[ccp4bb] השב: Re: [ccp4bb] Sister CCPs

Dear George, I'm not sure it's a good idea since the wet work and coputational work are quite often linked. For example preparation of heavy atom derivatives and handling the data, to which bb would you send questions related to this subject? To both bb's? Wouldn't that make life even more

[ccp4bb] השב: Re: [ccp4bb] Sister CCPs

The wet lab questions on ccp4bb are crystallography related in most if not all cases, aren't they? I'm quite sure that people send more general wet lab questions to other bb's. Boaz הודעה מקורית מאת Robbie Joosten robbie_joos...@hotmail.com תאריך: 12/02/2014 21:22

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

of your data. There is a limit to what refinement programs can do when there is a real problem in the data which is not taken care of properly. My 2p thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] CCP4-6.4.0 Update 010

Hi, Is the refmac5 indeed 5.8.006? The current ccp4 version 5.8.0049. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972

Re: [ccp4bb] off-topic: protein losing FAD during purification

diffracting crystals. Unless of course you have good reason to believe that the apoprotein is more stable, in which case dialysis could be the way to go in order to get all (??) the FAD out. My 2p thoughts. Good luck, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben

Re: [ccp4bb] off-topic: protein losing FAD during purification

Hi Stefano, On top of all that has been suggested you should also be aware of the effect of pH and buffer composition on the apo-holoenzyme equilibrium during purification and crystallization. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev

Re: [ccp4bb] ligand occupancy

Hi Monica, You can refine the ligand occupancy in refmac as explained here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html or in phenix, whichever program you're using. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University

Re: [ccp4bb] crystallographic confusion

and get out the effective resolution based on your criteria? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646

Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?

Hi, It's pdb2pqr problem (unknown residue). I guess you ran pdb2pqr prior to running APBS, if not, you should. So, you should submit your question to either the APBS or pdb2pqr BB's. They are very helpful people. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben

Re: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge?

Hi Nadir, Which One do you use? I may have missed it in the thread. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992

Re: [ccp4bb] Solvent channels

. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D

Re: [ccp4bb] Input reflection file for refmac runs

Hi Dilip, You've been doing the right thing. Just keep at it. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8

Re: [ccp4bb] question about powder diffraction

and Oxford dictionaries agree on that too. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] very informative - Trends in Data Fabrication

How about such a footnote to Table 1: The resolution of data is 3A in the a direction, 3.5A in b direction and 5A in the c direction Wouldn't this do the trick? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

been through recently, unwillingness to provide data to Editor/Reviewer may well raise questions. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8

Re: [ccp4bb] Anomalous SAXS

of literature on the method and results on many metal proteins (I'm familiar with the EXAFS results on haemoglobin which caused quite a stir at the time). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail

[ccp4bb]

Hi, I think you'll find the Jligand tutorial on the York site very helpful in that regard. It's well worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647

Re: [ccp4bb] PDB deposition of internally truncated protein

the information about the missing piece and its position in the sequence. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8

Re: [ccp4bb] Calculation of volume/size of cavity

Hi, You could try CASTp (http://sts.bioengr.uic.edu/castp/). If your protein is in the pdb it may well be in their database, if not, just upload it. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

being obsolete, is yes it is since a long time? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

MIRAS doesn't count, only MIR (If I understand the original question correctly). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972

Re: [ccp4bb] Question on Symmetry Axis Notation Convention

Hi, Isn't there a notation 2 subscript 1 superscript x (one on top of the other) for 2-fold screw along x for example? and likewise for y and z? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone

Re: [ccp4bb] information received through the AFC: iycr2014

Et alors, what will this mean for us? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] information received through the AFC: iycr2014

And perhaps all crystallographers will have to wear those blue hats during conferences or even during data collection sessions at syncrhotrons. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8

Re: [ccp4bb] Chiral volume outliers SO4

be cured. As Ian pointed out computational chirality (Pasteur must be spinning in his grave right now) is addressed nicely in the cif file (chirality both). My 2p. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] Heme incorporation in expressed protein

Hi, You may find helpful suggestions in Kiyoshi Nagai's papers (mid 80ies) who did this with haemoglobin (I could be wrong but I think he was the first to do this). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105

Re: [ccp4bb] peptide fragment

as it pointed to the way MHC's recognize peptides. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] refmac5, SIGF/SIGIMEAN labels

88.74 117.37 1.90 Q SIGF 7 NONE0.0329367.6 0 100.00 764.82 764.82 117.37 1.90 F FC 8 NONE0.0 360.0 0 100.00 179.27 179.27 117.37 1.90 P PHIC Boaz Boaz Shaanan, Ph.D

Re: [ccp4bb] Pairwise distance calculation

Hi, ProSmart (in 6.3.0) might be your friend here. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646

Re: [ccp4bb] CC1/2, XDS and resolution cut off

)? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB

Re: [ccp4bb] calculating dialectric properties of enzyme active site

. As for the hydrophobicity - there are hydrophobicity scales around (whether you believe them or not is a different matter) which you can use to display on the surface, again by Pymol or Chimera (and probably many other programs). My 2p/2c thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences

Re: [ccp4bb] Stabilization of crystals and ligand exchange

(although not impossible). This may help you decide which way to go for obtaining the ligand-free structure. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype

Re: [ccp4bb] Different residue type with same number in refmac?

Yes. It's not different from two alternate conformations of the same residue as far as refmac is concerned. Just name one AXXX, the other BYYY and give them each occupancies less than 1. Refmac5 will handle them properly. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] usefulness of cacodylate?

). Meanwhile, the admins can use the money for their needs. Clever people, right? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992

Re: [ccp4bb] vitrification vs freezing

? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

Re: [ccp4bb] Equilibrium Relative Humidity matching

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 This leads to a counter-intuitive observation - it is only

Re: [ccp4bb] cc1/2

and also in the CORRECT.LP. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] refining against weak data and Table I stats

Hi, I'm sure Kay will have something to say about this but I think the idea of the K K paper was to introduce new (more objective) standards for deciding on the resolution, so I don't see why another table is needed. Cheers,           Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben

[ccp4bb] FW: [ccp4bb] refining against weak data and Table I stats

they report. I think it's another tool that will show case-by-case dependence. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8

Re: [ccp4bb] archival memory?

But why? I thought the idea emanating from the thread was to go the other way around for long time archival, i.e. computer -- Sumerian (or Babylonian) clay. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] PEG refinement

Hi, I usually pick up the one that fits best the map (there are several PEG monomers in the ccp4 monomer library to choose from). You should bear in mind that PEG's are a mixture of molecules, quite often floppy, so whatever fits best is the best choice. Good luck, Boaz Boaz

Re: [ccp4bb] Very sad new - Roger Fourme

impressed by Roger's professional qualities and his gentle personality. Please pass my sincere condolences to his family. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647

Re: [ccp4bb] Very sad new

Sorry, the sentence I quoted about Roger Fourme is on page 325 in Science is not a Quiet Life by Max Perutz (not 375). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype

Re: [ccp4bb] Who invented PDB format?

Dear George, Those folks (bioinformaticiens ?) are not interested in inter-molecular contacts, as far as I'm aware so they can't bothered less by the orthogonal coordinates used in pdb files. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev

Re: [ccp4bb] About NCS and inhibitors

Just a naive question: why apply NCS to ligands at all? Their contribution to the number of parameters and hence to the param/obs ratio, the main argument for applying NCS, is negligible, isn't it? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva

Re: [ccp4bb] PDB crawler

, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf

[ccp4bb] השב: Re: [ccp4bb] Vote for crystallography

Well done to you Fred for pointing this out to us. How did you comr across it? Cheers, Boaz ‏נשלח מהטלפון הנייד של Samsung הודעה מקורית מאת: vellieux frederic.velli...@ibs.fr תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: Re: [ccp4bb] Vote for crystallography Dear

Re: [ccp4bb] CCP4 Update victim of own success

you think you told them, which is why inspecting the log file helps. BTW, I find the GUI's (ccp4i or phenix) as great help in preparing the command file, certainly the skeleton which can then be modified and run via the command line if needed. Cheers, Boaz Boaz Shaanan, Ph.D. Dept

Re: [ccp4bb] Program or server to predict Kd from complex structure

Hi, PISA have something like this, I think, or at least deltaG estimate. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646

[ccp4bb] השב: Re: [ccp4bb] Curious electron density associated with Asp sidechain

Hi, it looks like gly-asp not asp-gly in this case, doesn'it? Cheers, Boaz הודעה מקורית מאת: Jonathan Cooper bogba...@yahoo.co.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: Re: [ccp4bb] Curious electron density associated with Asp sidechain Hello Tony is that

Re: [ccp4bb] refinement hanging--what am I missing?

thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin

Re: [ccp4bb] detectors on home sources

of service. This may mean quite often taking compromises and going perhaps not for the front-line state-of-art piece of equipment but rather for the sturdy, hard-working equipment. It worked for us very well. My 2p advice. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] The importance of USING our validation tools

with such a summary. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University

Re: [ccp4bb] Strange diffraction images

commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105

Re: [ccp4bb] just how bad can phases be and still help

, was it only when relatively better phases gave any interpretable density that it was known that the bad phases would help? -bryan Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] Twinning

to trace all the atoms and ligands. There is nothing much to build in the map too. Any suggestions to reduce the gap in R and Rfree. I couldn't use shelxl because of the resolution. Is it OK to stop refinement and submit the structure. with warm regards John Boaz Shaanan, Ph.D. Dept

Re: [ccp4bb] Summary: Symmetry of crystallographic stereographic projections?

Fax: +49-89-2180-76999 E-mail:    [EMAIL PROTECTED] *** Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] looking for a program

for a program (if there is one...) that would allow to list all interactions at a dimer interface (polar, ie hydrogen bonds and salt bridges, and non polar). Thanks in advance for your replies. Best regards, Fred. Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University

Re: [ccp4bb] nad woes - yet another question regarding ligand restraints

, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] fake images

or statistical analysis won't help you if you don't have access to the image.  This discussion started regarding a place for people who _want_ to deposit images; unfortunately some people aren't going to do it voluntarily. -Eric -- Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

picture, which I'm sure you'll find attractive. Please reply in private (i.e. not to the list) as this is a too serious issue. Kind regards,   Boaz Shaanan            - Original Message - From: Sehl Oediter sehloedi...@gmail.com Date: Wednesday, April 1, 2009 12:11 Subject

Re: [ccp4bb] Programs to detwin.

? Or there are some other good programs can do this? If the data has some pseudo-meroheral twin operators, can it be treated as same as merohedral operates? Thanks very much! Best Yang Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647

[ccp4bb] idiffdisp - two clicks to define a line does not work on a sector ?

are ignored by the indexing program. Saving the sector and reading it back in is not an option  in idiffdisp either, since it only suggests to save the sector as jpg. In ipdisp, which is no longer supported, this was possible.  Is it possible to add them to idiffdisp ? Cheers,     Boaz Boaz

Re: [ccp4bb] anisotropic/isotropic

could refine the macromolecule anisotropically and the waters isotropically it would result in better R values? Ivan -- I'd jump in myself, if I weren't so good at whistling.    Julian, King of Lemurs Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] MR from fo-fc

molecule. What are the file conversions do i need to do?  Can any one tell how to do this? Thanks in advance. yours sincerely, Murugan Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] rigorously compatible coordinate files

in the CCP4 suite, though one might exist. MOLEMAN2 doesn't seem suitable, either. Thanks, Charlie Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] Refmac bref MIXED failed

2010  15:28:12 #CCP4I MESSAGE Task failed Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] The color of GFP crystals?

much for your helpful information! Best wishes, * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax

Re: [ccp4bb] Free R with doubled cell edge

by convincing opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.  ~Max Planck Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647

Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues

! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Phone: 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

On 2/9/11 5:08 PM, Jon Schuermann wrote: I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better. Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University

Re: [ccp4bb] Liquid nitrogen resistant flooring

cracking.  Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick --   Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

Re: [ccp4bb] CNS and protein structure refinement

to be different from the value given by Refmac at the end of the refinement?   Rex Palmer   Birkbeck College Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

[ccp4bb] problem of conventions

Excuse my naive (perhaps ignorant) question: when was the abc rule/convention/standard/whatever introduced? None of the textbooks I came across mentions it as far as I could see (not that this is reason for or against this rule of course).     Thanks,    Boaz Boaz Shaanan, Ph.D

Re: [ccp4bb] problem with pdb its symmetry molecule

This intertwined conformation is very possible and is reminiscent of Trp repressor (at least in the view you provided). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype

Re: [ccp4bb] Data processing suggestion

Hi, You could try XDS and input your unit cell from one crystal, then decide whether you're happy with the outcome for the other crystal. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 Skype

Re: [ccp4bb] Problem running shelxC/D/E

They should reside in the $CBIN directory for the gui to see them, is that where you have them installed? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan

  1   2   3   >