Re: [ccp4bb] mtz/cif file for depostion

Hi, I would try https://project-gemmi.github.io/wasm/mxdepo.html It worked nicely for me recently. Marcin Wojder, who wrote this package, will be happy to help you, I'm sure. Good luck, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105

Re: [ccp4bb] About model building

Hi, If you still have crystals left, you could soak crystals with KI3 and collect data at Cu wavelength for SAD phasing, which could help you to resolve the missing piece. Maybe. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Nov 4, 2023 10

Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

Hi, If you're using Sharp for phasing, it'll refine the positions and occupancies of the heavy atoms that Shelx has picked up in the first stage. I used Sharp a long time ago but I'm pretty sure it still works that way. My 2p. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion

Re: [ccp4bb] Ligand superposition!

Hi Rams, It's also worth looking into the Cambridge CSD suit. I'm pretty sure that there is a routine there for superimposing small molecules, i.e. ligands which will produce the matrices you need. How to put it on a script is another question. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life

Re: [ccp4bb] Ligand superposition!

will also bring the ligands to near superposition. -Using chimera/chimerax you can select protein residues within certain radius from the ligands, write out the pdb's and then perhaps superimpose those smaller pdb's. I have not tried this. Sorry I can't be of more help. Cheers, Boaz Boaz Shaanan, Ph.D

Re: [ccp4bb] British X-ray Crystallographers

Thanks for looking into this, Harry. Yes, I agree, optimism is the way to go. Best wishes, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On May 24, 2023 12:34, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: The

Re: [ccp4bb] British X-ray Crystallographers

Indeed! Will it perhaps be possible to watch the event by zoom? Or will a recording of it be availabe later on? Any idea? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On May 24, 2023 11:26, Harry Powell <193323b1e616-dmarc-r

Re: [ccp4bb] anomalous data usage

Hi Ian, The file that aimless/ccp4i produces is exactly as you describe. I noticed the weird output from aimless/ccp4i2 and hence don't use. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Mar 13, 2023 21:40, Ian Tickle wrote: Hi Gottfried

[ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel -- Forwarded message -- From: בעז שאנן Date: Dec 28, 2022 17:13 Subject: Re: [ccp4bb] Calculate charge on protein surface To: Rafael Marques Cc: Hi In ucsf-chimera you can "

Re: [ccp4bb] issue with running ccp4i2

Hi, Did you check the 'issues tab' on the ccp4 site? It lists remedies for ccp4i2 on various systems. It worked for me. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Dec 10, 2022 21:32, Prasun Kumar wrote: Hi Group I currently updated my

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Stephen, On top of Roberto's reply I was wondering whether the resolution of your structure and the ensuing s.d. of the bond length was taken into account by the refree. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Nov 28, 2022 19:29

Re: [ccp4bb] Copying NCS chain to heteroligomer

Hi Alessandro, Wouldn't it be easier/simpler to use the modified chain together with its (possibly) modified partner as a probe in MR to generate the completely modified 12mer? Just wondering. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Nov 17

Re: [ccp4bb] Regarding the correct space group identification

irradiated crystal volumes may enable to deal better with this nasty mixture of lattices. This is of course assuming that a search for different crystallization conditions has been exhausted. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Aug 1

Re: [ccp4bb] ccp4i2 qt error

Hi, Have a look at the 'known issues' tab on the ccp4 download page and you'll find solutions to the ccp4i2 problem for various OS. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Jun 24, 2022 12:21, hoh wrote: Hi I've update from ccp4-7

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, In case you don't have a cif file for the ligand, I would load the SMILES expression into acedrg (or use any other input option) to create a cif file which you can then read into Coot. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Jun 6

Re: [ccp4bb] Erica Saphire speaking at ALS Colloquium in 6 hours

Well said, Gerard. I join/support the plea. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On 8 Dec 2021 19:38, Gerard Bricogne wrote: Dear James, Thank you for this notification about what should be a captivating and inspiring talk

Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

Hi, Did you try to edit 'Model 1' to 'Model 0'? I seem to recall that it was reported on this bb as the solution to this problem. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On 7 Dec 2021 22:56, Yong Wang <3c4fc05cc53b-dmarc-r

Re: [ccp4bb] how to fix helices-sheets getting converted to coil,

Hi, As far as I recall (and I could well be wrong/not uptodate) Chimera reads the SS description on the input PDB and implements them. So you could perhaps edit the pdb to have the correct descriptions, as you wish. My 2p contribution. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion

Re: [ccp4bb] Problems with refining covalently linked heme cofactor

there has been a recent discussion on the issue. I'm sure Phenix people would guide through the necessary steps to get the Coot-Phenix combination to work. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bs

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Jun 2, 2021 16:59, Stefano Trapani wrote: Dear Stuart That does not work. "Transform coordinates" seems to move molecules, but not the crystal symmetry elements (no update of the crysta

Re: [ccp4bb] Analysis of NMR ensembles

and, not surprisingly, align usually with high B-factor regions in the corresponding crystal structures. In cases where such flexible regions are held by crystal contacts the situations would likely be different. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

Hi, Will it be possible to include the rama-z analysis in Coot (perhaps as a plugin)? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jan 18, 2021 22:47, Robbie Joosten wrote: Dear all, During the last CCP4 meeting, Oleg

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Hi all, Can someone point me to cases of glycoprotein structures in the PDB for which the old (traditional?) system of naming N or O linked chain was found inadequate? Thanks. Stay safe, Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Just curious, how does the result of the Phaser run  with the Alphafold model compare with a Phaser run using the Arcimboldo phased model as a probe? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Dec 4, 2020 00:32, Anastassis

Re: [ccp4bb] [RESOLVED]partially restrained mode?

Hi Bernhard, Always trust Google. A most powerful tool to unearth Garib's hidden hints .  Cheers,           Boaz      Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University

Re: [ccp4bb] Regarding difference in ITC and structure data

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

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot o

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi, Just in case nobody has pointed this out yet (which I doubt) "google ccp4 documentaion" or just "doc" will give you several lists+docs  of current and old ccp4 programs, included and absent from ccp4i2. Cheers, Boaz Boaz Shaanan, Ph.D. Department of Life

Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

Hi, You can try the SSM from the pdbe tools, also described in Krissinel and Henrick (2004), Acta D63, 366-380. It worked for us nicely on a similar problem of a dimeric structure. Cheers, Boaz. Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva

Re: [ccp4bb] visual mask editor - why

Hi Bernhard, Did you consider trying 'polder' in the phenix package? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On May 28, 2020 21:17, Bernhard Rupp wrote: Maybe I should explain an example: Say coot detects an unmodelled

Re: [ccp4bb] linux issue- Ubuntu specific?

noticed the erratic delay in ccp4i. I didn't notice it under 14.04 (my previous OS). Stay safe,           Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University of the Negev

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

Hi Artem, Indeed it seems, as you mentioned, that you have to go ahead and determine the structure, particularly if you've gone a few steps ahead already (pure protein, crystals, data?).  Good luck, Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer

Re: [ccp4bb] problem in structure solution of multidomain protein

Hi, One other option is to run MR in Phaser in one run with the tetramer made of the 4 monomers as model 1 and the single monomer as model 2. The gui offers this option and there is also an example in the documentaion.  Cheers, Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion

Re: [ccp4bb] Question about losing reflections when refining in PHENIX

refinement. There are several options in the data input part of the gui.   Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Oct 29, 2019 00:05, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: Hello, it

Re: [ccp4bb] tNCS incompatible with cell dimensions

Wouldn't c222 or c222(1) be included in the Phaser run if all orthorhombic sg's were requested? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On May 31, 2019 23:37, Diana Tomchick wrote: Your native Patterson

Re: [ccp4bb] Last few months updates, updated coot, ccp4i2, imosflm, etc

Hi, For now, until there is a complete new version, I think that if you pick up the latest build from the ccp4 site it includes all the updates. I could be wrong though, but the CCP4 people will confirm this (or not). Cheers,   Boaz     Boaz Shaanan, Ph.D

Re: [ccp4bb] cavities in protein structures

Hi Claudia, Another possibility is CastP: http://sts.bioe.uic.edu/castp/index.html They also have a Pymol plugin. I have not used this plugin since I'm displaying the CastP o/p files in UCSF-chimera which handles them nicely. Cheers,             Boaz     Boaz Shaanan, Ph.D

Re: [ccp4bb] Sugar-Pi-stacking

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

Re: [ccp4bb] Unknown electron density blob

Hi, Could it be a segment of peg3350?   Cheers,               Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University of the Negev  Beer-Sheva 84105

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

these days, and for good reasons, isn't it?   Best regards,                    Boaz   Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-Gurion University of the Negev  Beer-Sheva 84105

Re: [ccp4bb] XDS questions

Hi, I do this by editor (and cut / paste). Clumsy but works. Let me know if you find a more elegant way. Cheers, Boaz Original message From: Wei Wang Date: 21/11/2016 19:05 (GMT+02:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] XDS questions

Re: [ccp4bb] Model parts rearrangement

Hi Bernhard, symmatch in the ccp4 suite comes to mind but also any superposition program will superimpose your scattered pieces onto the relevant part of your reference structure, won't it? Cheers, Boaz Original message From: Bernhard Rupp (Hofkristallrat a.D.)

Re: [ccp4bb] Improving MR map contrast

Hi Rhys, Just to add onto Herman's suggestions: filling space with waters/atoms is actually what Arp-wArp is doing in the process of building the model. Perhaps you could also try that? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev

Re: [ccp4bb] Rfree below Rwork

Just wondering about Eleanor's interesting remark: would the Rf Rw go as low as reported by Wolfram (0.22) in case of a wrong space group? 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] Refmac refinement R factors going up..... TLS issue?

Hi Christian, I usually send the pdb back to the tlsmd server after any manipulation of the model just to be on the safe side. I'm not sure whether that'll make any difference in your case but it's perhaps worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences

Re: [ccp4bb] Residual density feature

, 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

Re: [ccp4bb] Auto-proteolysis

Hi, How certain are you that what you see is the result of auto-proteolysis and not proteolysis by a contaminating protease? Have you used protease inhibitors (of all sorts) during purification? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev

Re: [ccp4bb] CYS mod

Hi, As I've just written to David, maybe it's sulfenic acid (result of radiation damage?). I've had those in some cases. See attached scheme for the chemistry and other possibilities for Cys modification by oxidation. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion

Re: [ccp4bb] cutaway view of the electrostatic potential

to this address:chimera-users-requ...@cgl.ucsf.edu 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 972-8-646-1710 From: CCP4

Re: [ccp4bb] Residue positional validation

Would it not be a good idea to include EDSTATS in ccp4i? I couldn't find it there. 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] Basic Anomalous Scattering Theory

time ago, perhaps they do these days. 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] error message in xds

) and SPOTS.XDS (where spots coordinates are stored). Other things to check would be the origin coordinates. 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] Blob Game

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] imosflm error

Hi, I suggest you upgrade to ccp4-6.5 in the first place. I used to have this problem (or a similar one) with the initial 6.4 release but it has been fixed with later updates. In 6.5 it's completely gone (I'm using Centos 6.6) Cheers, Boaz Boaz Shaanan, Ph.D. Dept

[ccp4bb] השב: [ccp4bb] pdb2pqr generation

Hi, I don't recall having this problem with pdb2pqr through the apps link. Did you try it? If all fails I suggest that contact the apbs/pd2pqr support. They're very helpful. Boaz הודעה מקורית מאת abhishek jamwal jamwalabhis...@gmail.com תאריך: 09/12/2014 8:29 (GMT-05:00)

Re: [ccp4bb] Intensities and amplitudes

as the atomic model improves). I may have misunderstood you completely, but do you mean that the Fobs's will be recalculated as the model improves (this is where French-Wilson comes into effect, right)? Or only once during refinement? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] Question about enzyme behavior

consider using Parthon oil (or something similar) as cryo-protectant so it will coat your crystal in the glove box and will also reduce oxidation? Good luck, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa

Re: [ccp4bb] XDS

Hi, Another option to do it in xds (following advice of a Kay) is to rename the frames you don't like differently than the template. Boaz Original message From: Almudena Ponce Salvatierra maps.fa...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb]

Re: [ccp4bb] XDS

Hi, Also, if you go from XDS to aimless with the INTEGRATE_ASCII.HKL or XDS_ASCII.HKL file, aimless has an option to omit batches (frames) as you wish from scaling or merging. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev

Re: [ccp4bb] Reliable criteria to tell Anomalous or not?

Also, if you process your data using XDS, it'll give you good indication for the strength of the anomalous signal. I find the XDS and Aimless indications to agree quite well. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

Re: [ccp4bb] ATP library file in REFMAC

Or use Grade: http://grade.globalphasing.org/cgi-bin/grade/server.cgi which gives the correct bond length. 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

Re: [ccp4bb] off topic

a thought. Good luck with the reviewer. 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

Re: [ccp4bb] Jligand help

Hi, A trick that has worked for me a few times is to skip the regularization stage in Jligand, although some may argue that it's illegal. If your ligand/cofactor has a decent geometry without regularization it may well work for you too. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life

Re: [ccp4bb] Heavy Atom Phasing

for the SeMet crystals and just didn't get well diffracting crystals, 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: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

[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

[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] 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] 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

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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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