Re: [ccp4bb] request for help about a 2-crystal drawing tool...

On Sunday, 25 August 2019 18:28:35 Laurent Maveyraud wrote: > Dear CCP4ers, > > a long time ago (something like 10 years, or even more), I used an applet > available on the internet for drawing small schematic 2D crystals (see > below). You had the possibility to draw a small motif (in my case s

Re: [ccp4bb] [OT] Structure-related pun needed urgently

On Thursday, 15 August 2019 13:42:10 Gerard DVD Kleywegt wrote: > Dear CCP4BB-ers, > > Once again I turn to you in my hour of need. I *urgently* need a > side-splittingly funny, and ideally punny, structure-related > sentence/statement/claim/expression to put in a speech bubble attached to a >

Re: [ccp4bb] Ligand identification

On Thursday, July 18, 2019 1:02:25 PM PDT Nicola Evans wrote: > > I have an unidentfied blob of density at a crystal contact region. I > > tried inputting a magnesium ion there, it was clearly incorrect but it > > improved the R-factors by 3, so I would really like to identify the > > correct molec

Re: [ccp4bb] Difference in the TLS origin calculation

On Saturday, 27 April 2019 06:35:11 Deepali Verma wrote: > Dear all, > > While depositing the PDB to RCSB, the following query was raised about the > TLS. Kindly advise to reporting the correct value of TLS origin > > *Query: *Please note that the reported TLS origin differs from the > calculated

Re: [ccp4bb] Normalization of B-factors

On Thursday, 09 August 2018 10:45:07 Pavel Afonine wrote: > > I (personally) think the best answer from these was to look at the > > TLS-subtracted residuals (ie. total B-factor - TLS component) — can’t > > remember who sent it, off the top of my head. > > > > TLS is just an approximation, sometim

Re: [ccp4bb] Python3 and MTZ

On Thursday, 07 June 2018 16:55:55 Markus Gerstel wrote: > On 6 June 2018 at 20:28, Ethan Merritt wrote: > > > On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote: > > > Right you are Kay. It would be very weird to start developing things on > > Python 2.7 right

Re: [ccp4bb] Python3 and MTZ

On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote: > Right you are Kay. It would be very weird to start developing things on > Python 2.7 right now. Its days are numbered: https://pythonclock.org/ I would take a contrarian view. Given the instability of python development, the promise to l

Re: [ccp4bb] Electron density

On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote: > Dear all, > > I am currently refining a structure and found a intriguing electron density > at the protein surface (pictures attached, the Fo-Fc map is contoured at > >3.5 sigma). My first candidates were molecules from my protein prep or > cr

Re: [ccp4bb] B-factor standardization

On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote: > Dears, > > everybody knows that B-factors may change amongst different crystal > structures and that they need to be standardized when different protein > crystal structures are compared. > > If I am not wrong, I remember that someone

Re: [ccp4bb] PDB redo and biased/unbiased R-free

On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote: > Dear all, > > I was looking at a 3 angstrom structure from 2015 with relatively bad > statistics, so I decided to look at the pdb-redo of said structure. > Surprisingly, pdb-redo statistics are even worse. You say "even worse", but the

Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

On Friday, 10 November 2017 05:29:09 Keller, Jacob wrote: > >>62500 is < 40^3, so ±20 indices on each axis. > 50Å / 20 = 2.5Å, so not quite 2.5Å resolution > > Nice--thanks for calculating that. Couldn't remember how to do it off-hand, > and I guess my over-estimate comes from most protein cryst

Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

On Friday, 10 November 2017 00:10:22 Keller, Jacob wrote: > Dear Crystallographers, > > I have been considering a thought-experiment of sorts for a while, and wonder > what you will think about it: > > Consider a diffraction data set which contains 62,500 unique reflections from > a 50 x 50 x 5

Re: [ccp4bb] A challenging Molecular replacement

On Tuesday, 18 July 2017 00:01:59 CDaddy wrote: > I am a structural biologist who is teaching X-ray crystallography. Recently I > noticed that BrlR structure (5XQL) was solved using molecular replacement > with a search model of very low similarity. I am very interested in this > structure becau

[ccp4bb] TLSMD server status

The TLSMD server has been bandaged and splinted and is back on its feet, if hobbling a bit. This is a short-term fix. Replacement hardware expected sometime next week. Go ahead and submit your jobs, but don't be too surprised if the server has a relapse. Thanks to everyone who offered to discuss

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

On Thursday, 26 January 2017 11:03:12 PM Claire Smith wrote: > Hello, > > I would like to ask a question related to a recent thread regarding > bad/missing density. > > I have used SAD to solve the structure of a protein at about 2.6Å > resolution. Phenix build a good portion of it (about 50%) an

Re: [ccp4bb] Calculation of generalised R-factor?

On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote: > Hi Dirk, > > > I want to check the validity of the refinement of anisotropic B-factors vs. > > TLS + isototropic B-factors using the Hamilton R-value ratio test as > > described in Ethan Merritt's paper "To B or not to B", Acta Cryst

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

On Monday, 28 November 2016 08:35:44 PM Pavel Afonine wrote: > I find Lothar's comments regarding H and RSRZ excellent! I would think of > it as a pretty much bug report. I hope developers at that end listen. This > goes very well in line with Phoebe's comment earlier today. I guess I'm a bit surp

Re: [ccp4bb] local coordinate uncertainty / SFCHECK questions

nt piece of the model from crystal A into your working model for crystal B, refine a bit (maybe only B factors or TLS), and see whether the resulting R/Rfree value are different from those you previously had for the crystal B model. You could then try the complementary excercise by placing th

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

On Wednesday, 20 May 2015 05:32:00 PM William G. Scott wrote: > > On May 20, 2015, at 5:38 AM, Randy Read wrote: > > > > Thanks, as always, to everyone for a thoughtful discussion! > > > Alternatively, as a scientific community, perhaps it is finally time for us > to untwist Clippy, bending hi

Re: [ccp4bb] strange pattern

On Thursday, 02 April 2015 02:21:48 AM Gert Vriend wrote: > The following article was rejected by 'our' journal... > > http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/april_fools__day_special_papers.htm > >

Re: [ccp4bb] A basic question about Fourier Transform

On Tuesday, 20 January 2015 10:18:35 PM Chen Zhao wrote: > Dear all, > > I am sorry about this slightly off-topic question. I am now a graduate TA > for crystallography course and one student asked me a question that I > didn't ask myself before. I don't have enough knowledge to precisely answer >

Re: [ccp4bb] Normal mode refinement

On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote: > Dear All, > Thank you very much for valuable suggestions and educating me on the normal > mode refinement. Actually, I am trying to refine a protein (cytosolic > domain and trans-membrane domain). I found a solution through PHASER and > de

Re: [ccp4bb] Space group numbers

On Saturday, 04 October 2014 10:26:51 AM Kay Diederichs wrote: > I do agree that in your use case it may be helpful to order a long as the symmetry is unknown. I also do understand that the H-M > symbols allow to describe the different settings, but this is a level of > complication that is not nec

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote: > Does anyone know if Molprobity has recently changed the standard bond lengths > and angles that it uses ? > > Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond > angle (deviations of 8-10 sigma) for AMP

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

On Friday, 13 June 2014 10:12:50 AM Tim Gruene wrote: > Hi Ethan, > > Maybe I miss something, but whenever an error in one of the cif-files > has been reported, be it directly to Garib, or publicly on the ccp4bb, > Garib (I assume) fixed very quickly - I don't quite understand why we > need a new

Re: [ccp4bb] Confusion about space group nomenclature

On Sunday, 20 April 2014 10:14:56 AM Ethan Merritt wrote: > On Sunday, 20 April 2014 01:35:33 AM Bernhard Rupp wrote: > > Hi Fellows, > > > > > > > > because confusion is becoming a popular search term on the bb, let me admit > > to one more: > >

Re: [ccp4bb] Confusion about space group nomenclature

On Sunday, 20 April 2014 01:35:33 AM Bernhard Rupp wrote: > Hi Fellows, > > > > because confusion is becoming a popular search term on the bb, let me admit > to one more: > > What is the proper class name for the 65 space groups (you know, those): > > > > Are > > (a)these 65 SGs the

Re: [ccp4bb] crystallographic confusion

On Saturday, 19 April 2014 02:52:38 PM Zbyszek Otwinowski wrote: > Why not improve "effective resolution" to include consideration of solvent > content? Due to constant packing density of proteins, it would become a > synonim (by appropriate transformation) to number of observations per > modelled

Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

On Tuesday, 04 March 2014 01:33:58 PM wu donghui wrote: > Dear Tim, > > Here I attached the config.log file for your help. I have tried to use > either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1), or > g++-4.2.1(/Applications/Xcode.app/

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

On Sunday, 23 February 2014 09:16:41 PM Andreas Förster wrote: > On 22/02/2014 10:15, Mark van Raaij wrote: > > But I would really want to make a general comment - not ALL structures > > can be better than the average! > Except structures from the Lake Wobegon Center for Structural Biology, > o

Re: [ccp4bb] Rmerge of Images

On Thursday, 13 February 2014 04:46:51 AM Keller, Jacob wrote: > Dear Crystallographers, > > Where can I find the definition of the R vs batch reported in scaling? > Specifically I am wondering whether it is cumulative (each new frame versus > all previous ones pooled together) or something else

Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote: > One thing I find confusing is the different ways in which d is used. > In deriving Braggs law, d is often presented as a unit cell dimension, > and "n" accounts for the higher order miller planes within the cell. It's already been

Re: [ccp4bb] TLS refinement and ANISOU records

On Thursday, August 08, 2013 01:51:34 pm Omid Haji-Ghassemi wrote: > Dear Robbie, Marcus and Reginald, > > Thanks again for your replies, I truly appreciate the help. > > The B-factors was set to 20 when performing TLS refinement so I don't > think that is the problem. > > I also tried Marcus's

Re: [ccp4bb] TLS refinement and ANISOU records

On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi wrote: > Dear all, > > I was about to deposit a few structures to the pdb when I noticed the mean > B-factors were larger than one might expect. > > All the structures were refined using TLS refinement. > > During refinement in Refmac t

Re: [ccp4bb] mmCIF as working format?

On Wednesday, August 07, 2013 04:54:39 pm Jeffrey, Philip D. wrote: > Nat Echols wrote: > > Personally, if I need to change a chain ID, I can use Coot or pdbset or > > many other tools. Writing code for > > this should only be necessary if you're processing large numbers of models, > > or have

Re: [ccp4bb] mmCIF as working format?

On Wednesday, August 07, 2013 04:00:16 pm Ed Pozharski wrote: > On 08/07/2013 05:54 PM, Nat Echols wrote: > > Personally, if I need to change a chain ID, I can use Coot or pdbset > > or many other tools. Writing code for this should only be necessary > > if you're processing large numbers of mod

Re: [ccp4bb] post to ccp4bb

On Monday, 22 July 2013, Katherine Donovan wrote: > Hi All, > > I have a data set that was collected to about 2.2A, which I have processed in > either P21 (to 2.4 A) or C2221 (2.25A). So I'm confused. You may not know what the spacegroup is, but you are processing the same spots either way. Why

[ccp4bb] How to disable auto-renaming of files in ccp4i refmac menu?

I dearly love ccp4i, but there is one aspect of the interface that drives me to distraction. When I type (or paste) an input file name (let's say input.mtz) into the refmac menu, ccp4i changes various output file names automatically according to some scheme that doesn't at all match my work flow.

Re: [ccp4bb] Definition of diffractometer

On Wednesday, June 19, 2013 11:11:01 am Edward A. Berry wrote: > Somewhere I got the idea that a diffractometer is an instrument that measures > one > reflection at a time. Is that the case, and if so what is the term for > instruments > like rotation camera, weisenberg, area detector? (What is a

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

On Sunday, 09 June 2013, Theresa Hsu wrote: > Dear all > > A question for the cross-trained members of this forum - for small sized > proteins, is NMR better than crystallography in terms of data collection > (having crystals in the first place) and data processing? How about membrane > protein

Re: [ccp4bb] anomalous scattering server down?

On Saturday, 01 June 2013, Edward A. Berry wrote: > Is Ethan Merritt's anomalous scattering page at: > http://www.bmsc.washington.edu/scatter/ > down or moved, or the firewall I'm behind is blocking it? The UW, in its infinite wisdom, scheduled a power outage today so that they could replace the

Re: [ccp4bb] atomic coloring for the color blind

On Friday, May 31, 2013 01:34:51 pm Phoebe A. Rice wrote: > I feel badly that one of my undergrads had trouble telling an O from a C in a > pymol homework set because he's color blind. (The assignment involved telling > me why the a GTP analog (GDPCP) wasn't hydrolyzed). > Is there a handy by-ato

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for "true multiplicity"?

On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote: > > The use of the term redundancy (real or otherwise!) in crystallography > is potentially misleading as the normal usages means superfluous/ surplus > to requirements. That may be true in the UK, but on this side of the pond "redundancy"

[ccp4bb] A crystallographer on Mars

The _New Yorker_ frequently publishes decently written articles on a huge variety of topics. Occasionally they come out with one about science, sometimes with a focus on a public policy issue, sometimes a biographical piece about a mainstream or not-so-mainstream scientist, sometimes a serialized

Re: [ccp4bb] CCP4 Update victim of own success

On Thursday, April 11, 2013 01:53:16 pm David Schuller wrote: > On 04/11/13 13:36, Ethan Merritt wrote: > > On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote: > >> Eugene - that's great. I too run a small suite of Macs (12) and was trying > >> to find

Re: [ccp4bb] CCP4 Update victim of own success

On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote: > Eugene - that's great. I too run a small suite of Macs (12) and was trying to > find a practical way of updating all those machines remotely. The command > line version of CCP4um will be very useful. Another option for a set of mach

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

On Sunday, 17 March 2013, Pavel Afonine wrote: > Hi Ethan, > > > I would place the expected resolution break-even point at more like > > 1.2 - 1.3 A. But that's only an expectation, not a rule to rely on. > > You should justify anisotropic refinement of a structure on the basis > > of its own pa

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

On Sunday, 17 March 2013, Pavel Afonine wrote: > Hi Sonali, > > regarding isotropic vs anisotropic parameterization of your individual > ADPs: apart from common sense and theoretical considerations, this is also > in great part software dependent. > > I can't speak for other programs, but for phe

Re: [ccp4bb] first use of synchrotron radiation in PX

On Saturday, 16 March 2013, James Holton wrote: > The first report of shooting a protein crystal at a synchrotron (I > think) was in 1976: > http://www.pnas.org/content/73/1/128.full.pdf > that was rubredoxin > > The first PDB file that contains a "SYNCHROTRON=Y" entry is 1tld > (trypsin), which

Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?

back to Fs somehow. Ethan > Maybe use old truncate with the notruncate option > Phil > > Sent from my iPad > > On 12 Feb 2013, at 18:48, Ethan Merritt wrote: > > > On Tuesday, February 12, 2013 12:39:57 am Phil wrote: > >> "Scale constant" in Aimless o

Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?

m nowadays, I would > > convert to a shelx hkl file and use xprep for the merging and statistics > > -- that's "painless". > > > > Cheers, > > > > Jens > > > > On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: > >> Hi all, >

[ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?

Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI

Re: [ccp4bb] B-factors

On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote: > Hi all, > > I have been refining twinned data (at 3.1 A resolution) using refmac. My R > and Rfree values are 19.6 and 26.2 respectively with NCS restraints and > isotropic B-factor refinement.. I am not sure weather it is a good id

Re: [ccp4bb] CASP ROLL needs your structures!

designating it to be a new fold" 2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011 Structure and genetic analysis of the arterivirus nonstructural protein 7α Ethan Merritt > The lack of such targets makes it probl

Re: [ccp4bb] About NCS and inhibitors

On Monday, January 07, 2013 12:10:17 pm Edward A. Berry wrote: > The idea is (whether it's valid or not) to apply the information from > both sites simultaneously. If the density is pretty ambiguous and one side > tends to drift off into an alternate conformation and the other drifts off > into ano

Re: [ccp4bb] vitrification vs freezing

On Thursday, November 15, 2012 10:14:54 am Raji Edayathumangalam wrote: > Hi Sebastiano, > > Elspeth Garman howls bloody murder everytime someone says they "froze" > their crystals. I think her issue is with the description of the process of > successfully flashcooling crystals in the presence of

Re: [ccp4bb] vitrification vs freezing

On Thursday, November 15, 2012 09:13:58 am you wrote: > > Hi folks, > I have recently received a comment on a paper, in which referee #1 (excellent > referee, btw!) commented like this: > > "crystals were vitrified rather than frozen." > > These were crystals grew in ca. 2.5 M sodium malonate,

Re: [ccp4bb] side chain density

On Friday, 09 November 2012, Faisal Tarique wrote: > Dear all > > i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22 > and 25 respectively..the Ramachandran plot shows 90% of the residues in the > most favorable region and with 6 residues in generously allowed and no > resid

Re: [ccp4bb] Ca or Zn

> Prof John R Helliwell DSc > > > > On 31 Oct 2012, at 04:53, Ethan Merritt wrote: > > > On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: > > > >> The coordination is indicative but not conclusive but, as I responded to > >> the

Re: [ccp4bb] Ca or Zn

On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: > The coordination is indicative but not conclusive but, as I responded to the > original poster, I think the best approach is to use anomalous scattering. > You can measure just below and above the Ca edge, Actually, you can't.

Re: [ccp4bb] PNAS on fraud

On Friday, October 19, 2012 10:12:44 am Colin Nave wrote: > This is worth looking at as well. Suggests most papers should be retracted! > http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 A paper claiming that all papers are false, by someone named Ioannidis? I wonder i

Re: [ccp4bb] PNAS on fraud

On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: > > Le Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)" > a écrit: > > I had a look to this PNAS paper by Fang et al. > I am a bit surprised by their interpretation of their Fig. 3: > they claim that

Re: [ccp4bb] anisotropic refinement

On Thursday, October 11, 2012 11:50:37 am Rex Palmer wrote: > Dear CCP4'ers > With the occurrence of more and more high resolution protein structures does > anyone know at present how many such structures have been successfully > refined anisotropicall?� When we tried to categorize refinement pr

Re: [ccp4bb] B-iso vs. B-aniso

On Monday, September 17, 2012 11:31:53 am Yuri Pompeu wrote: > Dear community, > > The protein model I am refining has 400 amino acids (3320 atoms). > Some real quick calculations tell me that to properly refine it > anisotropically, I would need 119,520 observations. Given my unit-cell > dimens

Re: [ccp4bb] Aimless and Pointless

On Wednesday, 12 September 2012, Cosmo Z Buffalo wrote: > Hi all, > > I am currently trying to perform a quickscale in iMosflm 7.0.9 after I > integrate in an R 32 space group. Unfortunately, both Pointless and Aimless > are both giving me a best solution space group of P 43 3 2. After analyzi

Re: [ccp4bb] Off-topic: Best Scripting Language

On Wednesday, September 12, 2012 07:32:54 am Jacob Keller wrote: > Dear List, > > since this probably comes up a lot in manipulation of pdb/reflection files > and so on, I was curious what people thought would be the best language for > the following: I have some huge (100s MB) tables of tab-delim

Re: [ccp4bb] Refmac: ADP is non-positive

). Residue 3 is the > lowest-numbered residue in its chain. B-factors of N, CA of residue 4 are > 38, 33A**2, respectively. Could refmac just be taking exception to the > missing N atom? > > -- Forwarded message -- > From: Ethan Merritt > Date: Tue, Jul 24,

Re: [ccp4bb] How to identify unknow heavy atom??

On Tuesday, July 24, 2012 10:22:18 am Nat Echols wrote: > On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba > wrote: > > 1- if i have anomalous peak of unknown heavy atom, How can i identify this > > heavy atom in general. (different methods) > > > > 2- in my case, i see anomalous peak in heavy ato

Re: [ccp4bb] Refmac: ADP is non-positive

On Tuesday, 24 July 2012, wtempel wrote: > CCP4ers, > > a log file from Refmac_5.7.0027 presents me with this line: > > > Problem with the ADP of the atom N A 3 ADP is non-positive > -1.7740907E+35 > > > I did not explicitely refine ADPs or TLS. > Should I modify my model when I

Re: [ccp4bb] Chiral volume outliers SO4

On Sunday, 15 July 2012, Dale Tronrud wrote: >There are good reasons for maintaining "order" in this human-induced > numbering scheme. A common operation is to superimpose two molecules > and calculate the rmsd of the positional differences. This calculation > is not useful when the Val CG1 a

Re: [ccp4bb] do you think it is interesting?

On Monday, June 18, 2012 02:06:46 pm Alexander Scouras wrote: > > I'm further racking my brain to figure out a biological implication of this > > behaviour, I thought something like plaque formation but I can't find > > support in literature. > > > There are a variety of domain swapped crystal

Re: [ccp4bb] Question on Symmetry Axis Notation Convention

On Thursday, June 14, 2012 12:06:13 pm James Stroud wrote: > Hello All, > > I would like to discuss symmetry axes, but I'm not sure what the notation > convention is. For example, I'd like to say something about a 2(1) along the > x-axis, but the phrase "the 2(1) symmetry axis along x" is a bit

Re: [ccp4bb] how to interpret DALI search results

On Tuesday, June 12, 2012 02:29:13 pm Jerry McCully wrote: > > Dear ALL; > > After we solved our structure by anomalous scattering, we did a DALI > search. Here are the results but it is not easy to draw meaningful > conclusions whether our structure represents a novel fold or is homolo

Re: [ccp4bb] lithium incorporation in refmac

On Friday, June 08, 2012 11:35:25 am Faisal Tarique wrote: > Dear all > > i have downloaded lithium coordinates for the density i guess is for > lithium but i think while refinement in refmac is not taking lithium into > the consideration. If you see density, it might not be lithium :-) > i wan

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

On Tuesday, 05 June 2012, Stefan Gajewski wrote: > Hey! > > I was just wondering, do you know of any recent (~10y) publication that > presented a structure solution solely based on MIR? Without the use of any > anomalous signal of some sort? A text search for "MIR" returns 1377 PDB structures ove

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote: >The resolution limit of the data set has been such an important > indicator of the quality of the resulting model (rightly or wrongly) > that it often is included in the title of the paper itself. Despite > the fact that we now want to

Re: [ccp4bb] Deposition of riding H

On Saturday, 12 May 2012, Yuri Pompeu wrote: > If you used riding hydrogens throughout refinement and arrived at a final > model that you believe best describes your x-ray data to a certain level of > accuracy (Rvalues, geometry, map CC, etc...) would you not be invalidating > the whole refineme

Re: [ccp4bb] P21221 to P21212 conversion

On Monday, May 07, 2012 02:00:43 pm Phil Jeffrey wrote: > On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt > > Scaling is done in a point group, not a space group. > > My quibble with this statement is that the output reflection data from > Scalepack differs depending on what sp

Re: [ccp4bb] P21221 to P21212 conversion

gt; > On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt wrote: > > > On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: > > > Hi all, > > > I was wondering if anyone knows how to convert the P21221 to P21212 > > > spacegroup in HKL2000. I scaled the data s

Re: [ccp4bb] P21221 to P21212 conversion

On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: > Hi all, > I was wondering if anyone knows how to convert the P21221 to P21212 > spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I > got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point gro

Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files

On Friday, April 27, 2012 11:23:13 am Florian Schmitzberger wrote: > Dear All, > > With my most recent PDBe deposition, in addition to the native data, I > had intended to deposit the anomalous data, used for structure > determination, and make it available for download. This turned out to >

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

On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: > If you want to make a big splash, then don't complain about > being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Cent

Re: [ccp4bb] mtz2cif capable of handling map coefficients

On Thursday, April 05, 2012 10:48:16 am Oliver Smart wrote: > > On Thu, 5 Apr 2012, Ethan Merritt wrote: > > > On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote: > >> Fc doesn't contain the weighting scheme used in the creation of the map > >> coeff

Re: [ccp4bb] mtz2cif capable of handling map coefficients

om an mtz or cif file containing Fo and Fc but no map coefficients. It is true that usually you want to have a value for the FOM or other weight avalailable also. cheers, Ethan > Phil Jeffrey > Princeton > > On 4/5/12 12:00 PM, Ethan Merritt wrote: >

Re: [ccp4bb] mtz2cif capable of handling map coefficients

On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote: > It seems that deposition of map coefficients is a good idea. > Does someone have an mtz2cif that can handle this? Maybe I missed something. What is accomplished by depositing map coefficients that isn't done better by depositing Fo

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

On Sunday, 01 April 2012, Kendall Nettles wrote: > > What is the single Latin word for troll? > > Kendall > According to Google Translate, it is Troglodytarum. But I'm dubious. I thought trolls lived under bridges rather than in caves. Except for the ones who inhabit the internet, of course.

Re: [ccp4bb] REFMAC5 residues with bad geometry

On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.) wrote: > >phenix.refine allows any number of alternate conformers. > > Hmm. quoting our old friends from the validation circuit: Where freedom > is given, liberties will be taken True, but... [warning: back of t

Re: [ccp4bb] Substituting zero vs. Fc for unobserved reflections

[Snipped from the full message, which is appended below] > The program that kept showing me two forms bound was not > substituting Fcalc for unobserved reflections. So, I turned on the option > to substitute Fcalc, and the minor form disappeared � the density looked > like it did in the second pro

Re: [ccp4bb] a question about protein sequences in the PDB

On Monday, 26 March 2012, Francois Berenger wrote: > Dear list, > > If I take all the fasta files for proteins in the PDB, > are the sequences complete? > > I mean, do they have holes sometimes (missing amino acids)? In theory the SEQRES records describe the sequence of the entity that was cryst

Re: [ccp4bb] sudden drop in R/Rfree

On Friday, 02 March 2012, Regina Kettering wrote: > Rajesh; > > I am not sure that you have a high enough data:refinement parameters ratio to > refine TLS. > It just adds more parameters to refine that can lead to over-refinement of > your model, > especially at the 3.3 A. I'm afraid you've

Re: [ccp4bb] Extra positive density seen after TLS refinement?

On Saturday, 18 February 2012, Naveed A Nadvi wrote: > Dear crystallographers, > > > > I am fairly new in crystallographic work and structure determination, but I > thought this would be the best place to post my questions. We had collected > structural data for a protein that diffracted to 3

Re: [ccp4bb] Crystal Structures as Snapshots

On Friday, February 10, 2012 12:51:03 pm Jacob Keller wrote: > Interesting to juxtapose these two responses: > > James Stroud: > >How could they not be snapshots of conformations adopted in solution? > > David Schuller: > > How could that possibly be the case when any structure is an average of a

Re: [ccp4bb] off-topic: "special" format for multiple sequence (protein) alignment

On Thursday, 02 February 2012, you wrote: > Dear members, > > Apologize for this off-topic question. I am looking for a protein sequence > alignment tool which is capable to generate a particular output file > similar to the attached format (please see the attached picture). I have > been looking

Re: [ccp4bb] writing scripts-off topic

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,C++, visual basic? What you descri

Re: [ccp4bb] New Faster-than-fast Fourier transform

On Friday, 20 January 2012, Jim Fairman wrote: > New Fourier transform algorithm supposedly improves the speed of Fourier > transforms get up to "a tenfold increase in speed" depending upon > circumstances. Hopefully this will get incorporated into our refinement > programs. > > http://web.mit.ed

Re: [ccp4bb] MAD

On Thursday, 19 January 2012, Ian Tickle wrote: > So what does this have to do with the MAD acronym? I think it stemmed > from a visit by Wayne Hendrickson to Birkbeck in London some time > around 1990: he was invited by Tom Blundell to give a lecture on his > MAD experiments. At that time Wayne

Re: [ccp4bb] Merging data collected at two different wavelength

On Wednesday, 18 January 2012, Soisson, Stephen M wrote: > But if we were to follow that convention we would have been stuck with > Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, > MuRDER. You could switch that to Multiple Energy Resonant Diffraction Experiment but

Re: [ccp4bb] RMSD of side chains

s > a lot. > > Secondly, for Ethan Merritt, I am seeking the information for comparing the > side chains RMSD for better comparison of structure. Please correct me if i > am wrong, i want to elaborate more on what i am thinking. If we have refine > the structure well so that issue of ro

Re: [ccp4bb] RMSD of side chains

On Friday, 13 January 2012, Appu kumar wrote: > Dear ccp4 users, >Would you please guide me how to calculate > the RMSD of side chains alone without considering C-alpha backbone. > Is/are there any program/programs availble which do this job. I want > to know the RMSD of

Re: [ccp4bb] Always Modelling Anomalous Signal

On Tuesday, January 10, 2012 02:46:21 pm Ian Tickle wrote: > Jacob, > > Actually the R factors including the Bijvoet pairs would be higher, > because the uncertainties in F(+) and F(-) are higher than that of > F(mean) by a factor of about sqrt(2). R factors will always be higher > for unmerged d

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