Re: [ccp4bb] TCL/TK and BLT distro for Mac Leopard

I've been fighting a similar problem here on linux. My solution was to "downgrade" the tcl + blt packages to use tcl version 8.4. Tcl version 8.5 is not working happily here with ccp4i. That still leaves me with a few CCP4 components that complain about version incompatibilities, but I assume tho

Re: [ccp4bb] Citations in supplementary information are invisible

On Friday 22 February 2008 08:11, William Scott wrote: > Hi Citizenry: > > This is worth reading: > > http://www.nature.com/nature/journal/v451/n7181/full/451887d.html > > Without knowingly doing so, I've short-cited coot and probably other > crystallographic software in this way. I hope one >

[ccp4bb] New higher-throughput server for TLSMD analysis

%% New higher-throughput server for TLSMD analysis %% http://skuld.bmsc.washington.edu/~tlsmd We have upgraded the TLSMD web server, and invite you all to try it out. The new server is faster, and can handle multiple jobs in parallel. It does additional pre-screening of sub

Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments

On Tuesday 04 March 2008 11:13, Stephen Graham wrote: > Hi all, > > I would like to generate a structure-based multiple sequence alignment > using 4 structures. I have already generated pairwise alignments for > each 'pair' of structures (6 alignments in all). Is there a program > out there that

Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

Of course, non-positive definite tensors may also be the result of a refinement that has simply gone bad. I'm not saying the model should be accepted without further inspection! Ethan Merritt [*] American readers: s/wooden/aluminum/ British readers:s/baseball/cricket/ &g

Re: [ccp4bb] intersection curve of cone with cylinder

On Thursday 20 March 2008 06:45, [EMAIL PROTECTED] wrote: > In topology, long time ago, I was taught that these are indeed > 'intersection curves of surfaces of the second order'. Emphasis on surface > being second order, not the curve. This was in Russian, which means that > the English terms may

Re: [ccp4bb] Rant: B vs TLS, anisou, and PDB headers

On Monday 31 March 2008 08:58, [EMAIL PROTECTED] wrote: > In the end, we're solving all these structures because we believe (or > at least hope) that they'll be useful for understanding > biology. That means that biologists should be able to understand > what we deposit. Agreed, but... > When

[ccp4bb] TLS analysis of sugars [ was Re: [ccp4bb] cryo-cooling]

On Tuesday 10 June 2008 07:15, Oganesyan, Vaheh wrote: > I apologize for using BB to address a person (Ethan Merritt, U. of > Washington). > His e-mail address mentioned on TLSMD page is not operational. I'm here, at the same Email address as always. > Good morning Ethan, &g

Re: [ccp4bb] birefringent spacegroups

On Thursday 12 June 2008 11:19, Philippe DUMAS wrote: > Hello, > > A short comment of historical interest: the first theory about "double > refraction in crystals" (with explicit calculation of the index ellipsoid) > goes back to 3 memoirs by A. Fresnel in 1821 and 1822. So, we are even in > "olde

Re: [ccp4bb] B-factor problem

On Tuesday 17 June 2008 09:08:24 am Sampath Natarajan wrote: > Dear All, >I am refining a structure with 2.5A resolution by refmac5. I > could find the solution by MR using molrep. After fitting the model, I > refined the structure again with 0.3 weighting term, but the output PDB file

Re: [ccp4bb] Friedel vs Bijvoet

On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote: > Please some one tells me if I'm wrong ... but I though that indeed one > is NOT supposed to measure anomalous difference from reflections h and > h' if those are related by one of the symmetry operator of the point > group... This statement

Re: [ccp4bb] Friedel vs Bijvoet

On Thursday 26 June 2008 11:35:31 am Bernhard Rupp wrote: > Let's try this again, with definitions, and pls scream if I am wrong: > > a) Any reflection pair hR = h forms a symmetry related pair. ??? Maybe you meanh' = hR >R is any one of G point group operators of the SG.

Re: [ccp4bb] 2D deviation plot

On Thursday 17 July 2008 09:48:08 Shawn Leeds wrote: > Dear all, > > I am trying to generate 2D Ca deviation plots for my superimposed molecules > as needed for publication. I am wondering what is the program of choice for > such a purpose? I tried Lsqkab in CCP4, but wasn't sure what's the most

Re: [ccp4bb] Rwork and Rfree in Sfcheck

On Monday 11 August 2008 16:54, Lisa Wang wrote: > Hello all, > I have a complex structure with resolution 2.7A The total molecular weight > is 80KD, and about 10% is disordered. I refined this structure to R and > Rfree 25.5% and 29.7% with CNS. I also tried refmac5, but the R and Rfree > have no

Re: [ccp4bb] truncate ignorance

On Monday 08 September 2008 12:30:29 Phoebe Rice wrote: > Dear Experts, > > At the risk of exposing excess ignorance, truncate makes me > very nervous because I don't quite get exactly what it is > doing with my data and what its assumptions are. > > From the documentation: > ==

Re: [ccp4bb] truncate ignorance

On Monday 08 September 2008 13:29:24 Jon Wright wrote: > Borhani, David wrote: > > ... > > but I think pretty much everyone has converged on using it for the > > past many years. > > Many small molecule crystallographers seem to refine on intensity and so > avoid need this procedure. I would ra

Re: [ccp4bb] disulfide bonds, SE sample, and Xray absorption edges

On Thursday 25 September 2008 08:45:10 Michael Jackson wrote: >   This data was collected at 0.97960 Angstroms which is close to the peak >   Xray absorption edge for Se but does anyone know if a disulfide has any >   absorption edge overlapping here? http://skuld.bmsc.washington

Re: [ccp4bb] refmac and average B factors

On Saturday 04 October 2008 18:32:00 Engin Ozkan wrote: > Hi everyone, > > I was in the middle of creating a "Table 1" for a finished structure and > was puzzled by one number. It is the average B factor, especially in > the case of TLS-refined structures. In this case, the average reported >

Re: [ccp4bb] Choosing TLS groups.

On Wednesday 12 November 2008 02:54:54 Ian Tickle wrote: > > All - I was just in a discussion about TLS and one thing that came out > that I hadn't been aware of is that for the Biso restraints Refmac > restrains the difference between the 'residual' Bs, i.e. with the TLS > contributions subtracte

Re: [ccp4bb] Program to fill unitcell randomly

On Monday 01 December 2008 10:28:34 Edward A. Berry wrote: > Ethan A Merritt wrote: > > On Friday 28 November 2008, Mueller, Juergen-Joachim wrote: > >> Dear all, > >> does anybody know a program to > >> fill an unit cell a,b,c randomly by an arbitrary number > >> of spheres (atoms)? > > > > First

Re: [ccp4bb] Program to fill unitcell randomly

andomly > chosen sample from a uniform probability distribution, but it is this > sample that the OP is requesting- so I would rephrase your question: > does he want _a random sampling from_ a uniform probability distribution > throughout the lattice, or ... > Ed > > Ethan Merrit

Re: [ccp4bb] tortion angle restraints in REFMAC

On Thursday 04 December 2008 11:50:30 Huiying Li wrote: > Thank you all for suggestions and explanations. I did not make it clear. The > tilt angle I wanted to restrain is the one from a C-OH bond to a plane > (The C is in the plane). The O atom of OH group is not in the planar > restraint in th

Re: [ccp4bb] refining anisotropy B factors on only a subset of atoms

On Tuesday 09 December 2008 11:22:04 Joseph Ho wrote: > Hello, > > I have a refined 1.8A structure that I wonder if I could squeeze out some > anisotropy information. I did TLS refinement on the protein, and it helped my > Rfree. But I would like to ask a biological question based on the thermal

Re: [ccp4bb] XAS software

On Wednesday 17 December 2008 14:26:32 Eugenio De la Mora wrote: > Hi, > I have some XAS spectra but I'm new in the area. I'm looking for a free > software. I just want to normalize the data and compare between them. Any > suggestion? http://depts.washington.edu/uwxafs/ -- Ethan A Merritt Bi

Re: [ccp4bb] Depositing coordinates with riding hydrogens

On Wednesday 17 December 2008 15:53:42 Jonathan Winger wrote: > Hi all- > > Just wondering what the consensus is - should a structure refined with > riding hydrogens be deposited with the coordinates for the hydrogens > included? One could argue that, since they were used in the > refinemen

Re: [ccp4bb] Fwd: Twinning

On Tuesday 06 January 2009 08:35:19 Stephen Hare wrote: > Dear All, > > We are currently working on a structure of apparent P21 symmetry which > has been solved by molecular replacement. The data are to 2.7Å but the > Rfree will not drop below 30%. The density is clear for the model we > hav

Re: [ccp4bb] OT - Software articles / databases

On Friday 09 January 2009 10:11:55 Lucas Bleicher wrote: > I've been compiling a reference database and I've just noticed that it's > quite difficult to automatically retrieve references for most articles on > crystallographic software. Has anyone noticed that? > It seems that, for some reasons,

Re: [ccp4bb] structure (factor) amplitude

On Monday 12 January 2009 02:42:43 Ian Tickle wrote: > Also I did a 'Google vote' for the two terms. 'Structure amplitude' has > 11300 hits. 'Structure factor amplitude' has only 4750. So all round I > would say that 'structure amplitude' wins by a considerable margin. The field of crystagoogl

Re: [ccp4bb] structure (factor) amplitude

e amplitude." > >> > >> (1950 ed., Ch II, 1a (p27)) > >> > >> JPK > >> > >> *** > >> Jacob Pearson Keller > >> Northwestern University > >> Medical Scientist Training Program > >> D

Re: [ccp4bb] X-ray photon correlation length

On Thursday 29 January 2009 10:59:23 Bernhard Rupp wrote: > Ok, following seems to be correct: > > > > a) interaction length = mean free path : relevant for absorption > > b) correlation length = time correlation between photons : relevant for > multi-photon scattering > > c) c

Re: [ccp4bb] protein folds

On Wednesday 25 February 2009 08:20:14 Jayashankar wrote: > Dear Folks, > > The last novel proteins fold were from the yr 2007(pdb statistics), > From 2007 to till date no novel fold has been identified, If you reached this conclusion by looking at the PDB web site, you should note that the site

Re: [ccp4bb] images

On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote: > Dear all > > Before going into and trying to find a technical solution to the > problem it would be good if decide if we need images. As far as I know > if we face with a problem to solve and we know that it is necessary to > solve

Re: [ccp4bb] Crick-Magdoff and anomalous

On Monday 23 March 2009 14:34:24 Peter Zwart wrote: > Hi, > > > > If we then require that the rms change in intensity be greater than the > > average noise, then we can write down the requirement: > > sigma(I_P) < rms(deltaI) > > > . > > I_P/sigma(I_P) > 1.3*sqrt(MW/N_H)/fpp > > one can actually r

Re: [ccp4bb] two identical proteins in one asymmetric unit

On Tuesday 24 March 2009 12:20:17 Mischa Machius wrote: > Having dealt with quite a few cases of more than one molecule in the > AU (including a couple of dreaded 12-meric assemblies... bleah), I am > still looking for the best way to identify proper NCS operators for > the myriad of potentia

Re: [ccp4bb] Halide soaking

On Tuesday 31 March 2009 09:57:13 Jose Antonio Cuesta-Seijo wrote: > Hi! > > Normally the cell parameters, etc change very very little. You'll > only know if the bromides got in at the synchrotron by looking at the > fluorescence spectrum That won't help, normally. It only tells you that th

Re: [ccp4bb] Eleven plausible phasing elements remain unused

On Wednesday 01 April 2009 07:21:16 Thomas Womack wrote: > A perusal of the PDB reveals that the game of Periodic Table bingo still > has eleven rounds to run: > > scandium, titanium, germanium, zirconium, niobium, neodymium, > dysprosium, thulium, hafnium, bismuth and thorium remain absent from P

[ccp4bb] Cross-crystal density averaging and/or refinement

Hi all, I have an interesting problem case at the moment. We have crystallized the same 2-domain protein in two different, i.e. non-isomorphous, crystal forms. There is a decent homologous structure for one domain (about 40% of the total), but no known homologous structure for the larger second

Re: [ccp4bb] X-ray fluorescence: numbers for fluorescence lifetime and quantum yield

On Monday 20 April 2009 16:33:57 Jacob Keller wrote: > Hello Crystallographers, > > Is the assumption correct that x-ray fluorescence is exactly the same > process as occurs in the UV-vis range, but simply with higher-energy > photons? Yes. > If so, does anybody know of a source for number

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

On Wednesday 22 April 2009 09:23:19 Jacob Keller wrote: > Hello All, > > What is the reason that x-ray fluorescence is neglected in our experiments? > Obviously it is measureable, as in EXAFS experiments to determine anomalous > edges, > but should it not play a role in the intensities as well?

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

On Wednesday 22 April 2009 13:22:41 marc.schi...@epfl.ch wrote: > Quoting Ethan Merritt : > > > On Wednesday 22 April 2009 09:23:19 Jacob Keller wrote: > >> Hello All, > >> > >> What is the reason that x-ray fluorescence is neglected in our experiments?

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

On Friday 24 April 2009 11:28:16 Jacob Keller wrote: > Dear Dr. Holton and CCP4BBers, > > Are you saying that a resonant event is always accompanied by a fluorescence > event? If that were true, wouldn't the resonant event end up manifesting as > *negative* scattering component from the resonant

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

oratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-kell...@northwestern.edu > ******* > > - Original Message - > From: "Ethan Merritt" > To: "

Re: [ccp4bb] Computer hardware and OS "survey"

On Friday 01 May 2009, Link,Todd M wrote: > My home institution, in effort to cut costs, is making an effort to push > those of us on Macs onto PCs. Up till now they have been very generous via a > lease program for computer hardware, but that is changing given the current > economics. The ins

[ccp4bb] Another pointless question

I was very surprised recently when a run of pointless chose to transform my data into spacegroup I2 [*]. Here are excerpts from the output log: Selecting space group I 1 2 1 as there is a single space group with the highest score Space group confidence (= Sqrt(Score * (Score - Ne

Re: [ccp4bb] phasing with se-met at low resolution

On Wednesday 13 May 2009 09:30:06 Jacob Keller wrote: > > The reason is that you've missed out one important term: the atomic > > displacement parameters (B-factors), which describe a combination of > > thermal motion and positional disorder between unit cells. > > A somewhat niggling point: isn

Re: [ccp4bb] phasing with se-met at low resolution

On Wednesday 13 May 2009 10:22:54 Patrick Loll wrote: > Greg Petsko's group did something like this about a billion years ago > (yet, strangely, I remember the paper, even though I'd be stumped if > you asked me what I had for breakfast...) > > They covered the range from room temp down to ver

Re: [ccp4bb] phasing with se-met at low resolution

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

Re: [ccp4bb] [offtopic?] putting b-factors from two pdbs on the same scale and interpretation

On Friday 22 May 2009 11:10:16 Francis E Reyes wrote: > Hi all, > > Maybe this is more of a statistics/normalization question, but say you > have the same molecule crystallized in two different states. How would > you put their refined b-factors (directly from the pdb) on the same > scale an

[ccp4bb] mtz2various is broken [ was: Another pointless question ]

it is converting reports * Space group = 'I 1 2 1' (number 4005) cheers, Ethan > Keeping the obliquity of the cell small has some advantages: it may > make map viewing easier, and improve the accuracy of map interpolation > in programs which are a bit ca

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

1 'X, Y, Z' > 2 '-X, Y, -Z' > 3 'X+1/2, Y+1/2, Z+1/2' > 4 '-X+1/2, Y+1/2, -Z+1/2' > > The only thing I see is different is that your space group is shown as > 'I121' whereas mine is just 'I2' > > Hope this

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

On Thursday 11 June 2009, Ian Tickle wrote: > > -Original Message- > > From: Ethan Merritt [mailto:merr...@u.washington.edu] > > Sent: 11 June 2009 00:35 > > To: Ian Tickle > > Cc: CCP4BB@jiscmail.ac.uk; Phil Evans > > Subject: Re: mtz2various is brok

Re: [ccp4bb] PDB Validation Server

On Monday 06 July 2009, Cale Dakwar wrote: > Dear colleagues, > > Please excuse these naive questions but I am new to the field of structural > biology and need to ask it. > > 1) By submitting my structure to the PDB Validation Server for precheck and > validation, will my structure become public

Re: [ccp4bb] Best 3D stereo combination

On Saturday 11 July 2009, Warren DeLano wrote: > Along those lines, did anyone see "Up" in Stereo 3D? Does stereo 3D enhance > the experience enough for this to strike you as more than just a passing fad? > The future (cost) of stereo 3D molecular visualization may well lie in the > response o

Re: [ccp4bb] MAD wavelength

On Thursday 16 July 2009 10:15:51 Jerry McCully wrote: > > Dear All: > > Next week we are going to try some seleno-Met labeled crystals. > > We checked the literature to try to find out the peak wavelength that > has been used for SAD or MAD data collection. But they are slightly diff

Re: [ccp4bb] Scalepack error model?

On Friday 17 July 2009 11:40:09 Richard Gillilan wrote: > Does anyone know of a detailed rigorous discussion of how the > scalepack error model/Bayesian reasoning works? The scalepack manual > has no equations for this. I wouldn't call it a detailed rigorous discussion, but the equations are g

Re: [ccp4bb] SAD questions

On Wednesday 22 July 2009 10:03:19 Jacob Keller wrote: > I had thought that "dispersion" might be an allusion to "dispersive > differences" > which occur between corresponding amplitudes collected at different > wavelengths > due to differences in anomalous scattering. No. These terms were in

Re: [ccp4bb] *adobe-courier-medium-r*--8* font again: hklview

On Thursday 23 July 2009 04:57:58 Boaz Shaanan wrote: > Hi all, > > This has been brought up before but I'm not sure whether any solution has > been suggested and if so, what it was. > > hklview complains: > > ** xdl_view error in routine xdl_open_view ** > ** Unable to load *adobe-courier-me

Re: [ccp4bb] advice on laptop for crystallography

On Tuesday 28 July 2009 09:44:42 Nathaniel Echols wrote: > On Tue, Jul 28, 2009 at 8:05 AM, Salgado, Paula > wrote: > > Also, I did a little research and it seems few laptops could deal with the > > resolution requirements for HKL2000 - any thoughts on that as well? > > This is really still a pr

Re: [ccp4bb] space groups not supported by Refmac5

On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote: > Hi, > > I have a question; recently I have encountered a few space groups which are > not supported by Refmac5. Examples include I2 and P21221. This is not correct. Refmac is perfectly happy with these settings, although there are som

[ccp4bb] How to work around strange naming XYZIN convention?

Not sure this is the right place to ask, but... I'm trying to chain some ccp4 programs together via a script. It creates temporary files with arbitrary names based on the process id. The problem is that when I try to pass one of these files to the next program in the chain, as in: tlsanl XYZIN

Re: [ccp4bb] How to work around strange naming XYZIN convention?

tation it doesn't let you remove the extension altogether. Perhaps I didn't try the right thing? Given the hint to look in ccp4_general.c, I may be able to fix that. thanks, Ethan > > HTH > Martyn > > On Mon, 2009-08-24 at 17:30 -0700, Ethan M

Re: [ccp4bb] anisotropic temp for H2O

On Thursday 27 August 2009, Elad Binshtien wrote: > Dear all, > I run refmac5 on TLS & restrained refinement mode. my pdb input file contain > anisotropic temp for the amino acid and isotropic temp for the cofactors and > water. The refinement parameters is set on mixed isotropic/ anisotropic tem

Re: [ccp4bb] attachments

On Tuesday 15 September 2009, Ian Tickle wrote: > Yes, obviously it doesn't provide full equation formatting capabilities, > as in LaTeX for example, but at least one can type or paste in equations > containing for example the Greek 'sigma' character (upper or lower case > of course) or the 'square

Re: [ccp4bb] bond lengthening in atomic resolution structure

On Wednesday 16 September 2009 11:19:11 Ivan Shabalin wrote: > Dear all, > > I have an atomic resolution (1.1Å) structure of enzyme with the bound > cofactor NAD. During the analysis of the refined structure I found that > important double C=O bond of the cofactor in the active site was slightly >

[ccp4bb] Format issue with TLSIN/TLSOUT files - probably explains some refmac problems

Hi all, I have run into an issue that affects a number of CCP4 programs (and my own code as well). The problem Programs that produce TLSOUT descriptions of TLS parameters create a file using the equivalent of Fortran format (9F8.4) Here are two examples: TLS RANGE 'A 209.' 'A 220

Re: [ccp4bb] I compressed my images by ~ a factor of two, and they load and process in mosflm faster

On Friday 18 September 2009 12:47:20 Chavas Leo wrote: > Dear all -- > > I cannot remember exactly, but I thought we had a long discussion on > the rightness of using compressed images, especially when considering > the loss of information while doing so. > -- Leo -- > > On 18 Sep

Re: [ccp4bb] Format issue with TLSIN/TLSOUT files - probably explains some refmac problems

sn't specifically give a Fortran format statement > for TLS parameter, in it's discussion of REMARK 3 it often shows > a line of column numbers. I presume those lines indicate that > column numbers are important even for data in REMARK 3. > > Dale > > > Ethan Me

Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment

On Friday 16 October 2009 15:49:16 Demet Arac-Ozkan wrote: > Dear All, > > I have a few questions about protein structure and fold. I will appreciate > your suggestions: > We have the crystal structure of a protein and it looks like it might be a > new domain. > > 1) Our structure looks like t

Re: [ccp4bb] Difficult molecular replacement in R32 with pseudo translation

On Monday 19 October 2009 12:43:43 Jerry McCully wrote: > > Dear All: > > I got a problem with a data set in R32 space group with a resolution > of 2.6. > Pointless indicated that the space group was R32 and phenix triage showed > that there was a pseudotranslation in the ASU. > > My p

Re: [ccp4bb] Sigma Cutoff in HKL2000 Data Processing

On Thursday 22 October 2009, protein.chemist protein.chemist wrote: > What is the Sigma Cutoff that one should use for Data Processing using > HKL2000. You need to narrow your question. Which "sigma cutoff" are you talking about? Do you mean the one on the "Index" panel? It controls the automati

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] 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

[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] 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

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

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