[ccp4bb] question about DM

Hi all, Just a (naive?) question: how does one manage to introduce (and deal with) improper non-crystallographic symmetry in DM ? Or does one has to go to DMmulti for that (because, by definition, going from one crystal form to another crystal form is improper NCS) ? Ta, F. Vellieux

Re: [ccp4bb] Regarding refinement in Refmac5

Hi there, Not much information provided. How was the initial model refined ? Phenix ? It could be a problem with the Refmac refinement protocol (difficult to say with so little information) if you switched from Phenix to Refmac. How certain are you 1 - of the space group; 2 - that the crysta

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

Do you mean we should crush the helmets and solve the structure of the resulting powder blue coloured powder by crystallographic methods ? Sounds like a good proposal to be put forward to the UN to help them get rid of their used helmets ! David Schuller wrote: On 07/04/12 08:03, Vellieux

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

The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? F.V. Boaz Shaanan wrote: Et alors, what wil

[ccp4bb] information received through the AFC: iycr2014

Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux IYCr-FR.pdf Descript

Re: [ccp4bb] how to get phase of huge complex

Hi Lisa, hi all, Please do not discard the alternative method(s) of "conventional" heavy atoms. Co-crystallisation or heavy-atom containing mother liquor soaks. You may remember that "monster" complexes have been solved in the past by such methods, and sometimes there are difficulties in cryst

Re: [ccp4bb] P321 space group reindex problem

12 07:55, Vellieux Frederic wrote: Hi there, But: trigonal (and hexagonal) space groups "are" (usually?) polar. The cell axis "c" can go "up" or can go "down", and in order to get a consistent indexing you need to check both indexing systems

Re: [ccp4bb] P321 space group reindex problem

Hi there, I am not certain that the thread is "P321 space group reindex problem" any more. But: trigonal (and hexagonal) space groups "are" (usually?) polar. The cell axis "c" can go "up" or can go "down", and in order to get a consistent indexing you need to check both indexing systems whe

Re: [ccp4bb] phaser: high z score but no sol

Hi, If you have the correct solution, clashes may be due to loops. It may be an idea to clip these off for the molecular replacement calculations (loops might be shorter in the structure-to-be-solved than in the search model, they may have different conformations in the structure-to-be-solved

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

Hi, I think this practice (requesting the data) is getting more and more common these days with some "scientists" having published fake structures. You are far more protected from scientific misconduct when you provide the data to referees (this takes place through an editorial system - you s

Re: [ccp4bb] Temp Fact Variance Analysis

Typo (my fingers type faster than my brain...) Original Message Subject:RE: [ccp4bb] Temp Fact Variance Analysis Date: Thu, 1 Mar 2012 14:56:06 + From: Oganesyan, Vaheh To: Vellieux Frederic References: <4f4f8cb1.1070...@ibs.fr> Fred,

Re: [ccp4bb] Temp Fact Variance Analysis

Hi, You could try to lower the threshold used to contour the maps for these side-chains (middle mouse "button" if you have a 3 button mouse with a wheel in the middle). Quite often such side chains have lowish electron density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc ma

Re: [ccp4bb] MTZ file

Hi, The refinement program generates an mtz file with map coefficients (including difference Fourier coefficients) so you should use that one for model rebuilding in coot; for the next refinement rounds, at the beginning of each round you should provide the initial mtz file coming from data pr

Re: [ccp4bb] off-topic:schematic representations for secondary structure

I believe Procheck generates drawings such as those. It generates PostScript files, and if you need to have (eg) jpg files, a PostScript interpreter, screen capture and there you are (Gimp to select only the areas you're interested in) HTH, Fred. WENHE ZHONG wrote: Dear memebers, Thank yo

Re: [ccp4bb] MAD

For those of you interested, the reply to Tassos' question can be found here: http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system (on-line) as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file). McLaughlin, Terry and Zelinka. And

Re: [ccp4bb] MERGING THREE DATASETS

There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites w

Re: [ccp4bb] Movements of domains

A mixture between mathematical significance and biological significance as a part of the reply: you should also take into account the thermal vibrations of the atoms present in that domain, i.e. the "thermal ellipsoids" when you have one of the representations of anisotropic temperature factor

Re: [ccp4bb] raw data deposition

I must "say" that there were some emails exchanged between me and Gerard later, in which I pointed out that I wasn't against deposition of images (data frames). In fact, if SR sources kept user's data there would be one more structure from here in the PDB: HDD failure here, the data on a mirror

Re: [ccp4bb] raw data deposition

D Bonsor wrote: and allow someone else to have ago at solving the structure. I'd be careful there if there was a motion to try to implement a policy at SR sources (for academic research projects) to make it compulsory to publically release all data frames after a period (1 year ? 2 years ?

Re: [ccp4bb] Biological assembly

Hi, If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. N

Re: [ccp4bb] Phenix building residues not found in input sequence file

Could you have an unexpected "small subunit" (or some other situation) giving additional density that Phenix is building into ? In other words, how sure are you of what is present in the crystal ? This is because I remember the enzyme methanol dehydrogenase where there was a small subunit which

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

Just to add to what has been "said" (written) before: coiled coiled or simply helices can be very problematic for M.R.. Human sacrifice has never given any positive result (as reported in the literature as far as I know), but "heavy atom sacrifice" could be attempted ("heavy atom" includes in

[ccp4bb] important information for scientists with samples travelling via Lyon or Grenoble airports

Could be of importance to those who have to use the Lyon or Grenoble airports (to ship in or out), check out the update from Sept. 27, 2011. http://www.ill.eu/users/user-guide/safety/important-instructions-for-biological-samples/ Fred.

Re: [ccp4bb] Structure problem

Hi there, In crystallography there are so many places where you can have problems (and need to solve these problems) that I cannot list them all. "There is no twinning in the data" - you probably mean "the data does not seem to indicate the presence of twinning but there might be twinning";

Re: [ccp4bb] Crystypos [WAS: [ccp4bb] Mac OSX 10.7 Lion]

Well in fact, it all depends on the type of detector these small angels end up on and on the speed of this "godly" radiation. Only once you have considered both these elements can you say "poor little things". My 2p worth. Fred. Ed Pozharski wrote: The best X-ray related typo I ever seen was

Re: [ccp4bb] omit map calculation in CCP4

sadaf iqbal wrote: Hello everyone, Do anybody know the correct procedure for calculating omit map in CCP4, if one need to reduce the bias from the Molecular Replacement structure. I am confused about the two options, one is fft map calculation while the other is OMIT map calculation in Map &

Re: [ccp4bb] No reflections in resolution bin???"

james09 pruza wrote: Dear CCP4BBers, Refmac is giving the error " No reflections in resolution bin???" It seems there is no SigFP column. I wonder how to fix the problem. Thanks in advance. James If the error is indeed due to a missing SigFP column, there are 2 ways to go about it I

Re: [ccp4bb] Newbie Installation Question

Quoting you: "I type ccp4 and I get no error", what happens if you type "ccp4i" (followed by carriage return) ? Yuri wrote: I downloaded the package for RHEL5. My default shell is sh. But I can change environments. I have progrmas that I must run in tcsh. I tried sourcing sh and csh setups.

Re: [ccp4bb] Phaser and Molrep gave different solutions

Hi, It's not a bad idea to read the Phaser manual for molecular replacement; see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement Soon after the start, in a table on the right hand side, there is: TFZ score < 5, have I solved it ? No. Hence with a TFZ score of 3.8 you do not

Re: [ccp4bb] Data from old tapes

Plenty of old drives at ESRF, for that purpose. If you don't find any other way, I could always read them there (the ESRF is "in my backyard") and burn the data to DVD for shipping (or upload to megaupload - but our gov't is hunting down people who use such services, they think megaupload and o

Re: [ccp4bb] Strange density in arginine

The distance to your modelled water seems to be in agreement with an ionic interaction. What are the components of all buffers in the crystallisation components ? Fred. ruheng wrote: > Dear all, > > Recently we are working on an archaebacteria protein which was > expressed and purified from /E.co

Re: [ccp4bb] hello

Hi, The R-factor you mention, is it an R-factor before any refinement of the model ? Like an R-factor at the very beginning of the entire modeling procedure, right after molecular replacement ? If this is so: you should always compare such initial R-factors to the R-factors for the atoms pla

Re: [ccp4bb] XDS question

"the space group is I422" "do you have any other suggestion?" Yes, how certain are you of the space group? For myself, I'm never entirely certain of the space group until I have solved the structure... I always keep in mind the other possibilities for space group assignment, if need be. And so

Re: [ccp4bb] XDS question

Hi, I have a problem with the following sentence: "if I collect all spots I get good map, but it is impossible to solve the structure by molecular replacement" - if you have a good map (I assume electron density map) then the structure is solved... for me a good map is a map I can interpret.

Re: [ccp4bb] Change cell parameter

Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to b

Re: [ccp4bb] unsubscription request

Hi, What about the ccp4 web page, from which you can follow the link to http://www.ccp4.ac.uk/ccp4bb.php ? HTH, Fred. Angela (Shaoxu) Li wrote: Hi there, I wish to unsubscribe to the mailing list. But I'm unsure as to how I can do that. Your help will be greatly appreciated. Best wishes

Re: [ccp4bb] need proper suggestion http://scripts.iucr.org/cgi-bin/paper?ms0234

Afshan Begum wrote: Dear All, I have a severe prob lam to performed my ligand binding study with corresponding protein. I have taking the native diffraction data at 1.75 A and after that i have performed soaking as well co-crystallization experiment with my inhibitors. Problem is that at the

Re: [ccp4bb] {**SPAM**} [ccp4bb] screen kit

Hi, Hampton research claims that their Natrix series of screening kits is designed for nucleid acid and nucleic acid/protein complexes. http://hamptonresearch.com/product_detail.aspx?cid=1&sid=27&pid=8 Fred. dengzq1987 wrote: hello all, is there any screen kit that is highly effective for

Re: [ccp4bb] determining the domain for overexpression and crystallization

Hi, There's a whole bunch of programs that can help you "out there". The 2 methods I think of right now are DISPROT (there's a server I believe, http://www.ist.temple.edu/disprot/ ) - Must admit I haven't been to that one for quite a while; DISPROT provides areas of your sequence with high pro

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

Hi, I don't think XDS generates an Rpim value, does it? The XDS CORRECT strep provides the "old fashioned" Rsym (R-FACTOR) plus R-meas and Rmrgd-F. The curves look all the same though Fred. Ed Pozharski wrote: On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:

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

For myself, I decide on the high resolution cutoff by looking at the Rsym vs resolution curve. The curve rises, and for all data sets I have processed (so far) there is a break in the curve and the curve shoots up. To near vertical. This "inflexion point" is where I decide to place the high res

Re: [ccp4bb] Processing Laue data

Hi, A Laue diffraction pattern is a diffraction pattern recorded using polychromatic ("white") radiation. Hence the beam line optics is for focusing the radiation onto the sample (the crystal) but not to select a single wavelength (a monochromator). Just to make it simple to understand. Cont

Re: [ccp4bb] Problem with refinement and positive electron density

Judith Reeks wrote: Dear All, I am currently refining a structure using the latest experimental version of Refmac (5.6) and there seems to be a problem with my Fo-Fc map. There is a region where I have fitted residues to the electron density but after refinement there is still positive el

Re: [ccp4bb] .pir file

Hi Careina, Just an example of a pir file which I just generated (using Bart Hazes program mcfman): P1;>MALDH_ Just a title TKVSVVGAAGTVGAAAGYNIALDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVR QGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNP VDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEG

Re: [ccp4bb] Molrep with two models

The molecular replacement program does not know about your molecule being a single polypeptide chain. The problem is "fit two bodies" therefore the program fits two bodies. The centre of mass of whatever you wish to position is placed the "standard asymmetric unit" used by the program. If it ha

Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU

Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it

Re: [ccp4bb] CNS and protein structure refinement

Hi Rex, There will be small differences in particular due to the different ways of treating the solvent. How large of a difference are you talking about? Normally the difference should not be very large... And if this related to solvent effects, it will affect the low resolution reflections w

Re: [ccp4bb] adding gaussian noise to an mtz data column

lumn with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic wrote: Before re-inventing the wheel... Is ther

[ccp4bb] adding gaussian noise to an mtz data column

Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported to another format if

Re: [ccp4bb] Mg2+ or water

James Stroud wrote: On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an "open document presentation". It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp fi

Re: [ccp4bb] If it is a new structure?

Hi, Last couple of times I asked myself the same question ("what does it look like?") I used ssm (or PDBeFold as seems to be called now). http://www.ebi.ac.uk/msd-srv/ssm/ HTH, Fred. wrote: The structure of my protein is as shown as the purple one. Another one ,as shown as green,is homolo

Re: [ccp4bb] Space group vs. gap between Rwork and Rfree?

Hi Petr, Usually IDXREF suggests more than one Bravais lattice that is consistent with your diffraction images; hence it is (sometimes) worthwhile trying to INTEGRATE in all possible Bravais lattices and this allows you to eliminate a number of possibilities (poor profiles during integration,

Re: [ccp4bb] Structure based and motif based sequence alignment

Muhammed bashir Khan wrote: Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure

Re: [ccp4bb] Problem with finding of spots

Hi, I agree with what has been mentioned about "fuzzy spots". But what seems obvious as well is that the resolution for spot picking should be limited (to 3.5 or 4 A resolution). It is difficult to judge from an image of a diffraction pattern, but it seems to me from this image that the spots

Re: [ccp4bb] relationship between B factors and Koff

I can direct you to PDB entry 1EWY, where the average isotropic temperature factor for the major component of the complex is ca. 47 A**2 and that for the smaller component is ca. 69 A**2. Similar values than the ones you are reporting. I am assuming some sort of "disorder", or if you prefer, "w

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

I do not know if that's really cynical: I've had the case of a referee recommending manuscript rejection because the title of the manuscript was not appropriate. The editor followed the advice of the referee. A proper refereeing job would have been to suggest that the authors change the title o

Re: [ccp4bb] Regarding space group P1, P21

Dear Mohinder, What one should really do is to provide an accurate model (including the space group) of what is taking place in the crystal. For example, there was this case reported by Morales et al. (2000, Acta Cryst sect. D56, 1408-1412) of a complex of 2 proteins (i.e. identical situation

Re: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

Hi, For questions relating to a specific package (if it is in rpm format, I don't know what the Uuntu installation software uses as packages), you can use the rpm search web site http://rpm.pbone.net/ (in addition to http://www.rpmfind.net/ , can't search in rpmfind.net at the moment, it says

Re: [ccp4bb] Refinement

I second that. Incorrect space group assignment usually causes this behaviour of having R and R-free stuck at very high values. It is useful to go back to the data processing stage and carefully consider all Bravais lattices (and associated space groups) that the autoindexing routine finds cons

Re: [ccp4bb] protein ligand energy

Rex Palmer wrote: Can anyone reccomend a free download program that will calculate the energy of a protein/ligand complex? The ligand has been modelled in. Thanks Rex Palmer Birkeck College Hi Rex, I think any refinement program such as CNS will do this - problem is, since these programs

Re: [ccp4bb] which Linux workstation for crystallography to buy?

Hi, Frankly, any vendor or assembler of PC's will do. Things to make sure to have on your PC: an NVIDIA graphics board in order to get nice graphics (their Linux drivers are fine; I don't know their current range of boards, here we buy middle-range boards, not the cheapest ones that are speci

Re: [ccp4bb] unknown density

Hi, I did a little bit of "modeling" in your density (starting from a nicotinamide ring, the positioned nicotinamide is enclosed). The middle part looks suspiciously like a 6 membered ring. Could it be a molecule in a half-chair conformation? There is only the blob that is perpendicular to th

Re: [ccp4bb] changing spacegroup

Another possibility is with sftools, set spacegroup option Fred. PS not in ccp4i Graeme Winter wrote: Hi Tim, Is it as easy as reindex hklin a.mtz hklout b.mtz << eof symm P43212 eof This will simply (and correctly) reassign the symmetry operations. Is this what you meant? Best wishes, Gr

Re: [ccp4bb] .cv to .mtz conversion

ccp4i Reflection Data Utilities Convert to/modify/extend MTZ Input reflection file is in XPLOR/CNS format etc Fortran format (7X,3I5,6X,E12.4,7X,E12.4,6X,I2) Skip first 6 lines (if # is part of the .cv file) [I think, I have counted the space before the INDEx for example giving me

Re: [ccp4bb] pdf to text

What you could try to do is print out the pdf file, then locate a scanner with a suitable scanning software. Several scanning software have the possibility of generating word processing program output or ASCII format. Since the pdf file is text only (no figures etc) then it should be OK. You ju

Re: [ccp4bb] ccp4 start

Hi, I suggest that you locate the ccp4.setup file in the version of ccp4 that you have installed and edit it to have all the variables pointing at the correct directories. This means that you will have to locate the directory where ccp4 has been installed. I thought that the ccp4 installatio

[ccp4bb] interesting article about science funding in the "Financial Times"

Dear all, Giuseppe Zaccai showed me an interesting article about science funding (from F.T.). I thought it could be of interest to all of us since we have to apply for funding, and succeeding in securing funds is getting more difficult all the time. The scan of the article can be found on:

[ccp4bb] Competition organised by the Scientist: Proteopedia voted first place

Dear ccp4bb subscribers, I have just learned that Proteopedia (the wikipedia-style encyclopedia of macromolecular structures) has been voted winner in this year's competition organized by "the Scientist" ( http://www.the-scientist.com/ , readers and judges choice). So thanks to all who voted

[ccp4bb] Post-doctoral position available at IBS - please do not reply to me !

POST-DOCTORAL POSITION DATE OF AVAILABILITY : starting as soon as possible, for 2 years (ANR contract). TITLE : purification and crystallization of ABC transporters POSITION: the position is opened at the Institute for Structural Biology (IBS) in Grenoble in the team of Jean-Michel Jault and

Re: [ccp4bb] How to find out Rmerge from the refinements..?

Hussain Bhukyagps wrote: Dear all, i want to know that how can we find Rmerge from the refinements done in CNS..?? Hi, I think you have the terminology wrong: Rmerge (or Rsym nowadays when most diffraction data is recorded from a single crystal) is provided by the data frame diffraction s

Re: [ccp4bb] XSCALE

anna delprato wrote: Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP fi

Re: [ccp4bb] Accuracy of the position of coordinates

:41 AM, Vellieux Frederic mailto:frederic.velli...@ibs.fr>> wrote: > I would like to know the accuracy (error) of the position of the coordinates This is provided by the output of the refinement software. An example (CNS-refined structure, from the pdb header, there is an in

Re: [ccp4bb] Accuracy of the position of coordinates

> I would like to know the accuracy (error) of the position of the coordinates This is provided by the output of the refinement software. An example (CNS-refined structure, from the pdb header, there is an input file called "xtal_pdbsubmission.inp" REMARK 3 ESTIMATED COORDINATE ERROR. RE

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

heers -- Ian On Fri, Jul 30, 2010 at 9:24 AM, Vellieux Frederic wrote: Hi, You take the output mtz from the refinement program (let's assume it's called refine_1.mtz). Command line mode: sftools read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT PHI2FOFCWT

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi, You take the output mtz from the refinement program (let's assume it's called refine_1.mtz). Command line mode: sftools read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT PHI2FOFCWT FOFCWT PHI2FOFCWT cal col 3FO2FCWT col 1 col 3 + set types F P F P R F write 3fo2fc.m

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

Hi, To quote you: "even my P222 experimental envelop does have a 4-fold axis" - this is not suprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nome

Re: [ccp4bb] non-symmetric tetramer ?

Non-symmetric tetramers: you can check out Tete-Favier et al (1993), Acta Cryst. D49, 246: the quaternary structure was assumed to have local 222 symmetry. It turned out this was not exactly the case: the actual symmetry of the object (the molecule) was "pseudo" 2t2t2t. So in addition to 2-fold

[ccp4bb]

Vandana Kukshal wrote: hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 % identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetr

Re: [ccp4bb] problem in annealing

Hi, I think the MAXCHN "errors" has been "fixed" in recent versions of CNS. You must be using CNS v1.0 or v1.1. So either you download and install a recent version (the latest is v1.3), or you do as the error message suggests: you edit your anneal.inp file, you locate "MAXCHN=" or "MAXCHN ="

[ccp4bb] Fifth Max Perutz prize of the E.C.A. to Prof. Claude Lecomte

News just received from the French Crystallographic Association (and thus forwarded to ccp4bb): The fifth Max Perutz Prize of the European Crystallographic Association goes to to Professor Claude Lecomte from Nancy Université and CNRS, France. Claude Lecomte is recognised for his contribution

Re: [ccp4bb] Density peaks to build

Hi, Can't rotate the picture so that I can't see the distance between the nitrogen and the green blob. The green blob is elongated. Sometimes what happens is that you can have 2 waters (partial occupancies), in some unit cells in your crystals the water occupies site 1, in the other unit cel

Re: [ccp4bb] Need suggestion on classification of a protease

Hi, If you do not know anything about peptidase (protease) classification, I'd suggest you have a look first at the Merops peptidase data base: http://merops.sanger.ac.uk/ Will tell you what (type of) classes there are, for example (and based on what). Fred. Gowriishankar Raju wrote: Dea

Re: [ccp4bb] A strange case of MR

Hi Jeremy, Just looking at the stats: 1- you could try to remove the low intensity reflections (are they reflections, or are they just indices - it's difficult to say), i.e. the first 4 shells in your tables dealing with intensities; 2 - you could try to truncate the high resolution to 1.6 A.

Re: [ccp4bb] Perfect crystal with weird diffraction pattern

Hi Hui, I think most of us can't do much with rar archive files. This is a Windows "thing" I believe and my Linux system tells me "Archive type not supported"... Fred. hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 s

Re: [ccp4bb] Mysterious density

Blobology (a branch of macromolecular crystallography). You could maybe place benzoate in there (the 6 membered ring on "top" in the pictures), refine, compute a new map and see if you can make something out of it. Why benzoate: because the ring would find its place nicely in the "hydrophobic"

Re: [ccp4bb] OFF: Intein-chitin purification method

Petr Kolenko wrote: Dear all, I am working on crystallization of a protein purified using intein-chitin binding domain. There is 86% identity with protein with already known high-resolution structure, but I am not able to get any crystals. I heard that reversed phase chromatography is not goo

Re: [ccp4bb] measure of anamolous signal

Vandu Murugan wrote: Dear all, I have collected a 2.7 angstrom home source data with Cu-Kalpha source for a protein with 6 cysteines, with a multiplicity of around 23. I need to know, is there any significant anamolous signal present in the data set, since there is no good model for my pro

Re: [ccp4bb] Lodovico...

Dear all, A tribute to Lodovico (pictures + letters + a song) can be found on http://www.crystalerice.org/Erice2010/Lodovico/index.htm Fred.

Re: [ccp4bb] Prof. Lodovico Riva di Sansevenino passed away last night

Dear all, An obituary for Prof. Lodovico Riva di Sanseverino (in English, written by Prof. Carlo Mealli) can be found on http://www.cristallografia.org/uploaded/181.pdf (www.cristallografia.org is the web site of the Italian Crystallographic Association, Associazione Italiana di Cristallogra

Re: [ccp4bb] Matthews coefficient

Hi, No such thing as a stupid question. If the resolution is sufficient, arp_warp does a good job. But it is a reconstruction and REFINEMENT program. But checking the proper packing (that there are indeed contacts in the 3 dimensions of space to form the crystal): takes only 10 seconds using

[ccp4bb] voting on "The Scientist" web site for our macromolecular structures

Dear all, I think we all think that macromolecular structures are "the best" there is... And now we have a chance to "prove it" to the world. The Scientist is organizing a competition to elect "the best website". One of the competitors is the Proteopedia web site (http://www.proteopedia.org)

Re: [ccp4bb] molecular replacement

Hi there, If there are a few clashes (acceptable - usually surface loops that "enter" the surface part of another molecule or subunit) then you can delete the parts of loops that usually have poor density and that clash, refine, compute a new map and see if the loop can be traced (usually it

Re: [ccp4bb] PEG 1000

R.Srinivasan wrote: Dear All, I have got initial crystals in a condition with PEG 1000. The PEG 1000 stock we had in our lab was rock solid and when i heated it to about 50 degrees for 15 to 20 minutes it became a solution. We thought the compound has got out dated or something like

Re: [ccp4bb] Prof. Lodovico Riva di Sansevenino passed away last night

Dear bb, Here is the news received today from Paola Spadon (also in charge of the Erice schools of Crystallography): "Lodovico's funeral was done friday morning in Palermo in a very strict and private way. This was his strong will. We will remember him as he would have liked most, singing smi

[ccp4bb] Fwd: Re: [ccp4bb] creating new ligand cif file

Received from Peter Zwart: Original Message Subject:Re: [ccp4bb] creating new ligand cif file Date: Mon, 21 Jun 2010 07:08:18 -0700 From: Peter Zwart To: Vellieux Frederic References: <4c1f4f26.2070...@ibs.fr> it is the same format actually. 201

Re: [ccp4bb] creating new ligand cif file

There is an option in Phenix to generate the necessary cif file for Phenix refinement. But that's a Phenix file, not a REFMAC file (I think, I never tried taking the cif file generated by Phenix to use it in REFMAC). As an example, I am enclosing a cif file that was generated by Phenix for NAD.

Re: [ccp4bb] NOT Job Advertisement but model refinement

This has been told (written, in fact) on this bb many times. The purpose of refinement is not to bring the R-factor down, but to obtain a model that satisfies "best" all available data (including "biochemical" data). Anyway, as to what you can do: it's always possible to question the choice of

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

Hi Christian, Had exactly the same problem (converting an mmCIF file into a PDB). I located and installed CIFTr . The version I have running here is ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded it from. I think it one of the PDB associated files. Fred. Christian E

Re: [ccp4bb] Ligand present in only one monomer in NCS

Hi Andy, I'd say fairly common, and there can be several reasons. One is that the entrance of the active site (in case of crystal soaks) is blocked in some subunits. Also, different affinities in the different active sites, plus allosteric effects, are possibilities to consider. The latest e

Re: [ccp4bb] Far to good r-factors

Hi Paul, I've seen that type of behaviour before for low resolution structures. On such structures, either I have a very hard time getting at the same time a good geometry, "good" R-factors and satisfactory electron density, or things go very smoothly and all the statistics (model geometry,

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