[ccp4bb] {Spam?} Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

nction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia El 10/1

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia El 09/10/13 20:04, Navdeep Sidhu escribió: > John Bohannon

Re: [ccp4bb] announcement: (another) GUI for XDS

) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia El 26/06/13 19:46, Kay Diederichs escribió: > Hi Sebastiano, > > ok, I think I have the solution, and, hoping it's correct, have put it into > http://strucbio.biologi

Re: [ccp4bb] off topic:how to prevent DNA tetraplexe forming?

Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Help with curves+

soxy-riboses. I presume it is the same for RNA riboses. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] how to install coot on ubuntu 11.10

. Good luck, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia cootbuilddiffs.tgz Description: application/compressed-tar

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

re reminds me of those astronomers complicating the Ptolemaic system to "save the appearances". And this is what we, you can include myself, are doing. Until the bubble collapses? -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] DNA in coot

f Molecular and Structural Biochemistry > North Carolina State University -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Autoreply: [ccp4bb] A story of acetoacetate decarboxylase

Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Problem with getting Rfree and Rf down

s. >> >> The structure factors are also high but they get better as the crystals >> diffract better. >> >> Thanks >> >> Sam -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA) Third time is the charm?

entity other > than the intended recipient is prohibited. > -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] image compression

e I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] image compression

163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] image compression

>>> >>>>> Anyway, assume that someone did go through all the trouble to >>>>> make these >>>>> datasets "available" for download, just in case they are >>>>> interesting, and >>>>> annotated them as much as possible. There will be about 20 >>>>> datasets for any >>>>> given PDB ID. >>>>> >>>>> Now assume that for each of these datasets this hypothetical >>>>> website has >>>>> two links, one for the "raw data", which will average ~2 GB per >>>>> wedge (after >>>>> gzip compression, taking at least ~45 min to download), and a >>>>> second link >>>>> for a "lossy compressed" version, which is only ~100 MB/wedge (2 min >>>>> download). When decompressed, the images will visually look >>>>> pretty much like >>>>> the originals, and generally give you very similar Rmerge, >>>>> Rcryst, Rfree, >>>>> I/sigma, anomalous differences, and all other statistics when >>>>> processed with >>>>> contemporary software. Perhaps a bit worse. Essentially, lossy >>>>> compression >>>>> is equivalent to adding noise to the images. >>>>> >>>>> Which one would you try first? Does lossy compression make it >>>>> easier to >>>>> hunt for "interesting" datasets? Or is it just too repugnant to >>>>> have >>>>> "modified" the data in any way shape or form ... after the detector >>>>> manufacturer's software has "corrected" it? Would it suffice to >>>>> simply >>>>> supply a couple of "example" images for download instead? >>>>> >>>>> -James Holton >>>>> MAD Scientist >>>>> >> > -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Linux vs MacOS for crystallographic software

of the apple OS, they may change it in the next "upgrade". Example: NFS. Non-unix idioms are becoming so frequent in osx that one would say that it will soon depart completely from the BSD origins. But this is a quite subjective view, of course. However, if you compare the price/performance ratio, at least in Europe, you will come easily with an answer. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] refmac and DNA

DB. Cheers, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.u

Re: [ccp4bb] E. coli mutant strains

el.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

Le 25 mars 2010 à 16:43, Tim Gruene a écrit : > Hello Rebecca, > > this is merely a guess, but I think, it should work. > > As you calculate the electrostatic surface potential in pymol, it uses apbs. > apbs, if I remember correctly creates an intermediate PDB-file where the > B-factor column i

Re: [ccp4bb] ARP_wARP 7.1 release

y sure you need a 32-bit fink installation for this workaround to > work. You have to source /sw/bin/init.sh. > > Best, > > Mark > > On 12/26/09 6:51 AM, Miguel Ortiz Lombardia wrote: >> Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit : >> >> >

Re: [ccp4bb] ARP_wARP 7.1 release

/tasks and the task is not there. Best regards, Miguel Le 26 déc. 2009 à 13:51, Miguel Ortiz Lombardia a écrit : > Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit : > >> Dear all, >> >> A couple of people have pointed out problems when installing the ARP/wARP >&

Re: [ccp4bb] ARP_wARP 7.1 release

Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit : > Dear all, > > A couple of people have pointed out problems when installing the ARP/wARP > CCP4i GUI over 64-bit fink installations > of CCP4, in Mac OSX 10.6 Snow Leopard. Although I am not confident we > understand the problem 100%, it a

Re: [ccp4bb] to model or not to model, that's not the question

Le 17 nov. 09 à 12:40, Morten Kjeldgaard a écrit : Tim Gruene wrote: Yes, but models that can be validated against experimental data. The defining characteristics of computational models is that they (A) are 100% dependent on the algortihm, (B) can't be validated at all. Cheers, Morten

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

Le 15 nov. 09 à 12:54, Kjeldgaard Morten a écrit : On 14/11/2009, at 20.17, Miguel Ortiz Lombardia wrote: Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit : On 14/11/2009, at 18.55, Ronald E Stenkamp wrote: The rumblings here at the Univ. of Washington among the computational modelers is

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit : On 14/11/2009, at 18.55, Ronald E Stenkamp wrote: The rumblings here at the Univ. of Washington among the computational modelers is that some of their current models might be more representative of protein structures in solution than are

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

Le 14 nov. 09 à 10:53, Frederic VELLIEUX a écrit : Dear Bulletin Board, The following URL's may help people to understand crystallography (this was also pointed out to me by Ines Kahlaoui last night, I am so grateful to her): http://videolectures.net/mit3091f04_sadoway_lec14/ (for the B

Re: [ccp4bb] {Disarmed} Re: [ccp4bb] sulfur sad phasing

Le 11 nov. 09 à 14:26, Jürgen Bosch a écrit : Dear CCP4 community, (hijacking the thread) I so far failed to get a sulfur SAD phased structure and I blamed it on the low symmetry space group C2 plus weakish diffraction if you don't want to overexpose your crystal and be able to collect 20-30

Re: [ccp4bb] sulfur sad phasing

Le 11 nov. 09 à 13:16, Matthias Zebisch a écrit : Dear bb! What is the optimal wavelength for Sulfur SAD phasing? Is it 1.9A or should one go below that to reduce absorption/damage. Also, would the same wavelength be appropriate to maximize anomalous scattering to position chlorides, calcium,

Re: [ccp4bb] Jobs

Le 30 sept. 09 à 22:07, Christopher Law a écrit : I am just wondering if anyone else is getting just a little bit peeved that the BB is now primarily being used as a jobs board? -- Dr. Christopher J. Law, Queen's University Belfast Hi Christopher, Well, I quote from the CCP4 web site:

Re: [ccp4bb] trouble with imosflm cell refinement

Le 30 sept. 09 à 17:27, Graeme Winter a écrit : Dear Miguel, You may find that replacing the ipmosflm binary with the one from Harry's web page may be more reliable - typically these sorts of things come down to gfortran or g77 being a little keen in optimization. http://www.mrc-lmb.cam.ac.uk/

[ccp4bb] trouble with imosflm cell refinement

Dear all, I cannot get imosflm refining any cell, the program simply stalls: all you have is the little "E" at the top right rotating, but no messages, no errors, no crashes. 'Abort' doesn't have any effect either, nor it has the sequence 'Pause'-'Continue'. I have this problem with: OS:

Re: [ccp4bb] heavy atom derivative choice

Hi Sebastiano, Have a look at HATODAS: http://hatodas.harima.riken.go.jp/ Good luck, Miguel Le 15 juil. 09 à 14:33, Sebastiano Pasqualato a écrit : Hi all, I've got crystals of a protein of ca 200 residues, with 2 free cysteines, 5 histidines, 2 methionines. We have nice diffraction for

Re: [ccp4bb] Problem with 2 runs in scala

Thanks to all who answered! Removing "RUN 1 reference" did the trick Another idea was to simply: EXCLUDE batch 551 to 650 but then, smoothed scaling is not possible (to wide a gap ) Best regards, Miguel 2009/7/3 Miguel Ortiz Lombardia >: Dear all, I'm trying to sca

[ccp4bb] Problem with 2 runs in scala

Dear all, I'm trying to scale a dataset where 100 frames in the middle (25 degrees) are quite bad so I would like to exclude them. Because the angular range is too wide I can only do that by creating two runs. So far, so good. The problem is that even if my input contains these five lines

Re: [ccp4bb] problem starting refmac from ccp4i gui

Hi, If you were trying to re-run a job created with ccp4 6.1.0 or earlier, this is a known bug. Have a look at: http://www.ccp4.ac.uk/problems.php#6.1.1-programs If that is the case, there is a new refmac.tcl file that solves that problem. Best, Miguel Le 16 mai 09 à 12:42, Kay Dieder

Re: [ccp4bb] NCBHT: severe warning

Not nice either to air the address of someone who wrote you privately. Miguel Le 1 avr. 09 à 22:48, Marius Schmidt a écrit : Interesting, isn't it? :-), nice person. F*** Off.. it might be 1st April but most people are not interested about your shit sense of humour.. send them to your frie

Re: [ccp4bb] XDS and ESRF ID23-1 images

Hi Ronnie and others, Le 27 mars 09 à 15:02, Ronnie Berntsson a écrit : This might be a bit too obvious, but have you checked that the path to the images is correct? The path written in the input files generated on the beamline reflects where the images were located in the file tree there.

[ccp4bb] XDS and ESRF ID23-1 images

Dear all, Not a CCP4 question. We seem unable to process with XDS a set of images collected at ESRF ID23-1. Images can be open and processed by other software (adxv, mosflm...) They have appropriate read permissions and so has the directory where we run XDS. We use the latest XDS binaries

[ccp4bb] Plasmids and other material [Was: images]

Hi, I mostly agree with Artem, except on one point: As long as people publish most of the details necessary to reproduce the materials (protein samples and crystals) used in structure determination - the crystals may be reproduced 'by persons skilled in the art'. There is no need to even s

Re: [ccp4bb] Problem with multiple users running ccp4i on one machine

Dear ccp4i developers, Jumping into this issue a bit late... I have some criticism to make here, please take them friendly, I make them precisely because ccp4i is so useful. I presume there are good reasons behind the new design of CCP4i and its CCP4 DBhandler, but I think you have overlook

Re: [ccp4bb] PHENIX & BSS refinement

Hi Pavel, Thanks, it is clear now. I have a last concern, though. Does phenix impose minimal values to the refined ADPs? I guess it does not, for I have found nothing like that in the documentation. But, if it does so, are they imposed to the individual B-factors or the B-overall is also ta

Re: [ccp4bb] PHENIX & BSS refinement

Hi Pavel, We have also seen that the B factor jumps up in this last step (see bellow). Is anybody aware of this? This is because the trace of overall anisotropic scale matrix is added to atomic B-factors and subtracted from that matrix. This is exactly what CNS does (at least version 1

Re: [ccp4bb] Google marks CCP4 web site as a potential security threat

The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and ScienceDirect websites, among many others... including google.com! Hope it's a (short-lived) bug. Pedro The bug is for them to decide what we have or have not to consider as a threat and to force us to change our websites

[ccp4bb] Google marks CCP4 web site as a potential security threat

Dear all, While searching for some definition of rotations angles I have bumped into this very disagreeable indeed discovery: google adds now a step if you want to go to places _they_ consider as potentially dangerous. You can proceed that have to copy and paste the address yourself or te

Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...

Hi Tassos, I very much like Homolmapper: http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm You can map several conserved properties onto your structures, not just plain sequence. Best, Miguel Le 29 janv. 09 à 22:25, Anastassis Perrakis a écrit

[ccp4bb] ccp4i 6.1.0 and file paths

Dear all, I have a request to the developers of CCP4I. I find very bizarre and potentially quite confusing that the default value for file paths is not _strictly_ the project directory but, instead, any directory that you happen to choose a moment before using 'Full-path', for instance (s

Re: [ccp4bb] Superdex 200 PC columns

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, You're right, there are two cell path sizes in AKTA systems: 2 mm and 10 mm. I don't know what path had the SMART. You definitely need the second one if you want to work with low protein concentrations. Miguel En/na Juergen Bosch ha escrit: > H

Re: [ccp4bb] Superdex 200 PC columns

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robert, I have run those PC 2.3/30 with ~10 ug of protein (of course this depends on the protein) and still get a useful signal at 280 nm. If you don't have anything interfering at ~215 nm and your HPLC system can read at that wavelength, you can e

Re: [ccp4bb] rmsd calculation. .

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Excellent! Thank you Gerard, Miguel Gerard DVD Kleywegt escribió: >> But my understanding is that Iain's procedure gives the rmsds of the >> _aligned_ C-alphas, whereas Jenny actually seems to be more interested >> in those that she excludes from th

Re: [ccp4bb] rmsd calculation. .

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jenny and Iain, But my understanding is that Iain's procedure gives the rmsds of the _aligned_ C-alphas, whereas Jenny actually seems to be more interested in those that she excludes from the alignment. I may be wrong, but in these cases, I use lsq

Re: [ccp4bb] CCP4 GUI

on. The latter could be done as a hidden > folder, made visible according to an Expert switch in Preferences. > > As developers, we also have to think about long-term maintainability. > Options, in particular little-used options, can soon become out-of-date. > > m > > >

Re: [ccp4bb] CCP4 GUI

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I'm a well-known luddite as Eleanor says. However, I shamelessly confess that the CCP4 GUI is great. Not that I think this is necessary here, I'm sure most people agree with that. If I write now is because Martynn's e-mail have reminded me

Re: [ccp4bb] predicting protease cleavage sites in proteins?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bill, If you are interested in the physiological, known cleavage sites, you may also try one of the possible searches at the MEROPS database: http://merops.sanger.ac.uk/cgi-bin/show_substrate Cheers, Miguel En/na Manish C Pathak ha escrit: >

Re: [ccp4bb] process SeMet labelled data

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear ccp4bbers, I agree with Dirk. I have also noticed that much due to the way X-ray crystallography is evolving, a lot of students/early-postdocs find themselves "doing crystallography" in labs without a tradition in crystallography, even without "r

Re: [ccp4bb] MR in P1 space group

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Uhnsoo, AMoRe will not run the translation function for the **first** body (an hetero-dimer in your case) because in P1 the origin is arbitrary and hence fixed by the first rotation solution. Now, if you think that the first solution from the rotat

Re: [ccp4bb] human cDNA clones?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Andrew, Can you get cDNA from human cell lines? Perhaps one of your colleagues can provide you with a few microliters. You can amplify from there all the genes you need (provided they are transcribed in that cell line; therefore, better use cDNA fr

Re: nucleic acid helices

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Florian, You can use coot to create an ideal DNA! Simply: Calculate -> Other Modelling tools -> Ideal DNA/RNA Another possibility is 3DNA: (http://rutchem.rutgers.edu/~xiangjun/3DNA/) For analysis you could use 3DNA or Curves (http://www.ibpc.fr