[ccp4bb] Formageddon is upon us... Important news from wwPDB!

2013-05-24 Thread Gerard DVD Kleywegt
Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large

Re: [ccp4bb] Definition of diffractometer

2013-06-19 Thread Gerard DVD Kleywegt
Wait, so a geometer measures ges, an odometer measures ods, and a kilometer measures kils? --dvd On Thu, 20 Jun 2013, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ed, to me, an '-ometer' is a device that measures whatever you put in front of the 'o', so in case of

Re: [ccp4bb] Definition of diffractometer

2013-06-20 Thread Gerard DVD Kleywegt
is hyphenated kilo-meter, no kil-ometer, so the origin of that word is nothing to do with 'ometer'. Remembering stuff from your school days help a great deal understanding the world around you ;-) Best, Tim On 06/20/2013 01:14 AM, Gerard DVD Kleywegt wrote: Wait, so a geometer measures ges

Re: [ccp4bb] Definition of diffractometer

2013-06-28 Thread Gerard DVD Kleywegt
As for Gerard's follow up, I remind him of the immortal wisdom of Jack Handey: Maybe in order to understand mankind, we have to look at the word itself. Basically, it's made up of two separate words ? mank and ind. What do these words mean? It's a mystery, and that's why so is mankind.

[ccp4bb] Announcement: wwPDB Workshop on mmCIF/PDBx for Programmers, 20/21 Nov-13, Cambridge (UK)

2013-08-01 Thread Gerard DVD Kleywegt
wwPDB Workshop on mmCIF/PDBx for Programmers What, why and how? -- The world of the PDB will be changing rapidly and profoundly over the next few years. A major change will involve the transition from PDB to mmCIF/PDBx as the

Re: [ccp4bb] structural search for homologs in pdb?

2013-08-22 Thread Gerard DVD Kleywegt
On Thu, 22 Aug 2013, Gloria Borgstahl wrote: We have a protein sequence that probably contains OB folds. What is the best way to search for the top structural homologs to this sequence in the pdb? G Hi Gloria, If you expect decent sequence simnilarity to one or more proteins in the PDB,

Re: [ccp4bb] What kind of reflection data to deposit to PDB

2013-09-16 Thread Gerard DVD Kleywegt
Dear all, At present, unmerged data cannot be handled properly as part of a PDB deposition. One reason for this is that changes to the mmCIF/PDBx data model will be required (at the moment, hkl must be unique within the reflection data, which is logical for merged data but precludes handling

Re: [ccp4bb] What kind of reflection data to deposit to PDB

2013-09-17 Thread Gerard DVD Kleywegt
it. It is strange to hear on a discussion board that recently considered the advantages of depositing complete image data, that a case will have to be made for allowing the deposition of full unmerged datasets. ++Martyn On 16/09/2013 14:03, Gerard DVD Kleywegt wrote: Dear all, At present

Re: [ccp4bb] Electron density server

2013-10-26 Thread Gerard DVD Kleywegt
The server has been rebooted and appears to be working again. --Gerard On Fri, 25 Oct 2013, Rojan Shrestha wrote: Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan Best wishes, --Gerard

[ccp4bb] Stand-alone wwPDB X-ray validation server

2013-12-02 Thread Gerard DVD Kleywegt
Dear colleagues, The wwPDB partners are pleased to announce that X-ray structure validation reports can now be generated on demand by macromolecular crystallographers by using the new stand-alone wwPDB validation server. For the full scoop, see:

[ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-16 Thread Gerard DVD Kleywegt
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-18 Thread Gerard DVD Kleywegt
, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Gerard DVD Kleywegt ger...@xray.bmc.uu.se ? : CCP4BB@JISCMAIL.AC.UK Envoy? le : Mercredi 16

[ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-23 Thread Gerard DVD Kleywegt
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see

[ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-23 Thread Gerard DVD Kleywegt
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see

[ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-23 Thread Gerard DVD Kleywegt
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see

[ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-23 Thread Gerard DVD Kleywegt
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

2014-04-24 Thread Gerard DVD Kleywegt
Hi all, I don't know why my posting about validation reports re-appeared several times. The mail headers show that all 4 came through the domain ouhsc.edu but why they would be resent to ccp4bb is not clear, nor why this only happened with my posting. --Gerard

Re: [ccp4bb] 100.000?

2014-05-10 Thread Gerard DVD Kleywegt
See: http://www.wwpdb.org/news/news_2014.html#06-May-2014 Even if you don't deposit anything, we'll reach the 100,000-entry milestone with next Wednesday's release :-) --Gerard On Fri, 9 May 2014, mesters wrote: Great, just a few more structures to deposit and then 100.000 structures to

Re: [ccp4bb] 100.000?

2014-05-11 Thread Gerard DVD Kleywegt
:33 PM, Gerard DVD Kleywegt wrote: See: http://www.wwpdb.org/news/news_2014.html#06-May-2014 Even if you don't deposit anything, we'll reach the 100,000-entry milestone with next Wednesday's release :-) --Gerard On Fri, 9 May 2014, mesters wrote: Great, just a few more structures to deposit

Re: [ccp4bb] AW: [ccp4bb] map manipulation questions

2014-05-20 Thread Gerard DVD Kleywegt
MAPMAN contains several related options, e.g. CEll, SPacegroup, TRanslate and GTranslate, PAste (see the manual for caveats - http://xray.bmc.uu.se/usf/mapman_man.html ). Saving as an ASCII file and editing may also work, if you know what you are doing. --Gerard On Tue, 20 May 2014,

Re: [ccp4bb] EDSTATS for an extracted fragment

2014-06-11 Thread Gerard DVD Kleywegt
What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. However, conversely, if your modified model

[ccp4bb] Vacancies for scientific programmers in the EMDB team at the Protein Data Bank in Europe (PDBe)

2014-06-12 Thread Gerard DVD Kleywegt
Dear all, The EMDB team at the Protein Data Bank in Europe (PDBe; http://pdbe.org) has two vacancies for scientific programmers to work on an exciting new MRC and BBSRC funded project to help bridge the worlds of cellular and molecular structural biology. The project aims to develop: 1) a

[ccp4bb] CCP-EM positions now available

2012-04-05 Thread Gerard DVD Kleywegt
[Cross-posted from the 3DEM mailing list.] --Gerard -- Forwarded message -- Date: Wed, 4 Apr 2012 16:34:39 +0100 From: Helen Saibil h.sai...@mail.cryst.bbk.ac.uk To: 3DEM Mailing List 3...@ncmir.ucsd.edu Subject: [3dem] CCP-EM positions now available Dear Colleagues, We have

[ccp4bb] A creative and challenging job in science communication - join PDBe as its Outreach Coordinator!

2012-04-11 Thread Gerard DVD Kleywegt
Are you an aspiring science communicator who has a wonderful way with words? The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an enthusiastic 'jack of all trades', to coordinate its outreach activities. We are looking for someone who will raise the profile of PDBe through

Re: [ccp4bb] wwPDB and CCDC

2012-04-13 Thread Gerard DVD Kleywegt
Hi Paul, You saw the wwPDB/CCDC JPG in my PPT at GSK :-) Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means, amongst a number of other things, that wwPDB will be allowed to use Mogul in its validation pipeline and that wwPDB will be allowed to incorporate and redistribute

Re: [ccp4bb] sequence format conversion

2012-05-08 Thread Gerard DVD Kleywegt
A good tool should leave b as is: it is ASX (the standard ambiguity code for ASP or ASN). j, o and u are a different matter :-) http://www.uniprot.org/manual/non_std Selenocyteine [sic!] and pyrrolysine are represented in the sequence using the one-letter codes U for selenocysteine and O for

[ccp4bb] Quite interesting Lord of the RING

2012-05-31 Thread Gerard DVD Kleywegt
Hi all, E3 ubiquitin ligase is responsible for flagging proteins for degradation by transferring ubiquitin from a donor protein onto the molecule to be degraded. It is activated by phosphorylation of a tyrosine which promotes a huge conformational change, swinging its RING domain 180 degrees

[ccp4bb] Software and servers in Uppsala

2012-06-21 Thread Gerard DVD Kleywegt
Hi all, In the past couple of years, Mark Harris in Uppsala has developed a bunch of programs and servers that are useful for crystallographers, structural biologists and structural bioinformaticians. Some of his programs are listed here: http://xray.bmc.uu.se/markh/programs.html

Re: [ccp4bb] pdb sequence search

2012-06-23 Thread Gerard DVD Kleywegt
Because I want all the structures of a particular protein itself, not it's homologues. I just went through several cycles of reducing E-value down to If you know the UniProt accession code of your protein, then UniPDB is your friend - pdbe.org/unipdb If not, try pdbe.org/fasta where you can

[ccp4bb] Sunhats for plants

2012-07-09 Thread Gerard DVD Kleywegt
Hi all, Plants suffer from DNA damage caused by ultraviolet light in the same way that humans do. Unlike us though, they cant put on a sunhat (or move to England) to avoid the suns rays. Read more about how plants sense UV-B light and turn on a suite of genes to protect their DNA against its

[ccp4bb] A little bit of sunshine from the Protein Data Bank in Europe (pdbe.org)

2012-07-12 Thread Gerard DVD Kleywegt
Hi all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved and updated versions of its tools and resources. Below is a brief description of new features and services that have been released this summer (or what passes as summer in the UK). As always,

[ccp4bb] EDS server woes resolved

2012-07-20 Thread Gerard DVD Kleywegt
Dear all, The EDS server was unfortunately down for a number of days. However, as of yesterday it is up and running again. Apologies for the inconvenience. http://eds.bmc.uu.se/ --Gerard **

[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator

2012-10-09 Thread Gerard DVD Kleywegt
Hi all, The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an expert structural biologist to join the PDBe curation team at the EBI near Cambridge, UK. Applicants should be computer-literate and possess a recent PhD in some area of structural biology or structural

Re: [ccp4bb] fragment searching

2012-11-01 Thread Gerard DVD Kleywegt
This sounds like a job for SPASM. We used it to find instances of left-handed helices in the PDB. See: - SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419 - Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737 The database for SPASM hasn't been updated for a few years, but it may

Re: [ccp4bb] dihedral backbone generator

2012-11-13 Thread Gerard DVD Kleywegt
If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be done very easily (ever since it was programmed on Valentine's Day 1993, in fact - I even remember who my Valentine was :-) - see: http://xray.bmc.uu.se/usf/moleman_man.html#S13 - READ your original model (PDB

[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator

2012-12-19 Thread Gerard DVD Kleywegt
Hi all, The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit a junior structural biologist to join the PDBe curation team at the EBI near Cambridge, UK. Applicants should be computer-literate and possess a recent PhD in some area of structural biology or structural chemistry

Re: [ccp4bb] ligand restraints

2007-01-28 Thread Gerard DVD Kleywegt
I am refining a lectin-carbohydrate complex. The electron density clearly shows that a mixture of alpha- and beta-anomers of the sugar have bound in the crystal. How can i generate appropriate restraints for the carbohydrate with alternative conformations (i.e. alpha- and beta-anomer)? At the

Re: [ccp4bb] video zueras do tooby

2007-02-28 Thread Gerard DVD Kleywegt
hahaha! brazilian humour - always cracks me up! for those of you whose portuguese is a bit rusty, let me provide a quick and dirty translation: video de pessoas famosas em cada situa?ao!!! videos of famous pessaries in situation comedy clika o lik p/ ver o video se nao der disite a

[ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)

2007-03-01 Thread Gerard DVD Kleywegt
gruzi dirk, come on - lighten up a little! your reply wasn't funny or helpful either - just moralising. (by the way - 't is a strange fact that whenever i get any negative reactions to my own postings they stem *exclusively* from any or all of these three countries: the us, germany and

Re: [ccp4bb] RMSD of pairs of atoms?

2007-03-01 Thread Gerard DVD Kleywegt
Risking a potentially trivial question: Is there a program that will calculate the RMS of distances between specified (listed) atoms in two different structures? As far as I could see, LSQMAN will only compute same with same? lsqman does in fact calculate rmsd valus between arbitrary sets of

[ccp4bb] HIC-Update: Release 11.2 @ 2007-06-01 == 7,452 compounds

2007-06-05 Thread Gerard DVD Kleywegt
Dear structural(-ly interested) biologist ! HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and now contains information on 7,452 hetero-entities. This is the last HIC-Up version prior to the release of the remediated PDB. Hopefully, the remediation will improve the

Re: [ccp4bb] Morphing with mutations

2007-10-02 Thread Gerard DVD Kleywegt
Does anybody know, please, any alternative program or trick to transfom the side chain of a residues into its mutated counterpart, please, with a nice and smooth visual effect? Does LSQMAN, for example, sort this problem out? It is not clear to me reading the manual. no, it won't. however, in

Re: [ccp4bb] Morphing with mutations

2007-10-03 Thread Gerard DVD Kleywegt
What about to do a cartesian morphing with the mutated residue added (or removed) atoms having initial ( or final) coordinates taken from previous common atom? Will work? Coloring may be a factor... but with a manual editing perhaps... you mean, for instance, if you

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Gerard DVD Kleywegt
I thought that I would never have to disagree with both Eleanor and Tassos in the same email, let alone risk being burnt at a stake as a heretic for doubting the Gospel according to Kleywegt, but in my but ... but ... i haven't even said anything! i'm innocent! my name is being used in vain!

Re: [ccp4bb] Plz suggest me

2008-01-01 Thread Gerard DVD Kleywegt
We have crystallized a cyanobacterial phycoerythrin which having two (alpha subunit) in an assymetric unit and held together by only three hydrogen bonds. When we compare the A and B molecule the RMSD is 1.32. because they same sequences then how it is possible to that two molecules are

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Gerard DVD Kleywegt
Can you explain the define of the bond length and bond angel--especially bond angel--here? i leave the definition of angels (be they ideal or not) to clerics, but if you want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE OR TOO BUSY TO EXPLAIN THESE BASIC

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Gerard DVD Kleywegt
them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed i am shocked. i just checked with one of my 25 chinese students here and indeed even universities in china do not have access to a

Re: [ccp4bb] ideal bond length and bong angel

2008-01-10 Thread Gerard DVD Kleywegt
Please do NOT use the BB for abuse. thank you for your support. although i think some abuse of the english language is unavoidable in an international forum like this --gerard (more important issue: http://www.irrepressible.info/)

Re: [ccp4bb] PERL system call to CCP4

2008-01-14 Thread Gerard DVD Kleywegt
hi, I am writing a PERL script to execute a number of CCP4 commands (ncsmask, pdbset, and dm) in succession. I have tried using system call or PIPE command, neither of which work. The ccp4 scripts generated work independently on the command line. we do this in the eds map generation

Re: [ccp4bb] How to improve the density of another molecule in Asymmetric unit

2008-01-16 Thread Gerard DVD Kleywegt
ni hao, I have a question about how to improve the electron density. I have two indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the structure with PHASER and refined with CCP4i (Rfree = 0.29). For the first molecule, the density is very good, but for the second

Re: [ccp4bb] CCP4 for bioinformatics?

2008-01-21 Thread Gerard DVD Kleywegt
manipulate some sequences into various forms, and I was imagining a moleman homolog for bioinformatics (perhaps seqman?). as a matter of fact, i did write exactly that program nine years ago - http://xray.bmc.uu.se/usf/seqman_man.html :-) - not quite a 'ccp4 for bioinformatics' but indeed

Re: [ccp4bb] convert .cif to .mtz

2008-01-29 Thread Gerard DVD Kleywegt
I'm looking for a convenient way of converting a .cif structure factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT for example..? Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of errors when opening with coot.. doesn't coot have an 'import from EDS'

[ccp4bb] [Protein-crystallography] 2008 Kyoto Crystallographic Computing School - Sharing our knowledge (fwd)

2008-02-03 Thread Gerard DVD Kleywegt
not sure if this announcement has made it to ccp4bb yet ... --bruce -- Forwarded message -- Preliminary announcement for the 2008 Kyoto Crystallographic Computing School Sharing our knowledge August 18-23, 2008 Kansai Seminar House,

[ccp4bb] 2008 Kyoto IUCr Crystallographic Computing School - Sharing our knowledge (fwd)

2008-02-07 Thread Gerard DVD Kleywegt
Forwarded on behalf of Lachlan Cranswick. --dvd -- Forwarded message -- 2008 Kyoto IUCr Crystallographic Computing School - Sharing our knowledge (preliminary announcement) Kyoto Crystallographic Computing School Kansai Seminar House,

[ccp4bb] One small step for a crystallographer, one giant leap for mankind!

2008-02-07 Thread Gerard DVD Kleywegt
One small step for a crystallographer, one giant leap for mankind! (*) -- For those of you who didn't see it, the following was posted to the PDB mailing list last week: Announcement: Experimental Data Will Be Required for

[ccp4bb] Uppsala University Practical Protein Crystallization Course (U2P2C2)

2008-02-08 Thread Gerard DVD Kleywegt
Terese Bergfors will be organising her famous Uppsala University Practical Protein Crystallization Course again, from 15-19 September, 2008. For more information, see the course website at: http://xray.bmc.uu.se/terese/course/course.htm --dvd

[ccp4bb] HIC-Update: Release 12.1 @ 2008-03-03 == 7,870 compounds

2008-03-03 Thread Gerard DVD Kleywegt
Dear structural(-ly interested) biologist ! HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and now contains information on 7,870 hetero-entities. This is the first HIC-Up version after the release of the remediated PDB. A few changes had to be made to the

Re: [ccp4bb] into the looking glass

2008-04-01 Thread Gerard DVD Kleywegt
Dear James! Initially I was shocked by the profound implications of your discovery! I immmediately phoned my good friend, Sen. John McCain, to discuss the issue. As you know, Sen. McCain was an aspiring physicist back in the 1920s, when he was in his forties. He pointed me to a little known

Re: [ccp4bb] Multimer threading server

2008-06-03 Thread Gerard DVD Kleywegt
I have a sequence that I would like to model by threading onto each subunit of a homo-tetramer of a related protein (crystal structure). It doesn't work to thread each subunit individually and then 'recombine' the homodimer as a single PDB because the interfaces suffer from clashes and

Re: [ccp4bb] How to change R-free set?

2008-06-19 Thread Gerard DVD Kleywegt
I am currently refining a high-resolution structure that has many reflections (~180,000). I would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so. Any advice will be greatly appreciated. there is a bunch of commands in dataman to do this (and other things) to your

Re: [ccp4bb] Classic density map drawing!

2008-09-18 Thread Gerard DVD Kleywegt
I am trying to make a quite classic demonstration of electron density map sliced and contoured as (smoothed) isoheight curves. The sliced section is random and NOT along any main cell axes. I am curious if there is any crystallographic software can handle this, which will save me from writing

Re: [ccp4bb] Facebook for Neerds

2008-09-18 Thread Gerard DVD Kleywegt
RE: [ccp4bb] Facebook for NeerdsIf you would fourier transform the whole site, you could get myspace back, but where would you get the phases? errrm, phasebook? --dvd ** Gerard J. Kleywegt [Research

Re: [ccp4bb] Positions / CCP4 wiki

2008-10-07 Thread Gerard DVD Kleywegt
Many of the positions advertised on CCP4 (and elsewhere) are also copied to the 'Job openings' page of the Swedish Structural Biology Network (SBNet; http://xray.bmc.uu.se/sbnet/) by Henrik Hansson (Uppsala): http://xray.bmc.uu.se/sbnet/positions.html Note that this page also

Re: [ccp4bb] 3D modeling program

2008-12-06 Thread Gerard DVD Kleywegt
I suspect everyone is refering to Rost's twilight zone in sequence similarity where homology modeling trials had better be avoided. If so, the twilight zone would rather correspond to any indefinite or transitional condition(s) with no applicable or ever relevant binary constraint(s). actually,

Re: [ccp4bb] 3D modeling program

2008-12-06 Thread Gerard DVD Kleywegt
But how do we establish phylogeny? - Based on simple similarity! ah! the old rhetorical trick of changing the problem or question a posteriori! all i pointed out was that things can't be 25% homologous (well, i can think of a contrived example in which two four-domain proteins have one

Re: [ccp4bb] Transferring a Free R set.

2008-12-18 Thread Gerard DVD Kleywegt
a few öre's worth from sweden ... there is a surprising number of deposited ligand structures where re-refinement shows that the ligand is built into noise. nope, not surprised at all: - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=89 -

Re: [ccp4bb] Transferring a Free R set.

2008-12-23 Thread Gerard DVD Kleywegt
issue. Could I just confirm whether or not you think its necessary to transfer initial free R assignment to any new data sets or to isomorphous data sets such as substrate complexes. well, i would always do a slow-cool at the start so then it would not be necessary to transfer them ian

Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution

2008-12-24 Thread Gerard DVD Kleywegt
I struck with MR problem. MY target has 76% sequence identity with the model. I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. If you have any suggestions and or New programs I would like to try. that is odd. at 76% SI mol. repl. should normally be a breeze.

Re: [ccp4bb] structure (factor) amplitude

2009-01-12 Thread Gerard DVD Kleywegt
As suggested by Tassos, what we need now more than ever is some Dutch diplomacy so that he healing can really begin. Various people have argued for a shorter term (Brazilians, Pflugrath) and since I'm personally rather partial to Brazilians I would say we ought to go with that and shave off a

Re: [ccp4bb] Transfer Rfree flag

2009-01-30 Thread Gerard DVD Kleywegt
Can someone tell me if there is a relatively straightforward way of transferring Free R flags between two CNS format reflection files ? DATAMAN - http://xray.bmc.uu.se/usf/dataman_man.html#S63 --dvd **

Re: [ccp4bb] sparse matrix screen design

2009-01-30 Thread Gerard DVD Kleywegt
Are there any good free programs for the design of one's own sparse matrix screens? I am looking for something in the lines of a set of mixtures of what gives you the best coverage of, say, seven variables with five states each in 96 experiments. If memory serves, both Stefan Knight

Re: [ccp4bb] leela shetty sent you a Friend Request on Yaari

2009-02-14 Thread Gerard DVD Kleywegt
leela shetty wants you to join Yaari! Is leela your friend? Please respond or leela may think you said no :( This being Valentine's Day and all, am I the only one who is wondering if Leela and CCP4BB hit it off? --dvd **

Re: [ccp4bb] radiation damage

2009-02-27 Thread Gerard DVD Kleywegt
I even made the cover! And I hope that (after looking at the cover) all you BBers will forgive me just this once as this was clearly a once-in-a-lifetime opportunity. Or, at least, I HOPE only once. Congratulations, James. But surely you could have found a better example of medical imaging?

Re: [ccp4bb] Permanent industrial position for a PhD crystallographer in Munich, southern Germany

2009-04-08 Thread Gerard DVD Kleywegt
Only problem: it's in Bavaria... and we belive that you will need an excellent command of the German language both written and spoken to work here efficiently and live here happily. Dear das Doktor von Hannes! Ich das Jobb very interessiert ist worden worden geworden. Die Bayern placement

[ccp4bb] Three job openings for software engineers or scientific programmers at PDBe

2010-06-16 Thread Gerard DVD Kleywegt
The Protein Data Bank in Europe has *three* openings for software engineers or scientific programmers (one-year contracts): (1) The PDBe Team has an opening for a software engineer or scientific programmer to work in the NMR (Nuclear Magnetic Resonance) project. The post holder will work with

[ccp4bb] Welcome to the new PDBe website (pdbe.org)!

2010-07-01 Thread Gerard DVD Kleywegt
PDBe launches its redesigned website (pdbe.org) --- The Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched its redesigned website with lots of new features, enhancements and improvements. This so-called Midsummer Make-over is the first

[ccp4bb] Project Leader Electron Microscopy - position available at PDBe

2010-07-01 Thread Gerard DVD Kleywegt
The Protein Data Bank in Europe (PDBe; pdbe.org) has a vacancy for the Project Leader Electron Microscopy position. For more information: http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/w_10_059_ebi/index.html PDBe is the founder of the worldwide archive of 3D cryo-EM data, the

[ccp4bb] Introducing PDBeXplore - a browser of structural knowledge

2010-07-07 Thread Gerard DVD Kleywegt
Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB accession code, or by searches based on information regarding, for instance, a publication, a molecule name, a sequence or a related 3D structure. While these methods are valuable for locating a specific PDB entry or

Re: [ccp4bb] Question about the MStats utiliy in UPPSALA-mapman

2010-07-10 Thread Gerard DVD Kleywegt
Ni hao, (1) Will re m2 msk.mask ccp4 instead of re m2 msk.mask mask affect the results? Well, that depends entirely on what's in the file! The last parameter is your way of telling the program what the format of the file is. Mask means one of the MAMA-supported mask formats - ccp4 means a

Re: [ccp4bb] Judging a PDB

2010-07-13 Thread Gerard DVD Kleywegt
I am sorry, I have a very basic quarry regarding the PDB structures. How one can judge the quality of a deposited PDB data set? Suppose,for e.g., two PDB's have same R-values and have determined at same resolutions with same completeness. You may want to work your way through this tutorial:

[ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries

2010-07-15 Thread Gerard DVD Kleywegt
If you were born before the Dutch lost their first World Cup final, you may remember the days when everybody knew that PDB entry 1tim was the structure of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen egg-white lysozyme, etc. Unfortunately, life for a structural

Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries

2010-07-15 Thread Gerard DVD Kleywegt
http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here

[ccp4bb] Announcement: 2010 Cryo-EM Modelling Challenge and 2011 PSB Workshop

2010-07-15 Thread Gerard DVD Kleywegt
We are pleased to announce the 2010 Cryo-EM Modeling challenge and a PSB 2011 workshop, organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard Kleywegt. http://ncmi.bcm.edu/challenge * Modeling as a tool for interpretation of cryo-EM reconstructions * Cryo-EM

[ccp4bb] Update - PDBprints - salient, at-a-glance info about PDB entries

2010-07-16 Thread Gerard DVD Kleywegt
://pdbe.org/advancedsearch?text=lac+repressor If you want to read more about PDBprints, surf to: http://pdbe.org/pdbprints Thanks for your feedback! --Gerard On Thu, 15 Jul 2010, Gerard DVD Kleywegt wrote: If you were born before the Dutch lost their first World Cup final, you may remember

[ccp4bb] Introducing one-click access to PDB data at PDBe

2010-07-22 Thread Gerard DVD Kleywegt
Introducing one-click access to PDB data at PDBe When you visit the newly redesigned home page of the Protein Data Bank in Europe (PDBe; http://pdbe.org/), the panel in the centre of your screen (labelled Home) provides one-click access to PDB

[ccp4bb] SAXS/validation post-doc position available

2010-07-22 Thread Gerard DVD Kleywegt
There is an EMBL Interdisciplinary Post-doc (EIPOD) position available to work on the validation of low-resolution structural models obtained from small-angle X-ray scattering (SAXS). The project is a collaboration between EMBL Hamburg (Svergun), EMBL Heidelberg (Gavin) and the EBI (Kleywegt),

[ccp4bb] Introducing the PDBe Wizard - finding stuff on the PDBe website

2010-07-29 Thread Gerard DVD Kleywegt
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe website (PDBe; http://pdbe.org/), we introduced a new Wizard tool. The purpose of the Wizard is to help novice users find stuff on the site, be it one or more PDB or EMDB entries or information about PDBe tools,

[ccp4bb] Handy shortcuts to information on the PDBe website

2010-08-05 Thread Gerard DVD Kleywegt
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe (PDBe) website, we acquired the domain name pdbe.org and have used it to implement a number of shortcuts to many of our services etc. - http://pdbe.org/ - the new PDBe website - http://pdbe.org/1cbs - go directly to

[ccp4bb] Protein Data Bank in Europe roadshows and tutorials

2010-08-12 Thread Gerard DVD Kleywegt
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) offers a number of educational resources as part of its wider mandate for outreach and training within the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk/). As part of this commitment, we offer the PDBe roadshow

[ccp4bb] Job opportunities at the Protein Data Bank in Europe

2010-08-18 Thread Gerard DVD Kleywegt
There are three more vacancies coming up at the Protein Data Bank in Europe (PDBe; pdbe.org): - Head of PDBe Deposition and Annotation http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=MbkMjPUrEcTFkHhTczjobid=40182,2388233441 - 50% Oracle DBA/50% Senior Software Engineer

[ccp4bb] PDBePISA assembly, summary and XML data files available from the Protein Data Bank in Europe

2010-08-18 Thread Gerard DVD Kleywegt
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to announce the availability of PISA assembly files, summaries and associated XML descriptors for all relevant entries in the Protein Data Bank (PDB) archive for download and in-house analysis. PDBePISA

[ccp4bb] SIFTS mapping files between PDB and UniProt, Pfam, EC, CATH, SCOP, GO, etc. available from PDBe

2010-09-17 Thread Gerard DVD Kleywegt
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to announce the Structure Integration with Function, Taxonomy and Sequence (SIFTS) initiative, a close collaboration between PDBe and UniProt, that aims to improve the integration of the structural database and other

[ccp4bb] EMBL-EBI Services Survey

2010-09-20 Thread Gerard DVD Kleywegt
Dear colleagues, The EBI is carrying out a user survey about its services, collecting input from current and potential users. The survey lives here: http://www.surveymonkey.com/s/EMBL-EBI - It should take 10-15 minutes. - There are no compulsory questions. - You can be

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

2010-09-22 Thread Gerard DVD Kleywegt
Hi Ian, First, constraints are just a special case of restraints in the limit of infinite weights, in fact one way of getting constraints is simply to use restraints with very large weights (though not too large that you get rounding problems). These 'pseudo-constraints' will be

Re: [ccp4bb] I really need a file(such as .pdb) contains pseudo tanslation

2010-10-12 Thread Gerard DVD Kleywegt
For an older paper with several examples, see: Acta Cryst. (1993). D49, 505-512 [ doi:10.1107/S0907444993003737 ], Orientation of non-crystallographic symmetry axes in protein crystals, X. Wang and J. Janin My favourite example is 1cel: pdbe.org/1cel and pdbe.org/download/1cel (see:

[ccp4bb] Sweet and discreet tweets about helices and sheets - @PDBeurope

2010-10-14 Thread Gerard DVD Kleywegt
Following feedback from students, collaborators and other structural biologists, the Protein Data Bank in Europe (PDBe; pdbe.org) has become aware of a need for a social networking presence to strengthen the link with current and potential users of its resources. So if you would like to

[ccp4bb] Job opportunities at the Protein Data Bank in Europe (pdbe.org)

2010-11-11 Thread Gerard DVD Kleywegt
Hi all, We have two new openings at the Protein Data Bank in Europe (http://pdbe.org - part of the European Bioinformatics Institute in Cambridge, UK) to work in the Databases Services team: - Software/Database Engineer

Re: [ccp4bb] generating 2D projections

2010-12-01 Thread Gerard DVD Kleywegt
Not sure if this helps, but MAPMAN contains options to make 1D and 2D projections - see http://xray.bmc.uu.se/usf/mapman_man.html#S45 Many moons ago, I also wrote a script to generate general projections (e.g., onto the plane of an aromatic ring) using various USF programs - you may want to

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

2010-12-01 Thread Gerard DVD Kleywegt
This was one of the things that Indonesia was written for (a long time ago, in a galaxy far, far away), although I'm not sure if it will still run. If you're desperate, see http://xray.bmc.uu.se/~dennis/ --Gerard On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: Dear All; I have

Re: [ccp4bb] Can LSQKAB calculate RMSTAB for two pre-superposed structures?

2010-12-01 Thread Gerard DVD Kleywegt
If you have LSQMAN, this is trivial - read your superimposed files and use the RMsd_calc command - http://xray.bmc.uu.se/usf/lsqman_man.html#S59 --Gerard On Tue, 23 Nov 2010, Huiying Li wrote: Another question on RMSD: I have two structures of the same protein superposed with the LSQ

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