Re: [ccp4bb] coot-scripting

2011-02-09 Thread Bernhard C. Lohkamp
Hi Seema, for python scripting in Coot (and syntax) you may want to refer to the WIKI: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_Scripts or the manual: http://www.biop.ox.ac.uk/coot/doc/user-manual.html#Scripting I meant to complete a more comprehensive man

[ccp4bb] coot-scripting

2011-02-09 Thread Seema Nath
Hi, I'm using COOT-0.6 following the manual,but while trying to use (calculate>scripting>)>python or (calculate>scripting>)>scheme to write any command (say,set_show_origin_marker 0) it shows "BL WARNING:: Python syntax error! (Or you attempted to use an invalid guile command...) Py

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Hudel Luecke
James, I must admit not (yet) having read the "data processing paper PMID: 20389587" nor the 88 author paper. Nevertheless, I would like to comment on your remark "Personally, I was quite impressed by how good the R factors were, all things considered." If I am not mistaken, perfectly twinne

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread Das, Debanu
Hi Dale, Thanks for posting this interesting piece of history. My non-PX initiation into PX was through DEC too. On a summer internship in 1996 after my junior year, I landed up at this institute which had just received their new DEC ALPHA2000. My project was to write up a C code (I had rece

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread James Holton
The twin fraction for REFMAC was exactly 0.5. The individual crystals were not twinned (or at least I would be VERY surprised if they were), but they do belong to the space group P63, and autoindexing will give you one of the two possible axis conventions at random. So, of the 15445 crystals that

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Axel Brunger
I performed DEN-refinement with CNS using the same data and starting model, and obtained similar "twinned" R values and maps. The twin fraction is 0.5. Axel On Feb 9, 2011, at 3:29 PM, Jon Schuermann wrote: > According to the paper, the data was refined in REFMAC in 'twin mode' which, > I

[ccp4bb] ctruncate - FP=0?

2011-02-09 Thread Ed Pozharski
I observe under some conditions that ctruncate sets some reflections amplitudes to zero. AFAIU, this should not be happening as even negative intensities (there are none in this particular dataset) should produce FP>0 upon truncation. 66 out of ~23000 reflections are zeros after ctruncate is ap

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Jon Schuermann
According to the paper, the data was refined in REFMAC in 'twin mode' which, I believe, calculates the R-factor using a non-conventional R-factor equation which usually lower than the conventional R-factor. I believe this is dependent on the twin fraction which wasn't mentioned in the paper (o

[ccp4bb] CCP4i doesn't run

2011-02-09 Thread Yong-Fu Li
Hi, I am using CCP4 6.1.13 in Windows 7. It worked fine after installation, but now stopped running after I moved CCP4-DATABASE to a subdirectory for consolidation. So I uninstalled the whole program and removed folders (CCP4-Packages and Ccp4Temp) from C: drive, and then I downloaded it again and

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread James Holton
This was "molecular replacement" from 1jb0, so the phases came from the model. Probably more properly called "direct refinement" since all we did was a few cycles of rigid body. Personally, I was quite impressed by how good the R factors were, all things considered. -James Holton MAD Scientist

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

2011-02-09 Thread Roberts, Sue A - (suer)
I have used phaser to successfully solve a structure in P2x2x2x that had pseudo-translational symmetry. It was unable to correctly choose the space group, but after running phaser in all 8 possible space groups and inspecting the best solutions in each the correct solution was clear. Furthermo

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Bernhard Rupp (Hofkristallrat a.D.)
Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with a

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

2011-02-09 Thread Garib N Murshudov
molrep can deal with some of the PST cases. Garib On 9 Feb 2011, at 22:27, Phil Jeffrey wrote: > Is there a program that does ? I was under the impression that they were all > equally good/bad at this, because any solution that agrees with the PTS has > quite a high score and any solution tha

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

2011-02-09 Thread Phil Jeffrey
Is there a program that does ? I was under the impression that they were all equally good/bad at this, because any solution that agrees with the PTS has quite a high score and any solution that doesn't has a low score, irrespective of the correctness of the placement of the molecules. In one

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

2011-02-09 Thread Jon Schuermann
Just to add to Phil and Eleanor's response... I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better. Its probably not C-centered (as Eleanor mentions) and you should try t

Re: [ccp4bb] image file extensions

2011-02-09 Thread Phil Jeffrey
find . -name '*.osc' -or -name '*.img' -type f -size +3000 -print -exec bzip2 '{}' \; is a personal favorite, along those lines, with ample opportunities for customization. (If the above command line wraps, it's all supposed to be on one line) Phil Jeffrey Princeton On 2/9/11 2:46 PM, Davi

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Thomas Juettemann
Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton wrote: > > As one of the people involved (I'm author #74 ou

Re: [ccp4bb] image file extensions

2011-02-09 Thread David Schuller
On 02/09/11 09:49, Andreas Förster wrote: Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas /bin

[ccp4bb] Max F. Perutz International PhD Program Vienna 2011

2011-02-09 Thread Kristina Djinovic Carugo
Dear All, I would like to point your attention to: *Max F. Perutz International PhD Program Vienna 2011* The Max F. Perutz Laboratories is inviting applications from talented students all over the world for our graduate program. The institute is located at the Vienna Biocenter Campus - a maj

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread James Holton
As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the "minimum" number that were needed to get a useful data set. The b

Re: [ccp4bb] image file extensions

2011-02-09 Thread Georg Zocher
Dear Andreas, I had the same problem frequently and wrote a little python-script for compressing our images on our server. It might help you and you can easily modify the extension for which the script should search for... Best Regards, Georg -- code starts below #!/usr/bin/pytho

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Colin Nave
By "That's" I presume Bob means "the 0.01% bandwidth figure is" approximately the intrinsic bandwidth of a Si (111) monochromator. The 0.1% bandwidth in the title of the email is the standard bandwidth often used to define the output of synchrotron sources. When defining flux within a certain

[ccp4bb] First images of proteins and viruses caught with an X-ray laser

2011-02-09 Thread Thomas Juettemann
http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: "The team combined 10,000 of the three million snapshots they took to come up

[ccp4bb] N-terminal sequencing facility summary

2011-02-09 Thread Junyu Xiao
Dear all, Thanks for your hearty responses. Below is a summary for the information I received. Again, I really appreciate all the help. Best regards, Junyu 1. Yale University, University of Utah, and Wake Forest University are three that have core facilities which perform N-terminal seque

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Robert Sweet
That's approximately the bandwidth of a Si (111) monochromator. On Wed, 9 Feb 2011, Andre Luis Berteli Ambrosio wrote: Dear ccp4bb,   I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1% bandwidth” instead of simply “photons/s”. Where does the “1/0.1% bandwidth”

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread David Waterman
Dear Jacob, Regarding your second question, I stumbled across a relevant article on Wikipedia recently: en.wikipedia.org/wiki/Megahertz_myth Cheers, David. On 9 Feb 2011 13:53, "Jacob Keller" wrote: > I love hearing these types of stories, which have a few effects on me: > > -Admiration of those

[ccp4bb] image file extensions

2011-02-09 Thread Andreas Förster
Harry Powell had the most comprehensive answer, giving me the extensions that are used in mosflm: .img .mar* (i.e. .mar1600, .mar2300, etc) .mccd .osc .SFRM .sfrm .image .ipf .cbf In addition, finding files larger than a certain cutoff might do the trick too - especially if the objective is

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread Ethan Merritt
On Tuesday, February 08, 2011 11:47:04 pm Dale Tronrud wrote: > I see in the news that Ken Olsen has died. Although he was > not a crystallographer I think we should stop for a moment to > remember the profound impact the company that this man founded > had on our field. > > My first expe

Re: [ccp4bb] Detaching crystals from glass cover slides

2011-02-09 Thread Savvas Savvides
Dear Wataru check out the following entry on the CCP4-wiki on 'sticky crystals' which we compiled based on feeback from many crystallographers: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals Best regards Savvas Savvas Savvides Unit for Structural Biology @ L-P

Re: [ccp4bb] Detaching crystals from glass cover slides

2011-02-09 Thread Benjamin Apker
Hi Wataru, Have you tried Mitegen's polymer MicroTools? These tools have tips made from soft, flexible microfabricated polymer films and are specifically designed for this type of application. There is more information about them here ( http://mitegen.com/products/microtools/microtools.shtml

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Colin Nave
And before anyone else points out the mistake Flux in magnetism is the magnetic field (e.g. no. of lines) over a defined area. Some similarity to photons/sec over a defined area for x-ray sources Well I think this is right. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC

Re: [ccp4bb] image file extensions

2011-02-09 Thread Clement Angkawidjaja
.ipf if you have files from (old) image plate detectors. clement > Dear all, > > I'm trying to create some space on our server and want to compress all > x-ray data files. I'm wondering what extensions I should search for. > mccd and img come to mind easily. What other extensions are commonly >

Re: [ccp4bb] Detaching crystals from glass cover slides

2011-02-09 Thread Colbert, Christopher
Hi Wataru, I second Bill's suggestion. Additionally, you might want to migrate to a sitting drop setup and use the vacuum grease with that. It worked for me. Happy Fishing, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State U

Re: [ccp4bb] Detaching crystals from glass cover slides

2011-02-09 Thread Jim Pflugrath
Cool the coverslip on the opposite side of the crystal with a chip of dry ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I wonder if you can simply move the whole tray into a cooler temperature? You can imagine that the thermal expansion coefficient of the glass cover

Re: [ccp4bb] N-terminal sequencing

2011-02-09 Thread Prince, D Bryan
I think that this CRO can help you: Proteos 4717 Campus Drive Kalamazoo, Michigan 49008 269.372.3423 http://www.proteos.net Good luck! Bryan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Junyu Xiao Sent: Tuesday, February 08, 2011 2:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject:

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Colin Nave
Andre I should have replaced flux in my email by photons/sec to be clear (or at least a bit clearer). Flux in magnetism is the strength of the magnetic field per unit area so it is confusing to use the term in the way I did. Different fields use the same term for different purposes. Techn

Re: [ccp4bb] image file extensions

2011-02-09 Thread Jacob Keller
.osc 2011/2/9 Andreas Förster : > Dear all, > > I'm trying to create some space on our server and want to compress all x-ray > data files.  I'm wondering what extensions I should search for. mccd and img > come to mind easily.  What other extensions are commonly used? > > Thanks. > > > Andreas > >

[ccp4bb] image file extensions

2011-02-09 Thread Andreas Förster
Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas Förster, Research Associat

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Colin Nave
Andre The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness (flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an emittance rather than an acceptance. A typical perfect crystal monochromator might take (i.e. accept) a tenth of this. However, dependent on the range of

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread Peter Keller
Hi Jacob, On Wed, 9 Feb 2011, Jacob Keller wrote: Regarding the last point, does anybody have a good response to the Moore's law conundrum that some programs which will take, say, ten years to run now will take only ~1 year to run 8 years from now, making it futile to run the program now? Maybe

Re: [ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Jrh
Dear Andre For a continuum wavelength band source this unit is needed. A monochromator of a given type then extracts it's rocking curves worth of bandpass. Or in Laue diffraction a wide band is selected with eg a mirror cut off at short wavelengths and a filter or transmission mirror at long wav

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread Jacob Keller
I love hearing these types of stories, which have a few effects on me: -Admiration of those who worked with so little to produce so much -Thankfulness for the resources we have now -Excitement for the forthcoming technogies -Despair about using current technologies, knowing they will be supplanted

[ccp4bb] Graduate Student Summer Internship at Merck

2011-02-09 Thread Soisson, Stephen M
Hi Everyone, Merck Research Laboratories has an opening for a summer intern in the Structural Chemistry (X-ray crystallography) groups located in either Kenilworth, NJ or West Point, PA. The idea is to have someone comfortable with programming and mathematics to explore some computational ideas t

[ccp4bb] Application Scientist position at Agilent Technologies (formerly Oxford Diffraction), Yarnton, UK

2011-02-09 Thread Tadeusz Skarzynski
The Agilent Technologies' X-ray Diffraction department, located in Yarnton near Oxford, is looking for an Application Scientist to join a small team of highly-skilled chemical and macromolecular crystallographers. Your principle activities within the team will include macromolecular X-ray data

[ccp4bb] Why 0.1% bandwidth?

2011-02-09 Thread Andre Luis Berteli Ambrosio
Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of "photons/s/0.1% bandwidth" instead of simply "photons/s". Where does the "1/0.1% bandwidth" unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw... Is it simply defining some degree of acceptanc

[ccp4bb] group defs for refmac rigid body

2011-02-09 Thread Tim Gruene
Dear all, is there a short cut to define an entire chain as one group in the rigid body refinement of refmac, or do I have to explicitly name the starting and ending residues - that's a little tedious with several domains, and using a wild card would come very handy. Cheers, Tim -- -- Tim Gruen

[ccp4bb] Fw: RE: Preliminary studies

2011-02-09 Thread REX PALMER
--- On Wed, 9/2/11, geoffrey kamau wrote: From: geoffrey kamau Subject: RE: Preliminary studies To: rex.pal...@btinternet.com Date: Wednesday, 9 February, 2011, 9:03 Dear Dr. Rex Palmer, Thanks for the message. Yes, we have been using X-ray diffraction cameras, particularly with respect t

Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday

2011-02-09 Thread Robert Esnouf
At times DEC we innovative in ways that no hardware company today even comes close. But I guess innovation and commercial success do not go hand in hand. OK, this is abridged from Wikipedia, but much of it is true... Digital supported/developed the ANSI standards, especially the ASCII and mult

[ccp4bb] The 2nd Advanced Protein Characterisation and Crystallisation Course in Helsinki, Finland

2011-02-09 Thread tommi kajander
Dear all, I would like to draw your attention to the following protein crystallization and characterization course we are offering: 2nd Advanced Protein Characterisation and Crystallisation Course: May 2.- 6. 2011 The Biocenter Finland Protein crystallisation unit is again organising an

Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).

2011-02-09 Thread Eleanor Dodson
Yees - a translation of 0.5 along x means you must consider SGs P212121 and P2 21 21 since the absences will be present (at least at low resolution) with either SG. I dont know how good Phenix would be at distinguishing between z=0.233 and z=0.25 However even if the exact peak is at z0.25, i

Re: [ccp4bb] N-terminal sequencing

2011-02-09 Thread pankaj gupta
Dear Daniel, You can get it here as well... University of Pittsburgh Department of Biological Sciences Fifth and Ruskin Aves Clapp Hall 301 Pittsburgh PA 15260 email: hem...@pitt.edu ph: 412.624.0106 or Jack Presley Laboratory Manager UC Davis Molecular Structure Facility http://msf.ucdavis.edu