Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

2021-01-04 Thread Andreas Förster
ed office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED

[ccp4bb] Satellite meeting on MX raw image data formats, metadata and validation

2020-08-18 Thread Andreas Förster
of the meeting will only let the most dedicated scientists from the US attend. I hope to see many of you on Saturday. Andreas -- <https://www.dectris.com> Andreas Förster, Ph.D. Application Scientist Crystallography, Area Sales Manager Asia & Pacific Phone: +41 56 500 21 00 | Direct:

Re: [ccp4bb] number of frames to get a full dataset?

2020-06-29 Thread Andreas Förster
rrect. These minimum ranges for data collection rely on the crystal being > pre-oriented, which is unheard-of these days, although they can help if > someone is nagging you to get off the beam line or if your diffraction > fades quickly. Going for 180 degrees always makes sense for a well-behaved

Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread Andreas Förster
des symmetry and radiation damage? > > Thanks > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- <https://www.dectris.com> Andreas Förster, Ph.D.

Re: [ccp4bb] Dose in diffraction patterns?

2020-05-06 Thread Andreas Förster
ain information about the > x-ray absorbed dose? > > > > Thanks > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- <https://www.dectris.com> An

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

2020-03-19 Thread Andreas Förster
ge. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > ##

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

2020-03-19 Thread Andreas Förster
Hi Andreas, > > On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote: > > - The link to the raw data can be found inside the mmCIF file under > > _pdbx_related_exp_data_set.data_reference. Whether it's also shown on > one > > of the PDB sites is up to the designers

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

2020-03-19 Thread Andreas Förster
As someone who's done this (for one structure of minor significance), I would like to make a few comments: - I highly encourage deposition of raw data. Why would you not? Now that many labs are shut is the time to do it for all these datasets hiding somewhere on abandoned hard disk. These

Re: [ccp4bb] [3dem] Which resolution?

2020-02-23 Thread Andreas Förster
A very good point, Gerard, but maybe too late. It seems to me that a lot of microscopists have already given up this abundantly discussed question. They just call everything atomic resolution irrespective of whatever numerical value they arrive at by whatever means. All best. Andreas

Re: [ccp4bb] SeMet data

2019-08-27 Thread Andreas Förster
Dear Lindsey, I'm all with Nukri on this one. 12 Se atoms (whose incorporation you've shown) should be plenty to give you enough anomalous signal to phase the data and solve the structure. That's why I would do the simplest experiment first. Collect 360° of data at the peak energy, maybe a bit

Re: [ccp4bb] Better Beamline suggestion!

2019-08-19 Thread Andreas Förster
> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- <https://www.dectris.com> Andreas Förster, Ph.D. Application Scientist Crystallography Phone: +41 56 500 21 00 | Direct: +41

Re: [ccp4bb] cbf to sfrm

2019-07-30 Thread Andreas Förster
ad of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > #### > > To unsubscribe from the CCP4BB list, click the fol

Re: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets deadline 18th June!

2019-06-03 Thread Andreas Förster
Would it be fair to call it CCP40 now? Andreas On Mon, Jun 3, 2019 at 4:37 PM Paula Salgado wrote: > > > This year, CCP4 turns 40 and is celebrating in style with an event in > London. CCP4 has a strong focus on training the new generation of > crystallographers and developers so, as part

Re: [ccp4bb] beryllium chloride

2019-04-02 Thread Andreas Förster
uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > -- > > UT Southwestern > > Medical Center > > The future

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Andreas Förster
Yeah, good stuff: http://www.auspex.de/ All best. Andreas On Mon, Mar 25, 2019 at 10:45 AM CCP4BB < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Even if you can't see them, it may be worthwhile investigating with Auspex > (Parkhurst, Thorn, Winter & Waterman - sorry, I can't

Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Andreas Förster
--- > Aaron Finke > Staff Scientist, MacCHESS > Cornell University > e-mail: af...@cornell.edu > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUB

Re: [ccp4bb] suggestions for cryoprotectant

2018-10-20 Thread Andreas Förster
Dear Firdous, get some Mitegen sleeves and test your crystals at RT. Before you establish diffraction, there’s no need to agonize about cryo-conditions. Good luck! Andreas On Fri, 19 Oct 2018 at 23:57, Firdous Tarique wrote: > Dear members > > I have got beautiful crystal hits in SaltRx

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

2018-09-22 Thread Andreas Förster
Hi James, you’re probably aware of this but you can edit CBF headers in place with sed. That’s what I do when I make the detector on my diffractometer go closer than the hardware limit. All best - Andreas On Sat, 22 Sep 2018 at 00:51, James Holton wrote: > For teaching purposes I have found

Re: [ccp4bb] data processing with split/bad crystals

2018-07-16 Thread Andreas Förster
Dear Tommi, DIALS is good with multiple lattices. It might not have given you best results as part of the Diamond pipeline, but give it a try with the max_lattices=2 parameter during dials.index and see where it takes you. That said, you'll end up with worse statistics if you have two

Re: [ccp4bb] processing hd5 files from Dectris detector

2018-06-01 Thread Andreas Förster
lowing link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- <https://www.dectris.com> Andreas Förster, Ph.D. Application Scientist Crystallography, Scientific Sales Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: andreas.foers...@dectris.com DECTR

Re: [ccp4bb] Sulphur SAD at home source

2018-04-03 Thread Andreas Förster
amples and have an idea > of signal strength? > > Regards > Manoj > > > 2018-04-03 10:55 GMT-04:00 Andreas Förster <andreas.foers...@dectris.com>: > >> Dear Manoj, >> >> providing your crystals diffract to at least 2.5 Å and the sulfurs are >>

Re: [ccp4bb] Sulphur SAD at home source

2018-04-03 Thread Andreas Förster
people who have tried and failed would also be highly > appreciated. > > Thank you > Manoj Saxena > University of Puerto Rico > > > -- <https://www.dectris.com> Andreas Förster, Ph.D. MX Application Scientist, Scientific Sales Phone: +41 56 500 21 00 <+41%2056%205

Re: [ccp4bb] Eiger 16M detector in HKL2000

2017-12-18 Thread Andreas Förster
a few days), I wonder whether > someone can provide me your solution since this detector has been in market > for more than a year. Thank you for your help. > > Sincerely, > > Aidong > > -- <https://www.dectris.com> Andreas Förster, Ph.D. MX Application Scientist, Scie

Re: [ccp4bb] SHELXE: peptide occupancy refined to negative value

2017-08-14 Thread Andreas Förster
tween my data and SHELXE, which George was very quick to address. The latest version of SHELX (13 Aug 2017) does not throw this error and finishes chain tracing happily. Thank you, George. Andreas On Mon, Jul 10, 2017 at 5:51 PM, Andreas Förster < andreas.foers...@dectris.com> wrote: > Dea

Re: [ccp4bb] Pilatus Issues

2017-07-15 Thread Andreas Förster
e have recently noticed an issue with our Pilatus (biased pixels/vertical > lines). > I was curious as to whether anyone else has seen this or might know what > could have caused it? > > Best, > John > > > -- <https://www.dectris.com> Andreas Förster, Ph.D. MX Applicati

[ccp4bb] SHELXE: peptide occupancy refined to negative value

2017-07-10 Thread Andreas Förster
the error, SHELXE doesn't write phases. How do I get these? (I could do MR, but there must be a more elegant way...) Better yet, what might cause the "negative occupancy" error and how do I avoid it? Thanks and all best. Andreas -- <https://www.dectris.com> Andreas Förster, Ph.D

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

2017-04-21 Thread Andreas Förster
for the remaining part. But as I > dont see it, could the rest part be flexible? But again, this is not > reflected in the R factors (I would then expect low Rfree). > > Could it be that I still lack phases (due to partial occupancy of SeMeth > in N-terminal lobe ) and have to try to ge

[ccp4bb] Further information on the HDF5 read plugin for XDS

2017-03-23 Thread Andreas Förster
generic_close (error_flag) If you think you can write more efficient read routines for already supported formats, please contact Kay Diederichs. All best. Andreas -- <https://www.dectris.com> Andreas Förster, Ph.D. MX Application Scientist, Scientific Sales Phone: +41 56 500 2100 |

[ccp4bb] XDS plugin for efficient reading of HDF5 data

2017-03-23 Thread Andreas Förster
make the plugin better, to the benefit of the entire community. All best and happy data processing Andreas -- <https://www.dectris.com> Andreas Förster, Ph.D. MX Application Scientist, Scientific Sales Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email: andreas.foers...@dectr

Re: [ccp4bb] merge weak anomalous signal from multiple datasets

2015-03-01 Thread Andreas Förster
Hi Charles, I don't know what multiscale does. Probably the right thing. If the anomalous signal is weaker after scaling of multiple datasets, non-isomorphism might be at fault. Try Blend to scale your datasets. Blend is part of ccp4 and gives good graphical diagnostic feedback. Andreas

Re: [ccp4bb] Ramachandran maps

2014-12-11 Thread Andreas Förster
SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] CrystalClear tape rolls

2014-12-01 Thread Andreas Förster
Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology

Re: [ccp4bb] The phase problem

2014-11-05 Thread Andreas Förster
-Biotecnologia UNIFESP Laboratório de Biologia Estrutural Tel.: (12) 3309-9698 Rua Talim 330, Vila Nair CEP 12231-280 São José dos Campos - SP -- Andreas Förster X-ray Crystallograhpy Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] 3 letter code

2014-10-02 Thread Andreas Förster
to please tell me the 3 letter code for p nitrophenyl phosphate.. -- Regards Faisal School of Life Sciences JNU -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] XDS

2014-09-29 Thread Andreas Förster
crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

[ccp4bb] frozen pellet insoluble protein

2014-09-29 Thread Andreas Förster
-- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] is small dialysis tubes reusable??

2014-09-28 Thread Andreas Förster
of Biophysics National Institute of Mental Health and Neurosciences Bengaluru-29, Karnataka INDIA E-mail: manjula@gmail.com mailto:manjula@gmail.com Mobile no:+91-9538553356 http://www.nimhans.kar.nic.in/ https://www.nimhans.kar.nic.in/ -- Andreas Förster Crystallization

Re: [ccp4bb] Lattice Translocation Disorder Correction

2014-08-27 Thread Andreas Förster
as described in Wang et al (2004)?. Any input or sharing will be immensely helpful. Thanks a lot, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)*/ /*BARCELONA, SPAIN*/ / -- Andreas Förster Crystallization and X-ray Facility Manager

Re: [ccp4bb] dynapro DLS cuvettes

2014-08-15 Thread Andreas Förster
of a source of these cuvettes? Protein Solution doesn't exist anymore and Wyatt no longer has these. -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] Heavy Atom Phasing

2014-07-28 Thread Andreas Förster
a fair bit of time on optimization already). Thanks in advance, Rhys -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] rigaku micromax 007 cooling

2014-07-25 Thread Andreas Förster
, facilities people can change things and you'd never know until it's too late... Ed -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas Förster Sent: Thursday, July 24, 2014 10:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] rigaku micromax 007 cooling

[ccp4bb] rigaku micromax 007 cooling

2014-07-24 Thread Andreas Förster
with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

[ccp4bb] m_range_check error in aimless

2014-06-13 Thread Andreas Förster
and consequently ctruncate craps out because of no input file. This occurs with the temporary directory on NSF and local, and with one or two mtz files as input. How can I go beyond this? Andreas -- Andreas Förster Crystallization and X-ray Facility Manager

Re: [ccp4bb] NEW! Try depositing X-ray data using the wwPDB deposition system

2014-04-25 Thread Andreas Förster
://www.facebook.com/RCSBPDB -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] PyMol and Schrodinger

2014-04-23 Thread Andreas Förster
would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] Merging Data from Multiple Crystals

2014-03-29 Thread Andreas Förster
Contact James Foadi. http://diamond.ac.uk/Beamlines/Mx/I24/Staff/Foadi.html Andreas On 29/03/2014 1:21, Alexander Batyuk wrote: Dear Tassos, Do you know by chance whether BLEND is available? Best wishes, Alex

[ccp4bb] summary - small molecule crystallography

2014-03-25 Thread Andreas Förster
Thanks again for all the responses to my question about small-molecule crystallography. I almost regret having sent the student to the chemist. Trying this at home sounds like a fun afternoon. On the ccp4 wiki, there was already a section describing how to solve a small-molecule structure.

[ccp4bb] small molecule crystallography

2014-03-24 Thread Andreas Förster
to use software X to analyze data in space group P-43N would be welcome. Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-10 Thread Andreas Förster
if anybody has any ideas/thoughts what could be wrong/done I would greatly appreciate any insight. Kind regards, Matic -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

2014-02-23 Thread Andreas Förster
://www.cnb.csic.es/~mjvanraaij -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] Stereo monitor

2013-11-21 Thread Andreas Förster
___ -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

[ccp4bb] diffraction image repository

2013-11-20 Thread Andreas Förster
through well-thought out mask - upload any number of datasets (native, SeMet, etc) - make existence of datasets or datasets themselves public Any suggestions would be appreciated. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre

Re: [ccp4bb] Comparison of Water Positions across PDBs

2013-10-30 Thread Andreas Förster
that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

2013-10-23 Thread Andreas Förster
the iMosflm web site, put ipmosflm in my executable directory, and this seems to fix the problem. You should get the CCP4 folks to investigate this and propagate a fix. Cheers, -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural

Re: [ccp4bb] weekend puzzle

2013-09-17 Thread Andreas Förster
doesn't sit on a twofold. It might just remain undefined. Thanks anyway for all replies. Andreas On 13/09/13 17:50, Andreas Förster wrote: Dear all, a structure I'm refining is enjoying a free R factor of 18 but still suffers from mystery density that nothing in the crystallization

[ccp4bb] weekend puzzle

2013-09-13 Thread Andreas Förster
an idea of the size. http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png Happy guessing! Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology

Re: [ccp4bb] reversed stereo issue in coot and pymol

2013-06-20 Thread Andreas Förster
On 19/06/2013 6:44, jlliu liu wrote: I am sure if others have the similiar experience as me, sometimes when I launch pymol and coot, I got the reversed stereo view which is pretty annoying. I am using the ASUS VG278H LCD monitor... Thanks in advance for your advice. -- Andreas Förster

Re: [ccp4bb] Why the name aimless

2013-05-02 Thread Andreas Förster
Occasionally given to losing extremities. is that a good thing? Andreas On 02/05/2013 11:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a

Re: [ccp4bb] COOT running slow after upgrading to CENTOS 6.4 from 6.3

2013-03-20 Thread Andreas Förster
the python source code when it was running CentOS 6.3, could this be a problem? Zhijie -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

[ccp4bb] correction to: Post Doctoral Position at Imperial College London in Structural Biology

2013-02-28 Thread Andreas Förster
Dear all, the recent advertisement for a postdoc position in the Freemont/Zhang labs at Imperial had a small error in the job code needed to find it online. The correct code is NS 2013 047 IL Use it at http://www3.imperial.ac.uk/employment (Job search) to apply for the position. Closing

Re: [ccp4bb] ccp4 update

2013-01-16 Thread Andreas Förster
Ah, I see. This was part of update 10. Thank you. Andreas On 16/01/2013 2:51, Qixu Cai wrote: Dear Andreas Förster, You can use ccp4um (ccp4 update manage) to update CCP4 from command line. Best wishes, Q. Cai -- Andreas Förster, Research Associate Paul Freemont

[ccp4bb] ccp4 update

2013-01-14 Thread Andreas Förster
/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research

Re: [ccp4bb] vitrification vs freezing

2012-11-15 Thread Andreas Förster
you need to be 100% unambiguous. Cheers, Tim -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

[ccp4bb] map sharpening

2012-09-26 Thread Andreas Förster
difference between enabling/disabling map sharpening? Cheers, Rob -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

[ccp4bb] low-resolution refinement

2012-09-25 Thread Andreas Förster
break, but no maps are displayed. This is independent of the sharpening factor I choose (between 5 and 60). Thanks for your help. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

[ccp4bb] imosflm background definition

2012-09-17 Thread Andreas Förster
. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk attachment: backgroundSpots.png

Re: [ccp4bb] Various OSes and Crystallography

2012-08-09 Thread Andreas Förster
Mac OSX because of Time Machine, Illustrator and crystallographic software in one happy box. XP on a Virtual Box for emergencies (SAXS, AUC and ITC programs). Though with Microsoft and Apple both pushing towards gestures, fingertip interaction and tablets, Linux will be the only option for

[ccp4bb] NCS on multiple conformations

2012-06-29 Thread Andreas Förster
Dear all, ok, never mind. I defined either peptide conformation as part of the protein it binds to and applied NCS to that. Should have thought of that before sending out the question. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs

[ccp4bb] NCS on multiple conformations

2012-06-29 Thread Andreas Förster
way of dealing with this situation? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-02 Thread Andreas Förster
Dear Gerard, inside Germany it's apparently called German Humour. There's a Wikipedia entry for that as well. Go figure: http://en.wikipedia.org/wiki/German_humor Andreas (still living on Sunday time) On 02/04/2012 4:03, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-02 Thread Andreas Förster
That's pretty funny, isn't it? Andreas On 02/04/2012 6:52, Jacob Keller wrote: Sorry to beat a dead horse, but: * *Antiwitz* (/anti-joke/): A short, often absurd scene, which has the recognizable structure of a joke, but is illogical or lacking a punch-line. Example: /Two

Re: [ccp4bb] live streaming of ccp4 study weekend

2012-01-05 Thread Andreas Förster
, or Chrome using a Mac with OS 10.6.8. David Mueller -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Off topic: Kendrew Model

2011-11-01 Thread Andreas Förster
it in my dining room if I can get it in the door. Any suggestions would be appreciated. Cheers, Katherine -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Mac OSX 10.7 Lion

2011-09-19 Thread Andreas Förster
won't let you trash documents The operating system for the nanny state? http://www.reghardware.com/2011/09/07/apple_mac_os_x_lion_the_nanny_os/ One of the reasons why I'm sticking with Snow Lepoard for now Regards, Peter. -- Andreas Förster, Research Associate Paul Freemont

Re: [ccp4bb] Trying to digest PISA results

2011-09-05 Thread Andreas Förster
does not show anything, but the binding constant is really strong? Or vice versa, the binding is completely undetectable, but the functional assay shows something? JPK -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial

[ccp4bb] more Computer encryption matters

2011-08-18 Thread Andreas Förster
problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] BLT wish

2011-08-17 Thread Andreas Förster
/ccp4-6.2.0-c5/ccp4i/bin/loggraph line 5) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

[ccp4bb] protein segments from pdb

2011-08-10 Thread Andreas Förster
to open the pdb file with PyMOL and click on the ends, but a script/command would be much quicker. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] protein segments from pdb

2011-08-10 Thread Andreas Förster
PRO 21 SER 36 THR 28 TRP 5 TYR 13 VAL 26 HEM 0 WAT 0 SUL 0 END 0 DUM 0 Other 6 HTH Martyn On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote: Dear all, how do you extract segments from a pdb file, so that from an input pdb file you

Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13

2011-08-09 Thread Andreas Förster
, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window ccp4i works -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry

Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?

2011-07-28 Thread Andreas Förster
the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Andreas Förster, Research Associate Paul Freemont

Re: [ccp4bb] Fab:antigen complex crystallization!!!

2011-07-28 Thread Andreas Förster
for such problems which have routinely been practiced in their lab Also what is a good storage condition for the excess complex that you want to use later? I would really appreciate any suggestion,help, direction. Thanks ivan -- Andreas Förster, Research Associate Paul Freemont

Re: [ccp4bb] Lion kills moleman (and all other USF programs on the Mac)

2011-07-22 Thread Andreas Förster
, living or dead, is purely coincidental. ** -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0

2011-07-19 Thread Andreas Förster
-- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http

[ccp4bb] mutation and minimization - SUMMARY

2011-05-13 Thread Andreas Förster
, but not natively on Linux - mutate and regularize geometry in coot - phenix.pdbtools from the command line (might be able to minimize only part of the model) Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial

[ccp4bb] mutation and minimization

2011-05-12 Thread Andreas Förster
-- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

[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

[ccp4bb] image file extensions

2011-02-09 Thread Andreas Förster
is economizing disk space. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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

2010-12-20 Thread Andreas Förster
replacement. And both structures have much different, especially in B chain. If my structure is a new one? thank you for help. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http

Re: [ccp4bb] Protein sequencing service?

2010-11-24 Thread Andreas Förster
85kDa.Our funds are somewhat limited. Thanks in advance. Rex Palmer Birkbeck College, London RexPalmer2010.homestead.com -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http

[ccp4bb] database-assisted data archive

2010-08-18 Thread Andreas Förster
place (some file server that's periodically backed up) and let users browse through all the collected data of the lab with minimal effort later. I doesn't seem too hard to implement this, which is why I'm asking if anyone has done so already. Thanks. Andreas -- Andreas Förster

Re: [ccp4bb] database-assisted data archive

2010-08-18 Thread Andreas Förster
brilliantly - it is now pretty straightforward to access any data back to ~ 1998 I think.. Eleanor j...@ysbl.york.ac.uk Andreas Förster wrote: Dear all, going through some previous lab member's data and trying to make sense of it, I was wondering what kind of solutions exist to simply the archiving

[ccp4bb] summary - SAXS EM comparison

2010-07-28 Thread Andreas Förster
. Andreas On 23/07/2010 11:54, Andreas Förster wrote: Dear all, the other day I obtained SAXS data from which a low-resolution structural model was calculated. The model is simpler/less complex than one of the same protein that we obtained with cryo-EM. Is there a way to estimate theoretical SAXS data

Re: [ccp4bb] SAXS EM comparison

2010-07-26 Thread Andreas Förster
understand that there would be a huge amount of handwaving involved, but it might help us reconcile our models. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] N-terminal sequencing

2010-04-16 Thread Andreas Förster
that accurately but affordably makes N-terminal sequencing ? Thanks a lot in advance to everybody. Best regards, Xavier -- -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] slow graphic in mac 10.6

2010-02-15 Thread Andreas Förster
glxgears, it only shows about 1400 FPS. If I open pymol, I can actually see the images are flashing. Does anyone know why? Thanks a bunch. Rui -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] slow graphic in mac 10.6

2010-02-15 Thread Andreas Förster
reboot of the machine... Cheers, Serge. Le 15 févr. 2010 à 10:44, Andreas Förster a écrit : Hey Rui, for what it's worth, I had a very similar problem. I upgraded a MacBook Pro to OSX SP6 and got extra-slow graphics and a wildly flickering PyMOL window - only on the laptop screen, though

Re: [ccp4bb] DLS

2010-02-04 Thread Andreas Förster
: +48-61-8520532 Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/ 61-704 Poznan, Poland -- -- Andreas Förster, Research

[ccp4bb] arp/warp installation

2010-01-04 Thread Andreas Förster
- installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] arp/warp installation

2010-01-04 Thread Andreas Förster
On 4 Jan 2010, at 11:15, Andreas Förster wrote: Dear all, I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up to and including refmac version check (see log below). After that, a Badly formed number in an if test. What could be the issue? The system

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