Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Deepthi, is it just a typo, or do your last two sentences say that your data DO NOT scale in P312 but scale well in P321? Did you try pointless for space group determination? I have not used molrep for this purpose and cannot judge how reliable

Re: [ccp4bb] Who is using 64-bit Linux?

2012-04-05 Thread Harry Powell
Hi David I'm curious - do you mean running on a 32-bit Centos box or running the 32-bit Mosflm executable on a 64-bit Centos box? We did have one report of problems with the 32-bit exe on a 64-bit box, which (seemingly) randomly gave one of two different results (either the same failure

Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Clemens Vonrhein
Hi, On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote: Hello everyone I have a problem scaling the MAD data which was collected a week ago.The data was collected at 1.5A resolution using three wavelengths for Zn-MAD experiments. Scaling the data for MAD experiments, the number of

Re: [ccp4bb] arp_waters still available?

2012-04-05 Thread Victor Lamzin
Dear Bernard, arp_waters is a very old code and it gets even older as we speak. Try to use ARP/wARP version 7.2, where you can run the same task: from the command line ($warpbin/auto_solvent.sh) from the CCP4i GUI (ARP/wARP Solvent) from ArpNavigator (Model Solvent) There should be both 32 and

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread John R Helliwell
Dear 'aales...@burnham.org', Re the pixel detector; yes this is an acknowledged raw data archiving challenge; possible technical solutions include:- summing to make coarser images ie in angular range, lossless compression (nicely described on this CCP4bb by James Holton) or preserving 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

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Herbert J. Bernstein
Dear Colleagues, Clearly, no system will be able to perfectly preserve every pixel of every dataset collected at a cost that can be afforded. Resources are finite and we must set priorities. I would suggest that, in order of declining priority, we try our best to retain: 1. raw data that

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Roger Rowlett
FYI, every NSF grant proposal now must have a data management plan that describes how all experimental data will be archived and in what formats. I'm not sure how seriously these plans are monitored, but a plan must be provided nevertheless. Is anyone NOT archiving their original data in some way?

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bosch, Juergen
I would say everybody keeps probably too many junk datasets around - at least I do. And I run into the trouble of having to buy new TB plates every now and then. I think on average per year my group acquires currently ~700 GB of raw images (compressed), now if we were to only keep the useful

[ccp4bb] Category 4 Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Jrh
Dear Herbert, Category 4, in Manchester, we find is tricky, for want of a better word. Needless to say that we have collaborators on our Crystallography Research Service who request data sets from eg ten years ago, that are now urgent for publication writing up. So we are keeping everything,

[ccp4bb] Via Annual Reports...Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Jrh
Dear Roger, At the recent ICSTI Workshop on Delivering Data in science the NSF presenter, when I asked about monitoring, replied that the PIs' annual reports should include data management aspects. See http://www.icsti.org/spip.php?rubrique42 Best wishes, John Prof John R Helliwell DSc FInstP

[ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Francis E Reyes
It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Pete Meyer
Have you tried mtz2various (with cif output)? Pete Francis E Reyes wrote: It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote: It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? Maybe I missed something. What is accomplished by depositing map coefficients that isn't done better by depositing Fo

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Miller, Mitchell D.
I have not tried it, but the latest version of the rcsb program sf-convert is supposed to support it (see version 1.2 released March 23) http://sw-tools.pdb.org/apps/SF-CONVERT/index.html http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-2-00/documentation.html (Version 1.2 is not yet available as

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Phil Jeffrey
Fc doesn't contain the weighting scheme used in the creation of the map coefficients, so Fc would require some sort of program to be run to recreate those for both 2Fo-Fc and Fo-Fc maps. By which time you might as well run a single cycle of the refinement program in question to generate new

Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Deepthi
Hello I arrived at the p312 space group by running a self rotation function using MOLREP. The maps show the space group as p312. I was scaling the data individually for each wavelength. None of the three wavelengths are scaling are scaling in p312 space group. On Thu, Apr 5, 2012 at 2:17 AM,

Re: [ccp4bb] problem in scaling the Zn-MAD data

2012-04-05 Thread Matthew Franklin
Hi - Let me just add that P312 is a very uncommon space group for protein crystals, much less common than P321. (This doesn't mean you don't have it - it's just unlikely.) If you look at PDB statistics: P 3 1 2 : 12 structures P3(1) 1 2: 61 structures P3(2) 1 2: 85 structures P 3 2 1 :

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote: Fc doesn't contain the weighting scheme used in the creation of the map coefficients, so Fc would require some sort of program to be run to recreate those for both 2Fo-Fc and Fo-Fc maps. The viewers I am familiar with do this for

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Oliver Smart
On Thu, 5 Apr 2012, Ethan Merritt wrote: On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote: Fc doesn't contain the weighting scheme used in the creation of the map coefficients, so Fc would require some sort of program to be run to recreate those for both 2Fo-Fc and Fo-Fc maps. The

[ccp4bb] PDF position Structural Cell Biology - Michigan

2012-04-05 Thread Amir Khan
Hi, I would like to advertise a position on behalf of Prof. Lois Weisman ((Michigan). Interested parties should contact her directly (lweisman.off...@gmail.commailto:lweisman.off...@gmail.com). -Amir Postdoctoral Fellow Position Integration of high resolution structures with biology Seeking a

Re: [ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Ethan Merritt
On Thursday, April 05, 2012 10:48:16 am Oliver Smart wrote: On Thu, 5 Apr 2012, Ethan Merritt wrote: On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote: Fc doesn't contain the weighting scheme used in the creation of the map coefficients, so Fc would require some sort of program

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Dear John, Thank you for a very informative letter about the IUCr activities towards archiving the experimental data. I feel that I did not explain myself properly. I do not object archiving the raw data, I just believe that current methodology of validating data at PDB is insufficiently robust

[ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
Can MOSFLM work with image files of type .x (BNL X6A) ? I am having no luck... I know it can do .cbf (BNL X25) for instance. Thanks a lot

[ccp4bb] Position in Structural Biology of Signaling

2012-04-05 Thread Qiang Chen
There is an immediate opening for a protein crystallographer position in Harvard Medical SchoolÂ’s ChildrenÂ’s Hospital. The research is focused on the structural and functional investigation of Wnt signaling pathway. The project is the close collaborative efforts between Professors Xi He and

[ccp4bb] postdoctoral position at the NIH focused on understanding the mechanism of cytoskeletal regulators

2012-04-05 Thread ANTONINA ROLL-MECAK
Postdoctoral positions are available in the Cell Biology and Biophysics Unit headed by Dr. Antonina Roll-Mecak at the National Institute of Neurological Disorders and Stroke. The Roll-Mecak Laboratory is interested in understanding the interplay between microtubules and their regulators

Re: [ccp4bb] MOSFLM- Image compatibility

2012-04-05 Thread Yuri Pompeu
thanks for kindly pointing that out. (despite the level of stupidity on my part) Those were not the raw imgs... They were denzo output files. Its been a while.

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Ronald E Stenkamp
This discussion has been interesting, and it's provided an interesting forum for those interested in dealing with fraud in science. I've not contributed anything to this thread, but the message from Alexander Aleshin prodded me to say some things that I haven't heard expressed before. 1. The

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bernhard Rupp (Hofkristallrat a.D.)
I also don't really worry about the images as a primary means of fraud prevention, although such may be a useful side effect. These cases are spectacular but so rare that it indeed would not primarily justify the effort. That it can be a useful political instrument to make that argument and get

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Well, looks like my opinion about importance of data validation at the moment of their submission does not catch much support, it is sad but understandable. Automatic redoing the pdb structures by professionals is a good idea, I myself suggested a similar thing 10 years ago at Accelrys (we

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bernhard Rupp (Hofkristallrat a.D.)
Ojweh c) Discarding your primary data is generally considered bad form... Agreed, but it is a big burden on labs to maintain archives of their raw data indefinitely. Even IRS allows to discard them after some time. But you DO have to file in the first place, right? How long to keep is an

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Alright, if the image deposition is the only way out, then I am for it, but please make sure that synchrotrons will do it for me... On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Ojweh c) Discarding your primary data is generally considered bad form... Agreed,

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread Bosch, Juergen
How should they ? They have no clue which of the 20 datasets was actually useful to solve your structure. If you ask James Holton he has (suggested) to go back to the archived data after a certain time and try to solve the undeposited structures then :-) [Where is James anyhow ? Haven't seen a

Re: [ccp4bb] very informative - Trends in Data Fabrication

2012-04-05 Thread aaleshin
Did you play as a child a game called a broken phone? It is when someone tells something quickly to a neighbor, and so on until the words come back to the author. Very funny game. My original thesis was that downloading/depositing the raw images would be a pain in the neck for