Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear Ron, Re (3):- Yes of course the investigator has that responsibility. The additional point I would make is that the employer has a share in that responsibility. Indeed in such cases the employer university convenes a research fraud investigating committee to form the final judgement on continued employment. A research fraud policy, at least ours, also includes the need for avoding inadvertent loss of raw data, which is also deemed to be research malpractice. Thus the local data repository, with doi registration for data sets that underpin publication, seems to me and many others, ie in other research fields, a practical way forward for these data sets. It also allows the employer to properly serve the research investigations of its employees and be duely diligent to the research sponsors whose grants it accepts. That said there is a variation of funding that at least our UK agencies will commit to 'Data management plans'. Greetings, John 2012/4/5 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 sky is not falling! The errors in the birch pollen antigen pointed > out by Bernhard are interesting, and the reasons behind them might be > troubling. However, the self-correcting functions of scientific research > found the errors, and current publication methods permitted an airing of the > problem. It took some effort, but the scientific method prevailed. > > 2. Depositing raw data frames will make little difference in identifying and > correcting structural problems like this one. Nor will new requirements for > deposition of this or that detail. What's needed for finding the problems is > time and interest on the part of someone who's able to look at a structure > critically. Deposition of additional information could be important for that > critical look, but deposition alone (at least with today's software) will not > be sufficient to find incorrect structures. > > 3. The responsibility for a fraudulent or wrong or poorly-determined > structure lies with the investigator, not the society of crystallographers. > My political leanings are left-of-central, but I still believe in individual > responsibility for behavior and actions. If someone messes up a structure, > they're accountable for the results. > > 4. Adding to the deposition requirements will not make our science more > efficient. Perhaps it's different in other countries, but the administrative > burden for doing research in the United States is growing. It would be > interesting to know the balance between the waste that comes from a wrong > structure and the waste that comes from having each of us deal with > additional deposition requirements. > > 5. The real danger that arises from cases of wrong or fraudulent science is > that it erodes the trust we have in each others results. No one has time or > resources to check everything, so science is based on trust. There are > efforts underway outside crystallographic circles to address this larger > threat to all science, and we should be participating in those discussions as > much as possible. > > Ron > > On Thu, 5 Apr 2012, aaleshin wrote: > >> 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 >> and requires a modification. >> Implementation of the raw image storage and validation will take a >> considerable time, while the recent >> incidents of a presumable data frauds demonstrate that the issue is urgent. >> Moreover, presenting the >> calculated structural factors in place of the experimental data is not the >> only abuse that the current >> validation procedure encourages to do. There might be more numerous >> occurances of data "massaging" like >> overestimation of the resolution or data quality, the system does not allow >> to verify them. IUCr and PDB >> follows the American taxation policy, where the responsibility for a fraud >> is placed on people, and the agency >> does not take sufficient actions to prevent it. I believe it is inefficient >> and inhumane. Making a routine >> check of submitted data at a bit lower level would reduce a temptation to >> overestimate the unclearly defined >> quality statistics and make the model fabrication more difficult to >> accomplish. Many people do it unknowingly, >> and catching them afterwards makes no good. >> >> I suggested to turn the current incidence, which might be too complex for >> burning heretics, into something >> productive that is done as soon as
Re: [ccp4bb] negative difference density around sulphur and oxygen atoms
This could well be due to radiation damage - S are often affected, also Glu and Asp side chains. It is hard to know what to do since the effects are time related. If you have high redundancy maybe you could not use he later batches? Otherwise maybe just relax the B factor restraints and let them show the loss of atoms.. The trouble with that is that you have to relax all side-chain B restraints which may not be so appropriate for ILE say... Eleanor On Apr 4 2012, Chris Meier wrote: MessageDear all, I am refining the X-ray structure of a protein:Data to ~2A were collected at a latest-generation synchrotron.The 2fo-Fc maps are crisp, the model of the protein is complete and I am reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). However, I am seeing a lot of negative difference density, especially around sulphur atoms (negative density around -9 sigma) and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with negative density around -6 sigma). Has anyone observed this before? I have found CCP4bb postings discussing radiation damange of suplphur atoms(e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ).Can this also happen with oxygen atoms? What would be an appropriate way to deal with this issue during refinement? Suggestions greatly appreciated. Thanks,Chris -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] problem in scaling the Zn-MAD data
You know that point group has two indexing conventions (h k l and -k,-h,-l if I remember - see the CCP4 documentation on alternate indexing and use pointless to sort it out.. Eleanor . Use pointless to check On Apr 4 2012, 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 rejections and chi2 values were very high even after adjusting the error-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] problem in scaling the Zn-MAD data
I don't see how a self rotation function can determine SG. If you processed data as P1 then found the SR maps showed 3 folds and 2 folds you might suspect that POINT GROUP!!! (Remember space groups are guessed on the basis of systematic absences - you don't really know that till you have a structure solution) At the integration stage it is important to choose a crystal class - e.g. trigonal with a=b and gamma = 120 The point groups then may be P3 P312 P321 P6 P6/mmm After integration a program like pointless checks for symmetry agreement. eg do h k l k (-h-k),l and -h-k,h,l agree well? In that case you probably have 3 fold symmetry. And so on for other possible symmetry operators.. After that you can probably be confident of your point group. But as Clemens pointed out - there are different equally possible indexing conventions for some of these choices. You need to check pass 2 against pass 1, etc - see pointless GUI Eleanor On Apr 5 2012, Deepthi wrote: 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, Clemens Vonrhein wrote: 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 rejections > and chi2 values were very high even after adjusting the error-scale factor > and error model. The space group i used was p312 which i obtained by > running a self-rotation function in MOLREP. When i scale my data using p312 > spacegroup the chi2 and rejections were huge. But he data was scaling well > in p321 spacegroup. can anyone explain whats going on? When you say 'Scaling the data for MAD experiments': do you mean scaling the various scans for your 3-wvl MAD data in a single scaling job? Unless you already took care of this during data integration, remember that your separate scans could have been indexed differently and therefore don't match up. See eg. http://www.ccp4.ac.uk/html/reindexing.html for some lookup-tables in P312 and P321. You can use the CCP4 program 'reindex' on MTZ files if needed. But I guess most modern data-processing and scaling programs will take care of that automatically anyway? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
[ccp4bb] off topic: the effects of spontaneous oligomerization on crystallization
Dear All, I have a 100KD protein which elutes as a mixture of 90% monomer and 10% dimer on HPLC, if I pool the monomer fractions and reload them onto the column, the elution profile is still 90% monomer plus 10% dimer, and the same is true if I do so to the dimer peak. Collectively, there seems to be a equilibrium between the monomer and the dimer. So far, I have not got crystals yet, since the purity of the protein is fairly high (99% pure), I am wondering if the lack of crystallization is caused by the heterogeneity introduced by the spontaneous oligomerization, and if so, what can I do to improve the homogeneity? Will a additive/detergent screen help (this is not a membrane protein)? Any comments will be greatly appreciated! Best, Joy
Re: [ccp4bb] off topic: the effects of spontaneous oligomerization on crystallization
If you have a DLS you can try playing with different [NaCl] or pH and see if you can push the equilibrium in one direction. Jürgen On Apr 6, 2012, at 11:41 AM, 杨贝 wrote: Dear All, I have a 100KD protein which elutes as a mixture of 90% monomer and 10% dimer on HPLC, if I pool the monomer fractions and reload them onto the column, the elution profile is still 90% monomer plus 10% dimer, and the same is true if I do so to the dimer peak. Collectively, there seems to be a equilibrium between the monomer and the dimer. So far, I have not got crystals yet, since the purity of the protein is fairly high (99% pure), I am wondering if the lack of crystallization is caused by the heterogeneity introduced by the spontaneous oligomerization, and if so, what can I do to improve the homogeneity? Will a additive/detergent screen help (this is not a membrane protein)? Any comments will be greatly appreciated! Best, Joy .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
[ccp4bb] Position Available: Technical Key Account Manager at Microlytic
*This posting is also available at *http://www.microlytic.com/careers . * * *Please submit a coverletter and C.V. to supp...@microlytic.com. **All general enquiries may be also be directed to this address.* * * *Position Summary:* Your primary focus will be the commercialization of Microlytic products into the workflow of a set of key accounts as well as other accounts. Your primary responsibility is to drive sales growth while maintaining existing business within the territory, in order to meet or exceed revenue goals. The position will involve significant travel to customer sites, primarily in North America, but from time to time worldwide, as the business may require, to reach our annual sales goals. Your day-to-day activities will focus on on-site meetings with customers, solving their technical problems and facilitating the integration of Microlytic products into their workflow. When you are not meeting with customers, you may be expected to work from our Massachusetts office. The ideal candidate will therefore reside in Boston. San Francisco or San Diego based candidates will also be considered. Compensation potential is in excess of $100,000. * * *ESSENTIAL DUTIES AND RESPONSIBILITIES:** * • Present product information and discuss crystallography research with customers and prospective customers in your assigned territory. • Meet or exceed revenue goals and other goals as assigned. • Leverage your technical expertise to meet or exceed your sales targets. • Increase our competitive advantage and enhance customer satisfaction • Build effective business and collaboration relationships with customers. • Prospecting to develop new accounts and arrange sales meetings. • Product demonstrations in the field. • Develop tactical plans to maximize revenues. • Complete and submit sales reports and documentation in a timely and efficient manner. • Provide regular reports on customer inquiries, and communicate successes, failures, best practices etc to improve the overall product offering. • Present technical seminars in person, via telephone or web conference • Gather and report customer and technical information • Represent Microlytic at tradeshows/exhibitions and other “on-site” events in order to promote crystallography products and services, receive feedback, network with customers and prospective customers. • Monitor competitive landscape and provide analysis of key findings to senior management. • This work will entail significant travel to customer sites. *Qualifications and experience:* • Ph.D. degree in life sciences • Minimum of 3 years lab experience with proven knowledge and understanding of structural biology, preferably within crystallography • Technical competency to interpret customer’s needs and identify solutions; to stay current in technical knowledge; to troubleshoot and to provide information back to customers in a helpful, courteous, positive and professional manner. • Sales experience is an advantage. • Excellent oral and written communication skills. • Experience in presenting technical materials in written and verbal form is critical. • Strong commitment to customer service and satisfaction. • Ability to effectively work on and manage many priorities at one time. • A clear and persuasive communication style, with the ability to gain trust and respect and to command attention both externally and internally. • A supportive and approachable team player, who is able to challenge in a constructive manner, yet not hesitate to show independent and creative thinking, and be able to compromise in order to accomplish the objective. • Must be self-reliant and a self-starter, with an entrepreneurial spirit, who is results oriented, has a sense of urgency, and has a competitive desire to succeed. *About Microlytic* Founded in 2006, Microlytic is an innovator and commercial provider of consumable laboratory products for the structural biology marketplace. Our mission is to provide a portfolio of innovative products that simplify the workflow, increase productivity and offer an attractive economic value proposition to our customers. For more information about Microlytic, please visit http://www.microlytic.com.
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear John, Your points are well taken and they're consistent with policies and practices in the US as well. I wonder about the nature of the employer's responsibility though. I sit on some university committees, and the impression I get is that much of the time, the employers are interested in reducing their legal liabilities, not protecting the integrity of science. The end result is the same though in that the employers get involved and oversee the handling of scientific misconduct. What is unclear to me is whether the system for dealing with misconduct is broken. It seems to work pretty well from my viewpoint. No system is perfect for identifying fraud, errors, etc, and I understand the idea that improvements might be possible. However, too many "improvements" might break the system as well. Ron On Fri, 6 Apr 2012, John R Helliwell wrote: > Dear Ron, > Re (3):- > Yes of course the investigator has that responsibility. > The additional point I would make is that the employer has a share in > that responsibility. Indeed in such cases the employer university > convenes a research fraud investigating committee to form the final > judgement on continued employment. > A research fraud policy, at least ours, also includes the need for > avoding inadvertent loss of raw data, which is also deemed to be > research malpractice. > Thus the local data repository, with doi registration for data sets > that underpin publication, seems to me and many others, ie in other > research fields, a practical way forward for these data sets. > It also allows the employer to properly serve the research > investigations of its employees and be duely diligent to the research > sponsors whose grants it accepts. That said there is a variation of > funding that at least our UK agencies will commit to 'Data management > plans'. > Greetings, > John > > > > 2012/4/5 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 sky is not falling! The errors in the birch pollen antigen pointed >> out by Bernhard are interesting, and the reasons behind them might be >> troubling. However, the self-correcting functions of scientific research >> found the errors, and current publication methods permitted an airing of the >> problem. It took some effort, but the scientific method prevailed. >> >> 2. Depositing raw data frames will make little difference in identifying >> and correcting structural problems like this one. Nor will new requirements >> for deposition of this or that detail. What's needed for finding the >> problems is time and interest on the part of someone who's able to look at a >> structure critically. Deposition of additional information could be >> important for that critical look, but deposition alone (at least with >> today's software) will not be sufficient to find incorrect structures. >> >> 3. The responsibility for a fraudulent or wrong or poorly-determined >> structure lies with the investigator, not the society of crystallographers. >> My political leanings are left-of-central, but I still believe in individual >> responsibility for behavior and actions. If someone messes up a structure, >> they're accountable for the results. >> >> 4. Adding to the deposition requirements will not make our science more >> efficient. Perhaps it's different in other countries, but the >> administrative burden for doing research in the United States is growing. >> It would be interesting to know the balance between the waste that comes >> from a wrong structure and the waste that comes from having each of us deal >> with additional deposition requirements. >> >> 5. The real danger that arises from cases of wrong or fraudulent science is >> that it erodes the trust we have in each others results. No one has time or >> resources to check everything, so science is based on trust. There are >> efforts underway outside crystallographic circles to address this larger >> threat to all science, and we should be participating in those discussions >> as much as possible. >> >> Ron >> >> On Thu, 5 Apr 2012, aaleshin wrote: >> >>> 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 >>> and requires a modification. >>> Implementation of the raw image storage and validation will take a >>> considerable time, while the recent >>> incidents of a presumable data frauds demonstrate that the issue is urgent. >>> Moreover, presenting the >>> calculated structura
Re: [ccp4bb] very informative - Trends in Data Fabrication
Ron makes an excellent point. Many institutions devote far more energy to limiting risk than to doing the right thing. This leads administrators to a frightening, but logical conclusion: The less science we do, the less chance of our doing something that could invite a penalty on the university. This translates into rules intended to head off bad behavior, but which in fact make it more difficult to do honest science, and increase the administrative burden (our IT group has already made great strides in this direction--if you can't connect to the network, then you can't use it to violate HIPAA!). So I agree that we should be cautious about "improvements." Pat On 6 Apr 2012, at 12:23 PM, Ronald E Stenkamp wrote: > Dear John, > > Your points are well taken and they're consistent with policies and practices > in the US as well. > > I wonder about the nature of the employer's responsibility though. I sit on > some university committees, and the impression I get is that much of the > time, the employers are interested in reducing their legal liabilities, not > protecting the integrity of science. The end result is the same though in > that the employers get involved and oversee the handling of scientific > misconduct. > > What is unclear to me is whether the system for dealing with misconduct is > broken. It seems to work pretty well from my viewpoint. No system is > perfect for identifying fraud, errors, etc, and I understand the idea that > improvements might be possible. However, too many "improvements" might break > the system as well. > > Ron > --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] UPDATED: Position Available: Technical Key Account Manager at Microlytic
In response to very welcomed suggestions from the bb, we have opened the hiring of this position to include non-Ph.D. candidates. Please see the updated posting below: Enquires and applications (coverletter and C.V) can be forwarded to j...@microlytic.com. The posting is also available at www.microlytic.com/careers * * *Position Summary:* Your primary focus will be the commercialization of Microlytic products into the workflow of a set of key accounts as well as other accounts. Your primary responsibility is to drive sales growth while maintaining existing business within the territory, in order to meet or exceed revenue goals. The position will involve significant travel to customer sites, primarily in North America, but from time to time worldwide, as the business may require, to reach our annual sales goals. Your day-to-day activities will focus on on-site meetings with customers, solving their technical problems and facilitating the integration of Microlytic products into their workflow. When you are not meeting with customers, you may be expected to work from our Massachusetts office. The ideal candidate will therefore reside in Boston. San Francisco or San Diego based candidates will also be considered. Compensation potential is in excess of $100,000. * * *ESSENTIAL DUTIES AND RESPONSIBILITIES:** * • Present product information and discuss crystallography research with customers and prospective customers in your assigned territory. • Meet or exceed revenue goals and other goals as assigned. • Leverage your technical expertise to meet or exceed your sales targets. • Increase our competitive advantage and enhance customer satisfaction • Build effective business and collaboration relationships with customers. • Prospecting to develop new accounts and arrange sales meetings. • Product demonstrations in the field. • Develop tactical plans to maximize revenues. • Complete and submit sales reports and documentation in a timely and efficient manner. • Provide regular reports on customer inquiries, and communicate successes, failures, best practices etc to improve the overall product offering. • Present technical seminars in person, via telephone or web conference • Gather and report customer and technical information • Represent Microlytic at tradeshows/exhibitions and other “on-site” events in order to promote crystallography products and services, receive feedback, network with customers and prospective customers. • Monitor competitive landscape and provide analysis of key findings to senior management. • This work will entail significant travel to customer sites. *Qualifications and experience:* • Ph.D. degree in life sciences preferred • Minimum of 3 years lab experience with proven knowledge and understanding of structural biology, preferably within crystallography • Technical competency to interpret customer’s needs and identify solutions; to stay current in technical knowledge; to troubleshoot and to provide information back to customers in a helpful, courteous, positive and professional manner. • Sales experience is an advantage. • Excellent oral and written communication skills. • Experience in presenting technical materials in written and verbal form is critical. • Strong commitment to customer service and satisfaction. • Ability to effectively work on and manage many priorities at one time. • A clear and persuasive communication style, with the ability to gain trust and respect and to command attention both externally and internally. • A supportive and approachable team player, who is able to challenge in a constructive manner, yet not hesitate to show independent and creative thinking, and be able to compromise in order to accomplish the objective. • Must be self-reliant and a self-starter, with an entrepreneurial spirit, who is results oriented, has a sense of urgency, and has a competitive desire to succeed. *About Microlytic* Founded in 2006, Microlytic is an innovator and commercial provider of consumable laboratory products for the structural biology marketplace. Our mission is to provide a portfolio of innovative products that simplify the workflow, increase productivity and offer an attractive economic value proposition to our customers. For more information about Microlytic, please visit http://www.microlytic.com.
[ccp4bb] Error in Scala
Hi everyone, Sorry for the newbie type problems, but I am just starting to use ccp4 for data processing. Here is my problem. After I index and integrate my images using iMOSFLM, I end up with the .mtz files that contains, AIUI, unmerged reflections. Next I should try to merge and scale experimental intensities, using SCALA. I am getting an error saying: Giving up Scala: Negative Scales task failed. Anything obvious I am missing? thanks a lot.
Re: [ccp4bb] Error in Scala
One quick thought is - are you trying to scale reflections that don't really exist? I.e are you trying to push your resolution a bit too much? Tony. Sent from my iPhone On 6 Apr 2012, at 20:29, "Yuri Pompeu" wrote: > Hi everyone, > Sorry for the newbie type problems, but I am just starting to use ccp4 for > data processing. > Here is my problem. > After I index and integrate my images using iMOSFLM, I end up with the .mtz > files that contains, AIUI, unmerged reflections. > Next I should try to merge and scale experimental intensities, using SCALA. > I am getting an error saying: > Giving up > Scala: Negative Scales > task failed. > > Anything obvious I am missing? > thanks a lot.
[ccp4bb] Positions in Structural Biology of Signaling and HIV-related Immunology
There are two immediate openings for protein crystallographer position in Harvard Medical School. One of the research projects is focused on the structural and functional investigation of Wnt signaling pathway. The project is the close collaborative efforts between Professor Xi Hes lab at Childrens Hospital and Jia-huai Wangs lab at Dana-Farber Cancer Institute. The other project is to study protective role of cellular immunity against HIV, which is a collaboration between Professors Bruce Walkers lab at Ragon Institute and Jia-huai Wangs lab. The successful candidate should have a Ph.D. in structural biology. The candidate will be responsible for determining crystal structure using X-ray crystallography. He/she should also have experience in molecular biology and protein biochemistry, capable in cloning and protein expression and purification. Interested candidates can email a CV, three contacts for reference, as well as an email address and a telephone number to Dr. Jia-huai Wang at jw...@red.dfci.harvard.edu. For more information regarding the Wang Laboratorie, please see the website: http://wang.dfci.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] Error in Scala
Do run the data through Pointless before Scala to check the point group. Try "scales constant" just to check that things aren't completely hopeless Phil On 6 Apr 2012, at 20:29, Yuri Pompeu wrote: > Hi everyone, > Sorry for the newbie type problems, but I am just starting to use ccp4 for > data processing. > Here is my problem. > After I index and integrate my images using iMOSFLM, I end up with the .mtz > files that contains, AIUI, unmerged reflections. > Next I should try to merge and scale experimental intensities, using SCALA. > I am getting an error saying: > Giving up > Scala: Negative Scales > task failed. > > Anything obvious I am missing? > thanks a lot.
[ccp4bb] scala - handling of anomalous data
Hi all, Can someone kindly explain what is that "match pairs related by inversion of indices" option doing for handling anomalous data? If I have collected the inverse beam data, does it mean I have to use this option to match the I+ and I- pairs in merging? But why does it lead to seriously incomplete data (compare to the merging data without the MATCH option ON)? Thanks, Matt -- Matthew L.H. Chu, PhD Postdoctoral Scholar - Weis Lab Department of Structural Biology Stanford School of Medicine
Re: [ccp4bb] scala - handling of anomalous data
I wouldn't recommend this option Phil On 6 Apr 2012, at 21:41, Matthew Chu wrote: > Hi all, > > Can someone kindly explain what is that "match pairs related by inversion of > indices" option doing for handling anomalous data? If I have collected the > inverse beam data, does it mean I have to use this option to match the I+ and > I- pairs in merging? But why does it lead to seriously incomplete data > (compare to the merging data without the MATCH option ON)? > > Thanks, > Matt > > -- > > Matthew L.H. Chu, PhD > Postdoctoral Scholar - Weis Lab > Department of Structural Biology > Stanford School of Medicine > >
Re: [ccp4bb] very informative - Trends in Data Fabrication
As famously observed by the Yes Minister teamthe dream outcome for any organization: http://www.youtube.com/watch?v=x-5zEb1oS9A&feature=youtube_gdata_player J Sent from my iPhone On 07/04/2012, at 3:16 AM, Patrick Loll wrote: > Ron makes an excellent point. Many institutions devote far more energy to > limiting risk than to doing the right thing. This leads administrators to a > frightening, but logical conclusion: The less science we do, the less chance > of our doing something that could invite a penalty on the university. This > translates into rules intended to head off bad behavior, but which in fact > make it more difficult to do honest science, and increase the administrative > burden (our IT group has already made great strides in this direction--if you > can't connect to the network, then you can't use it to violate HIPAA!). > So I agree that we should be cautious about "improvements." > Pat > > > On 6 Apr 2012, at 12:23 PM, Ronald E Stenkamp wrote: > >> Dear John, >> >> Your points are well taken and they're consistent with policies and >> practices in the US as well. >> >> I wonder about the nature of the employer's responsibility though. I sit on >> some university committees, and the impression I get is that much of the >> time, the employers are interested in reducing their legal liabilities, not >> protecting the integrity of science. The end result is the same though in >> that the employers get involved and oversee the handling of scientific >> misconduct. >> >> What is unclear to me is whether the system for dealing with misconduct is >> broken. It seems to work pretty well from my viewpoint. No system is >> perfect for identifying fraud, errors, etc, and I understand the idea that >> improvements might be possible. However, too many "improvements" might >> break the system as well. >> >> Ron >> > > --- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.l...@drexelmed.edu
