Re: [ccp4bb] Citations in supplementary material
Dear Jacob, Your posting reminds me of a Research Information Network Conference I went to in 2006 in London. Your views coincide with a presenter there, Peter Mika. His talk can be found at:- http://www.rin.ac.uk/news/events/data-webs-new-visions-research-data-web In his talk he referred to:- openacademia.org Peter Mika and I were on the Closing Panel; he advocated that refereeing is an imposition on a researcher's individual freedom and thus he/she should 'publish' their work on their own website. By contrast, I argued in favour of Journals and peer review, both with respect to my articles and my experiences as an Editor of more than one Journal. I would be happy to continue corresponding on this not least as publication should be a varied spectrum of options. Also I feel obliged to say that one cannot apply simply, by rote, 'Learned Society publisher is good', 'commercial publisher is bad'; there are exceptions in both camps. [in effect this was the tone of my last posting.] Greetings, John On Wed, Nov 17, 2010 at 8:13 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I guess the practice of being on your best behavior is good in terms of getting the research trimmed into shape, but there is a huge temptation to fudge things to get published, and to hide unpleasant artifacts, as can be seen by the many recent (and not so recent) scandals. Maybe as a lab website things would be more open. Also, having a comments section always seemed like an excellent idea to me, even for journals as they are, but would be really easy to implement in a website. I would love to read comments from others in the field about the papers I read, as sometimes people can help to point out gaping holes where one might not see them otherwise. It would be like journal club for the whole scientific community. Jacob On Wed, Nov 17, 2010 at 2:08 PM, Jrh jrhelliw...@gmail.com wrote: Dear Jacob Re journals out of the window:- Well, like democracy, journals may not be ideal but I believe other alternatives such as free for all personal website publishing, are worse. So, journals that are community driven offer an optimal approach, critically based on specialist peer review. That is why our community effort IUCr Journals I believe are so important. Open access, where we can sustain it financially, also can convey access to the widest readership ie that the high impact magazines currently, mainly, command. All best wishes, John Prof John R Helliwell DSc On 17 Nov 2010, at 18:28, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Supplementary info seems to me to be a double-edged sword--I just read a Nature article that had 45 pages of supplementary info. This means that you get a lot more for your money, but all of the methods and Why not have papers be as long as the authors want, now that almost everything is internet-based? It would make the papers much more organized overall, and would obviate the reference issue mentioned in this thread. To avoid them being too too long, reviewers could object to long-windedness etc. But, it would definitely make for a more complete lab notebook of the scientific community, assuming that that is what we are after. Incidentally, I have been curious in the past why journals are not going out the window themselves--why not have individual labs just post their most recent data and interpretations on their own websites, with a comments section perhaps? (I know there are about a thousand cynical reasons why not...) One could even have a place for reliability rating or impact rating on each new chunk of data. Anyway, it would be much more like a real-time, public lab notebook, and would make interaction much faster, and cut out the publishing middlemen. JPK On Wed, Nov 17, 2010 at 11:48 AM, Phoebe Rice pr...@uchicago.edu wrote: Another unfortunate aspect of this sort of editorial policy is that many of these papers contain almost no technical information at all, except for the supplement. I've started to avoid using Nature papers for class discussions becuase they leave the students so puzzled, and with a glossiness-is-all-that-matters idea of science. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Wed, 17 Nov 2010 17:12:26 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of John R Helliwell jrhelliw...@gmail.com) Subject: Re: [ccp4bb] Citations in supplementary material To: CCP4BB@JISCMAIL.AC.UK Dear Victor, I strongly support the stance that is in the Acta D Editorial. Manfred Weiss worked very hard assembling those details and over quite some time; he deserves our thanks. Greetings, John On Wed, Nov
[ccp4bb] off topic:question about helicase activity detect
Hi all, usually researchers detect the helicase activity using radio-labeled nucleic acid. if we increase the necleic acid lenght and concentration in the reaction mixture,can we employ non radio-labeled nucleic acid? Best regards, dengzq.
[ccp4bb] origin_shift in polar space group
Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
Re: [ccp4bb] Citations in supplementary material
The future of publishing will be (1) Publish your own work (2) Peer review by the entire community (3) Citation = Link #3 makes it work. Give it 25 years. The journals won't be in the position to lobby lawmakers to prevent this trend if we make sure the journals die so slowly that they don't realize it. James On Nov 18, 2010, at 1:14 AM, John R Helliwell wrote: Dear Jacob, Your posting reminds me of a Research Information Network Conference I went to in 2006 in London. Your views coincide with a presenter there, Peter Mika. His talk can be found at:- http://www.rin.ac.uk/news/events/data-webs-new-visions-research-data-web In his talk he referred to:- openacademia.org Peter Mika and I were on the Closing Panel; he advocated that refereeing is an imposition on a researcher's individual freedom and thus he/she should 'publish' their work on their own website. By contrast, I argued in favour of Journals and peer review, both with respect to my articles and my experiences as an Editor of more than one Journal. I would be happy to continue corresponding on this not least as publication should be a varied spectrum of options. Also I feel obliged to say that one cannot apply simply, by rote, 'Learned Society publisher is good', 'commercial publisher is bad'; there are exceptions in both camps. [in effect this was the tone of my last posting.] Greetings, John On Wed, Nov 17, 2010 at 8:13 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I guess the practice of being on your best behavior is good in terms of getting the research trimmed into shape, but there is a huge temptation to fudge things to get published, and to hide unpleasant artifacts, as can be seen by the many recent (and not so recent) scandals. Maybe as a lab website things would be more open. Also, having a comments section always seemed like an excellent idea to me, even for journals as they are, but would be really easy to implement in a website. I would love to read comments from others in the field about the papers I read, as sometimes people can help to point out gaping holes where one might not see them otherwise. It would be like journal club for the whole scientific community. Jacob On Wed, Nov 17, 2010 at 2:08 PM, Jrh jrhelliw...@gmail.com wrote: Dear Jacob Re journals out of the window:- Well, like democracy, journals may not be ideal but I believe other alternatives such as free for all personal website publishing, are worse. So, journals that are community driven offer an optimal approach, critically based on specialist peer review. That is why our community effort IUCr Journals I believe are so important. Open access, where we can sustain it financially, also can convey access to the widest readership ie that the high impact magazines currently, mainly, command. All best wishes, John Prof John R Helliwell DSc On 17 Nov 2010, at 18:28, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Supplementary info seems to me to be a double-edged sword--I just read a Nature article that had 45 pages of supplementary info. This means that you get a lot more for your money, but all of the methods and Why not have papers be as long as the authors want, now that almost everything is internet-based? It would make the papers much more organized overall, and would obviate the reference issue mentioned in this thread. To avoid them being too too long, reviewers could object to long-windedness etc. But, it would definitely make for a more complete lab notebook of the scientific community, assuming that that is what we are after. Incidentally, I have been curious in the past why journals are not going out the window themselves--why not have individual labs just post their most recent data and interpretations on their own websites, with a comments section perhaps? (I know there are about a thousand cynical reasons why not...) One could even have a place for reliability rating or impact rating on each new chunk of data. Anyway, it would be much more like a real-time, public lab notebook, and would make interaction much faster, and cut out the publishing middlemen. JPK On Wed, Nov 17, 2010 at 11:48 AM, Phoebe Rice pr...@uchicago.edu wrote: Another unfortunate aspect of this sort of editorial policy is that many of these papers contain almost no technical information at all, except for the supplement. I've started to avoid using Nature papers for class discussions becuase they leave the students so puzzled, and with a glossiness-is-all-that-matters idea of science. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Wed, 17 Nov 2010 17:12:26 +
Re: [ccp4bb] origin_shift in polar space group
HI Rojan, I'm not entirely clear that there is a problem. After superposition any origin shift that may have been present is removed: doesn't that solve your problem? Cheers -- Ian On Thu, Nov 18, 2010 at 10:11 AM, Rojan Shrestha ro...@riken.jp wrote: Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
Re: [ccp4bb] origin_shift in polar space group
If you want to shift the coordinates, just use a superposition program. If you want to know the exact shift to best match phases you need to CAD together phases calculated from each model, then use PhaseComparison (reflection utility) That will tell you the shft, and whether there is an allowed origin shift. Eleanor On 11/18/2010 10:42 AM, Ian Tickle wrote: HI Rojan, I'm not entirely clear that there is a problem. After superposition any origin shift that may have been present is removed: doesn't that solve your problem? Cheers -- Ian On Thu, Nov 18, 2010 at 10:11 AM, Rojan Shrestharo...@riken.jp wrote: Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
Re: [ccp4bb] Citations in supplementary material
On Nov 18, 2010, at 11:18, James Stroud wrote: The future of publishing will be (1) Publish your own work (2) Peer review by the entire community Although I have been remarkably bad at predicting the future, I still like attempting to do so ...! This will not happen ...! ;-) To be honest, I am not even sure its a great idea ... Let me outline what I think are problems of peer review: 1. 'review by last author name'. Very often the last author is well known, or a friend, and the reviewers' critical judgement takes a temporary leave of abesnse. 2. 'preferred reviewers'. a double edged sword .. think about it. 3. too much power of decision on editors (professional or academic) being able to reject papers without peer-review in many journals. 4. Bad refereeing - sometimes I wonder if people read the paper. 5. Lack of referee expertise: you get papers these days with: a structure, some biochemistry, some SAXS, some biophysics, and a cell based assay. Two or three people being able to pick up all the mistakes is very unlikely. Having outlines these, I can see ways that all can be amplified if you just publish all your work, and anybody can comment on it: Pairing to the above problems, you just amplify them: 1. Even more tempting to earn brownie points online! 2. you can ask your friends or I can ask your enemies to review 3. the other way around: far too many things out... how to filter ? 4. Lack of 'obligation', or even fear to make yourself look like a fool to the editors, will make commenting even more sloppy 5. People that think they are experts dwell on meaningless technicalities. Peer review is like democracy, its the worst publication system we can have, except the ones that have been tried or suggested ... A. (3) Citation = Link #3 makes it work. Give it 25 years. The journals won't be in the position to lobby lawmakers to prevent this trend if we make sure the journals die so slowly that they don't realize it. James On Nov 18, 2010, at 1:14 AM, John R Helliwell wrote: Dear Jacob, Your posting reminds me of a Research Information Network Conference I went to in 2006 in London. Your views coincide with a presenter there, Peter Mika. His talk can be found at:- http://www.rin.ac.uk/news/events/data-webs-new-visions-research-data-web In his talk he referred to:- openacademia.org Peter Mika and I were on the Closing Panel; he advocated that refereeing is an imposition on a researcher's individual freedom and thus he/she should 'publish' their work on their own website. By contrast, I argued in favour of Journals and peer review, both with respect to my articles and my experiences as an Editor of more than one Journal. I would be happy to continue corresponding on this not least as publication should be a varied spectrum of options. Also I feel obliged to say that one cannot apply simply, by rote, 'Learned Society publisher is good', 'commercial publisher is bad'; there are exceptions in both camps. [in effect this was the tone of my last posting.] Greetings, John On Wed, Nov 17, 2010 at 8:13 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I guess the practice of being on your best behavior is good in terms of getting the research trimmed into shape, but there is a huge temptation to fudge things to get published, and to hide unpleasant artifacts, as can be seen by the many recent (and not so recent) scandals. Maybe as a lab website things would be more open. Also, having a comments section always seemed like an excellent idea to me, even for journals as they are, but would be really easy to implement in a website. I would love to read comments from others in the field about the papers I read, as sometimes people can help to point out gaping holes where one might not see them otherwise. It would be like journal club for the whole scientific community. Jacob On Wed, Nov 17, 2010 at 2:08 PM, Jrh jrhelliw...@gmail.com wrote: Dear Jacob Re journals out of the window:- Well, like democracy, journals may not be ideal but I believe other alternatives such as free for all personal website publishing, are worse. So, journals that are community driven offer an optimal approach, critically based on specialist peer review. That is why our community effort IUCr Journals I believe are so important. Open access, where we can sustain it financially, also can convey access to the widest readership ie that the high impact magazines currently, mainly, command. All best wishes, John Prof John R Helliwell DSc On 17 Nov 2010, at 18:28, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Supplementary info seems to me to be a double-edged sword--I just read a Nature article that had 45 pages of supplementary info. This means that you get a lot more for your money, but all of the methods and Why not have papers be as long as the authors want, now that almost everything is internet-based? It would make the papers much more
Re: [ccp4bb] Citations in supplementary material
I agree with Tassos - and don't deny the power of evolution. Choice of journals, submissions, peer review, editorial assistance and citations are all in our hands - publishing has become what we have made it. We can argue that we want it differently (and to stay in the evolution terms: I also know of a number of life forms that do really stupid things), but it is not easy to play God, change things rationally and make it work. I like the online methods sections with e.g. Nature papers that also come with the pdf - they also count for citations, the citations are not within the manuscript allowance on numbers, they get peer reviewed and they actually leave quite a lot of space for readers to understand the experiments and for authors to cite methods properly. Easy fix in my mind. Also we do need printed journals still - I don't know how often I find great stuff that I didn't know to search for if I hadn't being going over it in a disconnected moment. Poul On 18/11/2010, at 11.47, Anastassis Perrakis wrote: On Nov 18, 2010, at 11:18, James Stroud wrote: The future of publishing will be (1) Publish your own work (2) Peer review by the entire community Although I have been remarkably bad at predicting the future, I still like attempting to do so ...! This will not happen ...! ;-) To be honest, I am not even sure its a great idea ... Let me outline what I think are problems of peer review: 1. 'review by last author name'. Very often the last author is well known, or a friend, and the reviewers' critical judgement takes a temporary leave of abesnse. 2. 'preferred reviewers'. a double edged sword .. think about it. 3. too much power of decision on editors (professional or academic) being able to reject papers without peer-review in many journals. 4. Bad refereeing - sometimes I wonder if people read the paper. 5. Lack of referee expertise: you get papers these days with: a structure, some biochemistry, some SAXS, some biophysics, and a cell based assay. Two or three people being able to pick up all the mistakes is very unlikely. Having outlines these, I can see ways that all can be amplified if you just publish all your work, and anybody can comment on it: Pairing to the above problems, you just amplify them: 1. Even more tempting to earn brownie points online! 2. you can ask your friends or I can ask your enemies to review 3. the other way around: far too many things out... how to filter ? 4. Lack of 'obligation', or even fear to make yourself look like a fool to the editors, will make commenting even more sloppy 5. People that think they are experts dwell on meaningless technicalities. Peer review is like democracy, its the worst publication system we can have, except the ones that have been tried or suggested ... A. (3) Citation = Link #3 makes it work. Give it 25 years. The journals won't be in the position to lobby lawmakers to prevent this trend if we make sure the journals die so slowly that they don't realize it. James On Nov 18, 2010, at 1:14 AM, John R Helliwell wrote: Dear Jacob, Your posting reminds me of a Research Information Network Conference I went to in 2006 in London. Your views coincide with a presenter there, Peter Mika. His talk can be found at:- http://www.rin.ac.uk/news/events/data-webs-new-visions-research-data-web In his talk he referred to:- openacademia.org Peter Mika and I were on the Closing Panel; he advocated that refereeing is an imposition on a researcher's individual freedom and thus he/she should 'publish' their work on their own website. By contrast, I argued in favour of Journals and peer review, both with respect to my articles and my experiences as an Editor of more than one Journal. I would be happy to continue corresponding on this not least as publication should be a varied spectrum of options. Also I feel obliged to say that one cannot apply simply, by rote, 'Learned Society publisher is good', 'commercial publisher is bad'; there are exceptions in both camps. [in effect this was the tone of my last posting.] Greetings, John On Wed, Nov 17, 2010 at 8:13 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I guess the practice of being on your best behavior is good in terms of getting the research trimmed into shape, but there is a huge temptation to fudge things to get published, and to hide unpleasant artifacts, as can be seen by the many recent (and not so recent) scandals. Maybe as a lab website things would be more open. Also, having a comments section always seemed like an excellent idea to me, even for journals as they are, but would be really easy to implement in a website. I would love to read comments from others in the field about the papers I read, as sometimes people can help to point out gaping holes where one might not see them otherwise. It would be like journal club for the whole scientific community.
Re: [ccp4bb] Citations in supplementary material
I like the online methods sections with e.g. Nature papers that also come with the pdf - they also count for citations, the citations are not within the manuscript allowance on numbers, they get peer reviewed and they actually leave quite a lot of space for readers to understand the experiments and for authors to cite methods properly. Easy fix in my mind. What Poul says about Nature, which is also my understanding, is in sharp contrast with the Cell group policy: Supplemental References Literature citations from within the Supplemental Information and unique to the Supplemental Information should be listed as Supplemental References. References that are already included in the main body of the paper should not be listed again. Please note that as references in Supplemental Information do not contribute towards citation measures for those papers, authors are encouraged, when possible, to include references in the main body of the paper. My experience with Elsevier, is that they like to listen to feedback and appreciate it. Nature seems to have fixed the problem with citations in Methods in a proper manner (which is largely true for all NPG journals, I think, at least NSMB will also do the Online Methods trick!). So, an important step would be that we as a community, take the steps to get everybody to follow that. So, lets start a petition? Maybe Victor that started this important thread could champion this and see it to an end !!! A.
Re: [ccp4bb] origin_shift in polar space group
OK now I understand. I couldn't find the script 'origin.com' you mentioned in the examples directory (at least from the filename I assume it's a script, not a MS-DOS program!), but it doesn't matter, I see the problem now. AFAIK there isn't a script in CCP4 that will do what you want entirely automatically, because it's actually quite a complicated problem in the completely general case of N molecules per a.u., though undoubtedly it could easily be scripted for the relatively simple case of 2 mols per a.u.. I'm assuming you don't simply want to superpose the molecules just for structural comparison purposes, you want to superpose the entire *crystals*, so that the calculated structure factors and hence the R factors (values) remained unchanged for the transformed structure. This means you can't use just arbitrary rotation/translation operators as would be generated by superposition programs such as SSM, you have to restrict it to crystallographically-allowed origin shifts. There are various programs which will do this, I wrote one called 'reforigin' but there are others which will do the same thing, and which have been mentioned in previous postings. So what you have to do is superpose the two 'A' molecules using reforigin or whatever (remember, as long as it applies only crystallographically-allowed origin shifts). There is of course a problem here: the chain ID 'A' is only an arbitrary label, so there's a 50% chance that the molecule you called 'A' in structure 1 might be called 'B' in structure 2 (and vice versa). This means you have to try both possibilities! Now you see why it gets complicated in the general case with molecules 'A', 'B', 'C', 'D' ... you have to try all combinations! While you are superposing A/2 on A/1 (or B/2 on A/1) you must also transform the other chain B/2 (or A/2) using the *same* operator (I think the program does this for you, or at least it will print the matrix that was used for the 1st pair) - you must not superpose it independently. Finally you need to transform the other molecule B/2 (or A/2) in the example above. For this you can only use space-group symmetry operators - you get only one chance to use the allowed origin shifts with the first pair of molecules, after that the origin is completely determined for the entire structure, hence only space-group symmetry can be used to transform subsequent pairs. For this I find it easiest just to view the structure on the graphics, work out which is appropriate space-group operator and apply it just to the 2nd molecule using PDBSET. Hope this is all clear - there are many traps here for the unwary! Cheers -- Ian On Thu, Nov 18, 2010 at 10:55 AM, Rojan Shrestha ro...@riken.jp wrote: Hello Ian: I am afraid that whether my problem is not clear to you. Here is brief description of the problem. When I tried to superimpose two structures having two or more copies in ASU for polar space group using symmetric operator, for one copies it used one origin and for next, another origin is used. So there is origins shift problem. Here is an example: applying 0.50 0.50 -0.69 Y,-X,3/4+Z to chain A applying 1.50 0.50 0.61 X,Y,Z to chain B WARNING: ./input.pdb chain B is on a different origin! I used origin.com to superimpose two models. Now I hope you get the insight of my problem. Do you have any idea to solve this problem? Regards, Rojan -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Thursday, November 18, 2010 7:42 PM To: ro...@riken.jp Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] origin_shift in polar space group HI Rojan, I'm not entirely clear that there is a problem. After superposition any origin shift that may have been present is removed: doesn't that solve your problem? Cheers -- Ian On Thu, Nov 18, 2010 at 10:11 AM, Rojan Shrestha ro...@riken.jp wrote: Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
Re: [ccp4bb] how to optimize small rod-shaped crystals
Hi, thank you for you reply. Could you tell me if you try to dye membrane protein crystal with detergent? Thanks. Y.B. 2010-11-18 yybbll 发件人： Matthew Bratkowski 发送时间： 2010-11-17 02:58:40 收件人： CCP4BB 抄送： 主题： Re: [ccp4bb] how to optimize small rod-shaped crystals I like using Izit dye from Hampton (http://hamptonresearch.com/product_detail.aspx?cid=4sid=41pid=33) to check if crystals are protein or salt. If the crystals are protein, the dye should absorb rather readily into the crystals and turn them blue, while the rest of the drop will eventually turn clear. Quite likely, excess dye will also crystallize out as well. Salt crystals will not soak in the dye, and the rest of the drop may remain blue for several days. Using Izit is easy and saves a lot of time. In my experience, I have gotten a lot of false positives from phosphate crystallization conditions, so you want to be sure that the crystals are not salt before you waste any time on optimizing them. Matt On Tue, Nov 16, 2010 at 3:23 PM, Ulli Hain haina...@msu.edu wrote: If you have a polarizer on your microscope you could see if they are extremely dichroic, in which case they may be salt. You could also open the well up and see if they are heavy - do they sink immediately when you lift them to the top of the drop? This could also indicate salt. But I agree with other posts that they do not seem to small to mount, especially with the new mesh loops they make. -Ulli Adelaide-Ulricke P. Hain Johns Hopkins University Bloomberg School of Public Health Biochemistry Molecular Biology Quoting yybbll yyb...@gmail.com: Hi, everybody, I try to crystallize one membrane protein. All crystals were grown by handing-drop vapor diffusion at 20 degree. A protein solution containing about 8-10mg/ml protein in 20mM Tris (pH7.5), 0.017% DDM, 100mM NaCl, 10% glycerol, 2mM DDT was mixed with an equal volume of a reservoir solution containing 45% PEG200, 0.1 M phosphate/citrate (pH4.2). First crystal appeared in the drop within 4 days. And one week a lot of crystals appeared in the drops. Our question is all of these crystals are too small to check them by X-ray diffraction and SDS-PAGE. We are not sure they are protein crystals or salt crystals. Our condition seems difficult to produce salt crystal. But I am a little warry because we use reloaded our sample to small Ni-resin column to reduce the concentration of detergent. Maybe some nickel ion dropped off, and then our protein sample contained some this ion. And nickel ion may react with phosphate, and then produced nickel phosphate crystal. Could somebody tell me if it is possible? I attach some photos of our crystals. Could somebody give me some suggestions about how to optimize this type crystal to get bigger crystal? Thanks a lot! Yibin 2010-11-16 yybbll Laurie Betts ? 2010-11-16 17:13:32 CCP4BB ??? ??? [ccp4bb] expression of Cys-rich small protein All - We are trying to express for structural studies a 257 AA eukaryotic intracellular (also possibly nuclear) protein (predicted to be single domain all-helical) that has 12 Cysteines. No known metal-binding function not that it couldn't happen. So far (E. coli) it expressed solubly as MBP fusion (with an N-terminal region deleted predicted disordered) until cleavage of MBP, then it's not soluble, including detergents added. THe MBP fusion is usually soluble aggregate so we assume that our part is not folded right. We have so far assumed it needs a lot of reducing agent (5 mM DTT or TCEP).Thinking of trying chaperones and insect cells next. Any experience out there that might help? Mostly I wonder about all the cysteines. Don't really know if that is the problem. Laurie Betts
[ccp4bb] A post-doctoral position in structural biology is available
A post-doctoral position in structural biology is available to train in structural biology of proteins of the urea cycle and arginine biosynthesis. The successful candidate will be mentored in generating and testing scientific hypotheses related to structural biology and biochemistry. He/she will work independently on projects under general guidance. Tasks will include design of study, collection and analysis of data, and reporting of results at conferences and in peer-reviewed manuscripts. Ph.D. or equivalent doctoral degree in molecular biology or related field. Majors Preferred: Biology, Biochemistry, Structural Biology, Molecular Biology, Cell Biology or Microbiology. The position will be open starting as soon as possible. Our institute helps to apply H1B visa for the potential candidate. Interested candidates should send a CV along with 3 letters of reference to: Dashuang Shi, PhD Center for Genetic Medicine and Department of Integrative System Biology Children’s National Medical Center George Washington University Washington, DC 20010 E-mail: d...@cnmcresearch.org Tel: 202-476-5817; Fax: 202-476-6014
Re: [ccp4bb] Digital microscope camera
Thanks all for the numerous answers ! I will post a summary of responses in a few days. -- Julian
Re: [ccp4bb] Citations in supplementary material
PLOS has the option of double blind review without author line references so that you can't even guess unless you are very familiar with the subject who the last author might be. Not sure though how many people have used this option. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Nov 18, 2010, at 7:21 AM, Anastassis Perrakis wrote: I like the online methods sections with e.g. Nature papers that also come with the pdf - they also count for citations, the citations are not within the manuscript allowance on numbers, they get peer reviewed and they actually leave quite a lot of space for readers to understand the experiments and for authors to cite methods properly. Easy fix in my mind. What Poul says about Nature, which is also my understanding, is in sharp contrast with the Cell group policy: Supplemental References Literature citations from within the Supplemental Information and unique to the Supplemental Information should be listed as Supplemental References. References that are already included in the main body of the paper should not be listed again. Please note that as references in Supplemental Information do not contribute towards citation measures for those papers, authors are encouraged, when possible, to include references in the main body of the paper. My experience with Elsevier, is that they like to listen to feedback and appreciate it. Nature seems to have fixed the problem with citations in Methods in a proper manner (which is largely true for all NPG journals, I think, at least NSMB will also do the Online Methods trick!). So, an important step would be that we as a community, take the steps to get everybody to follow that. So, lets start a petition? Maybe Victor that started this important thread could champion this and see it to an end !!! A.
Re: [ccp4bb] origin_shift in polar space group
Ah, looks like you are running one of my scripts! Although I called it origins.com, not origin.com. Someone must have renamed the file at some point. I have a newer (aka better) version of it here: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com which deals with the problem you seem to have encountered where two different chains in the moving model agree with the reference model, but with different origin shifts. This kind of thing happens a lot more often than you might think in molecular replacement and in heavy-atom finding programs. For example, consider trying to find two copies of the same protein in an asymmetric unit, using a crummy search model. After the first copy has been found, putting the second copy in the right place can (on occasion) have about as much dissonance as consonance with the first chain, and the best-scoring position of the second chain will then be found at random (often as not on another origin). I thought it was interesting to know when this happens, so I left that warning message in. However, as Ian pointed out, when you have a sliding origin, it can be hard to say exactly when an origin shift is the same or different. The new version of origins.com simply picks one and only one origin shift for all chains in the moving PDB file and then sticks with it. I have implemented a new approach wich uses electron density map deconvolution that seems to work pretty well, and does not rely on atom names being the same in the reference and moving PDB files. If you do have same-name atoms in both PDB files, then the CCP4 suite program reforigin or the Phenix program emma are both much faster than my script. However, if you get some satisfaction out of watching each origin get tried in turn, giving you a score for each, or if you have something like a rough chain trace and you want to compare it to a right answer PDB file, then origins.com might be the thing for you. Thanks! -James Holton MAD Scientist On Thu, Nov 18, 2010 at 4:26 AM, Ian Tickle ianj...@gmail.com wrote: OK now I understand. I couldn't find the script 'origin.com' you mentioned in the examples directory (at least from the filename I assume it's a script, not a MS-DOS program!), but it doesn't matter, I see the problem now. AFAIK there isn't a script in CCP4 that will do what you want entirely automatically, because it's actually quite a complicated problem in the completely general case of N molecules per a.u., though undoubtedly it could easily be scripted for the relatively simple case of 2 mols per a.u.. I'm assuming you don't simply want to superpose the molecules just for structural comparison purposes, you want to superpose the entire *crystals*, so that the calculated structure factors and hence the R factors (values) remained unchanged for the transformed structure. This means you can't use just arbitrary rotation/translation operators as would be generated by superposition programs such as SSM, you have to restrict it to crystallographically-allowed origin shifts. There are various programs which will do this, I wrote one called 'reforigin' but there are others which will do the same thing, and which have been mentioned in previous postings. So what you have to do is superpose the two 'A' molecules using reforigin or whatever (remember, as long as it applies only crystallographically-allowed origin shifts). There is of course a problem here: the chain ID 'A' is only an arbitrary label, so there's a 50% chance that the molecule you called 'A' in structure 1 might be called 'B' in structure 2 (and vice versa). This means you have to try both possibilities! Now you see why it gets complicated in the general case with molecules 'A', 'B', 'C', 'D' ... you have to try all combinations! While you are superposing A/2 on A/1 (or B/2 on A/1) you must also transform the other chain B/2 (or A/2) using the *same* operator (I think the program does this for you, or at least it will print the matrix that was used for the 1st pair) - you must not superpose it independently. Finally you need to transform the other molecule B/2 (or A/2) in the example above. For this you can only use space-group symmetry operators - you get only one chance to use the allowed origin shifts with the first pair of molecules, after that the origin is completely determined for the entire structure, hence only space-group symmetry can be used to transform subsequent pairs. For this I find it easiest just to view the structure on the graphics, work out which is appropriate space-group operator and apply it just to the 2nd molecule using PDBSET. Hope this is all clear - there are many traps here for the unwary! Cheers -- Ian On Thu, Nov 18, 2010 at 10:55 AM, Rojan Shrestha ro...@riken.jp wrote: Hello Ian: I am afraid that whether my problem is not clear to you. Here is brief description of the problem. When I tried to superimpose two structures having two or
Re: [ccp4bb] origin_shift in polar space group
Hello: It is origins.com not origin.com. I made spelling mistake. I am sorry for it. I tried my problem. It performs better. Thank you very much. Regards, Rojan From: James Holton [mailto:jmhol...@lbl.gov] Sent: Friday, November 19, 2010 1:05 PM To: CCP4BB@jiscmail.ac.uk Cc: ro...@riken.jp Subject: Re: [ccp4bb] origin_shift in polar space group Ah, looks like you are running one of my scripts! Although I called it origins.com, not origin.com. Someone must have renamed the file at some point. I have a newer (aka better) version of it here: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com which deals with the problem you seem to have encountered where two different chains in the moving model agree with the reference model, but with different origin shifts. This kind of thing happens a lot more often than you might think in molecular replacement and in heavy-atom finding programs. For example, consider trying to find two copies of the same protein in an asymmetric unit, using a crummy search model. After the first copy has been found, putting the second copy in the right place can (on occasion) have about as much dissonance as consonance with the first chain, and the best-scoring position of the second chain will then be found at random (often as not on another origin). I thought it was interesting to know when this happens, so I left that warning message in. However, as Ian pointed out, when you have a sliding origin, it can be hard to say exactly when an origin shift is the same or different. The new version of origins.com simply picks one and only one origin shift for all chains in the moving PDB file and then sticks with it. I have implemented a new approach wich uses electron density map deconvolution that seems to work pretty well, and does not rely on atom names being the same in the reference and moving PDB files. If you do have same-name atoms in both PDB files, then the CCP4 suite program reforigin or the Phenix program emma are both much faster than my script. However, if you get some satisfaction out of watching each origin get tried in turn, giving you a score for each, or if you have something like a rough chain trace and you want to compare it to a right answer PDB file, then origins.com might be the thing for you. Thanks! -James Holton MAD Scientist On Thu, Nov 18, 2010 at 4:26 AM, Ian Tickle ianj...@gmail.com wrote: OK now I understand. I couldn't find the script 'origin.com' you mentioned in the examples directory (at least from the filename I assume it's a script, not a MS-DOS program!), but it doesn't matter, I see the problem now. AFAIK there isn't a script in CCP4 that will do what you want entirely automatically, because it's actually quite a complicated problem in the completely general case of N molecules per a.u., though undoubtedly it could easily be scripted for the relatively simple case of 2 mols per a.u.. I'm assuming you don't simply want to superpose the molecules just for structural comparison purposes, you want to superpose the entire *crystals*, so that the calculated structure factors and hence the R factors (values) remained unchanged for the transformed structure. This means you can't use just arbitrary rotation/translation operators as would be generated by superposition programs such as SSM, you have to restrict it to crystallographically-allowed origin shifts. There are various programs which will do this, I wrote one called 'reforigin' but there are others which will do the same thing, and which have been mentioned in previous postings. So what you have to do is superpose the two 'A' molecules using reforigin or whatever (remember, as long as it applies only crystallographically-allowed origin shifts). There is of course a problem here: the chain ID 'A' is only an arbitrary label, so there's a 50% chance that the molecule you called 'A' in structure 1 might be called 'B' in structure 2 (and vice versa). This means you have to try both possibilities! Now you see why it gets complicated in the general case with molecules 'A', 'B', 'C', 'D' ... you have to try all combinations! While you are superposing A/2 on A/1 (or B/2 on A/1) you must also transform the other chain B/2 (or A/2) using the *same* operator (I think the program does this for you, or at least it will print the matrix that was used for the 1st pair) - you must not superpose it independently. Finally you need to transform the other molecule B/2 (or A/2) in the example above. For this you can only use space-group symmetry operators - you get only one chance to use the allowed origin shifts with the first pair of molecules, after that the origin is completely determined for the entire structure, hence only space-group symmetry can be used to transform subsequent pairs. For this I find it easiest just to view the structure on the graphics, work out which is appropriate space-group operator and apply it just to the 2nd molecule using PDBSET.
[ccp4bb] Postdoc Position in TMC-BCM, Houston
NIH funded Postdoctoral scientist position is available to study the structure and function of proteins in Nitric Oxide-cGMP signaling cascade. These enzymes modulate the cellular level of cGMP or the cellular response to this crucial secondary messenger and represent therapeutic targets for treating many hypertensive diseases, such as arterial and pulmonary hypertension, heart failure and erectile dysfunction. For more information, please visit website http://www.bcm.edu/pharmacology/index.cfm?pmid=9685 The successful candidate should have strong background and experience in molecular cloning, protein purification and biophysical characterization and x-ray crystallography. The qualified candidates must have a PhD or equivalent. Competitive salary and benefits are offered based on experience and qualifications. The laboratory is located in Texas Medical Center campus, which provides an excellent environment for academia and research. The lab is well equipped including robotics to facilitate overproduction and crystallization of proteins and has ready access to the Berkeley ALS beamline in the framework of the molecular biology consortium. Applicants should submit a curriculum vitae and and arrange to have 3 letters of reference sent to Prof. Kim ( c...@bcm.edu). Applications will be accepted until the position is filled. -- CRITICAL-Stop the ACTA. http://www.eff.org/ Daniel Ra Lab Sysadmin Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax)
