Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
Hello, Indeed, rigged positions do exist. In places where it is compulsory to advertise positions but where the person who will get the job has been selected in advance and is known already at the time the job advertisement appears. This does happen in several countries worldwide. I do not agree much with ccp4bb wars but India has been known to hire Indian citizens only for permanent jobs (with government funding). Foreigners (as I was told by Indian scientists - whom I believe) are only allowed to be employed on soft money, i.e. fixed term fellowships that may be renewed. This is quite different however than claiming (as Sham does) that this is a rigged job, I personally do not know (I won't be sitting on the panel interviewing the candidates). But for those (worldwide) who are involved in arranging such rigged jobs, perhaps these people should make it clear in advance to the candidates: Look, we are only advertising this position because it is compulsory. Now if you want to practice giving a presentation of your results for a future job interview and come visit us, and perhaps stay on for a couple of days to visit the area, we'd be delighted to have you around. But do not expect to get a job with us. Just don't repeat this to anyone, in fact we are warning you by phone because there will be no traces of this conversation ever having taken place. This would be more fair to the people who apply - but this is only day dreaming I think. F. On 30/10/12 00:33, Phoebe A. Rice wrote: I have no idea about Bangalore, but I know from personal experience that already-filled job ads exist and waste everybody's time. One of the junior faculty jobs I intereviewed for in the 90s at a prestigious US medical school turned out to be just such a thing - before I went people in the know told me which inside post-doc would get the position, faculty turnout to my presentation was low, and even during the visit somebody told me they thought it would be an inside deal. And in the end, it was. I had much better things to do with my time. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu mailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
[ccp4bb] Call for abstracts: Structural Biology in the BioEconomy (SBBE) 2012
A conference on “*Structural Biology for the Bioeconomy: Infectious Diseases and Biotechnology*” will be held at the *University of Cape Town* from *1 December to 2012 to 4 December 2012*. The conference will immediately precede the annual conference of the Microscopy Society of Southern Africa (4-7 December 2012) and will be held in the same venue on the University of Cape Town campus. The conference website is http://www.sbbe.co.za and more about the organisers can be found here: http://www.sbbe.co.za/structural-biology-conference-organisers/ *Context* Work in the field of structure determination of protein and macromolecular complexes has made a real and significant impact on: • The understanding of the mechanism of infection by pathogens • The design of interventions in the form of drugs • The design of preventative measures such as vaccines, barrier creams etc. • The design of enzymes to make new industrial chemicals • The design of novel herbicides and pesticides • The design of energy efficient industrial processes exploiting engineered enzymes • The use of engineered enzymes for environmental remediation • The use of biomolecules to make novel “bionanomachines” • The understanding of biological events so that novel strategies for intervention in human health can be designed and produced or exploited to make new devices. The conference will focus on the above areas and will highlight structural biology and biophysics research of direct economic benefit. The purpose of the meeting would thus be to: • further understanding of the interaction between Structural Biology and Biophysics, • promote awareness and development of Structural and Biophysics and associated techniques at all levels in the Southern African region, • further the exchange of knowledge w.r.t the latest research, results, techniques, and ideas in all areas of Structural Biology and Biophysics, • showcase the rapidly emerging South African research in Structural Biology and Biophysics and the increasing numbers of excellent African researchers in this area, • enable the South African researchers and students to hear presentations of work by international counterparts, • network and explore the possibilities of both local and international collaborations/partnerships, as well as interdisciplinary interactions, • foster the educational and research potential of students interested in pursuing Structural Biology and/or Biophysics as a career or major research tool, particularly those young researchers from previously disadvantaged communities *Themed areas of focus:* The conference will focus on the following 3 themes: - *BioEconomy*: By focusing on industrial enzymes as well as their optimization with respect to their production, their thermal and chemical stabilization as well as their catalytic efficiency. These are classical areas of biotechnology, synthetic biology and nano-technology resulting in the large scale production of modified enzymes world-wide to produce a large array of chemicals and biological products under mild conditions. The rate of developing new products – both the enzymes themselves as well as commercial products obtained by their use – is particularly high in this area of research - *Health Innovation*: By addressing and analyzing molecular processes underlying infectious diseases. By investigating interacting proteins or enzymes critical to pathogenesis, the information obtained will directly flow into the generation of new drugs to eradicate these diseases. In the case of South Africa tuberculosis and HIV/AIDS result in particularly heavy burden on the population though other infectious diseases such as cholera and bacterial meningitis are also prevalent. - *Human Capital Development*: By providing access to excellent local and international researchers, postgraduate students will be exposed to cutting-edge research. Through personal contacts students and supervisors will be able to identify new exchange laboratories, allowing them to partly train in the partner country providing them with first-hand experience of methodologies and techniques not normally available to them. *Involvement of Young Scientists * Both the number and the size of research groups in Structural Biology are growing steadily in South Africa reflecting the growing interest and participation of postgraduate students at all levels in this discipline. In addition, interest in structural biological techniques and analyses is growing in allied specializations in biotechnology and the health sector, significantly increasing the pool of young scientists in from South Africa that will benefit from this three-day conference. We hope to attract *around 60 young scientists and students* from the various South African universities and from the CSIR. Thanks and kind regards, *Amanda Dominy* *Conference Organiser - SBBE 2012* Salamander Conference and Event Management Email:
Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
I think Fred is overstating the problem of compulsory adverts. There are also cases where the expected pre-selected candidate does not get the job as a better candidate appears. There are also cases where there is eventually no job for anyone. Another outcome of an interview is you don't get the advertised post but are mentored through a fellowship application or similar to that institution. Like not stating an age range compulsory adverts are practices designed to reduce prejudice or nepotism, but do not eliminate it. They do not completely change the attitude of panel members, but most scientists do look at the data in front of them. The system also works both ways, you get good candidates coming for a job, who are only after an offer to improve their pay negotiations at their home institute. Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX
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-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, given the test is written in proper English with proper grammer etc., I think you are actually asking for censorship. I am happy ccp4bb does not censor such emails, be they in accordance with one's opinion or not! Best, Tim On 10/30/2012 06:15 AM, Kavyashree Manjunath wrote: Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQj5K5UxlJ7aRr7hoRAum6AKDzlXQSoX827+OrPJOiWy1zF24pVgCgymMq Hgv5aAxCqVjSnONml1GSfx0= =KVPK -END PGP SIGNATURE-
[ccp4bb]
Dear Kavya, The CCP4BB is a closed community, in the sense that a user must subscribe to the list before being able to post and that subscription requests are handled manually rather than being granted by default. This is generally sufficient to stop spam, irrelevant advertisements and blatant trolling. It is a credit to the subscribers that this system works. We are a self-governing community in which it is only natural that contentious messages generate vigorous responses. Only very rarely have subscriptions been cancelled because of an abuse of the system. Indeed in most such cases this has been a result of the subscriber's email account being hacked and used without their permission. The sort of comment removed type moderation you might see on e.g. newspaper websites is neither possible on our email-based Bulletin Board, nor I believe desirable, as it goes against the spirit of the CCP4BB. -- David On 30 October 2012 05:15, Kavyashree Manjunath ka...@ssl.serc.iisc.inwrote: Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb]
Dear all Could we stop at this point. regards Garib On 30 Oct 2012, at 18:35, Kavyashree Manjunath wrote: Dear Sir, I agree to that. But I presume that this is a platform to discuss scientific problems and not a forum to discuss or pour out personal frustrations. There may be other channels for such grievances but not this. I was just hoping this does not become a social network wherein everyone are free to express anything. Thank you kavya -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, given the test is written in proper English with proper grammer etc., I think you are actually asking for censorship. I am happy ccp4bb does not censor such emails, be they in accordance with one's opinion or not! Best, Tim On 10/30/2012 06:15 AM, Kavyashree Manjunath wrote: Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQj5K5UxlJ7aRr7hoRAum6AKDzlXQSoX827+OrPJOiWy1zF24pVgCgymMq Hgv5aAxCqVjSnONml1GSfx0= =KVPK -END PGP SIGNATURE- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] Orientation of the crystal and it importance in data collection
Dear Professor, Thank you very much for suggestion. With kind regards B.Vijayakumar On Mon, Oct 29, 2012 at 5:13 PM, Peter Keller pkel...@globalphasing.comwrote: Dear Tim and B. Vijay, On Mon, 2012-10-29 at 12:02 +0100, Tim Gruene wrote: Dear B. Vijay, for single-wavelength (as opposed to Laue) X-ray crystallographic data collection it is in general helpful to mount your crystal in an arbitrary orientation. Well, this depends on the sample, and how you are going to solve the structure if you don't already know it for the crystal form that you have (i.e. MR, SAD, MAD etc). The overall oscillation range required for completeness depends on the orientation, and if your sample is radiation sensitive then achieving (near) completeness early can be helpful. If you happen to mount it such that a symmetry axis is parallel to the rotation axis, you may not be able to collect fully complete data. and also if the symmetry axis is a screw axis you won't have observed any systematic absences. So it may be a good idea to tilt the symmetry axis away from the rotation axis a bit. But (in some cases) not too far: apart from the rotation range issue, if you have one cell axis much longer than the others, putting it close to the rotation axis will reduce spot overlap, which can also be helpful. These factors (as well as others such as anisotropy of the sample) fight against each other, and the best compromise depends on the sample, the wavelength and the instrumentation that you are using. A truly arbitrary orientation risks getting it badly wrong. If you are unlucky you may then be unable to process the images and/or solve the structure (or at least have severe problems). Indexing routines figure out the orientation of your crystal. After integrating all reflections, the orientation is refined (depending on the integration program you use). For anomalous data you may want to collect in inverse beam mode which makes sure you collect Bijvoet pairs close in time and thus reduce the effect of radiation damage. As drawback you risk possible systematic errors in the Bijvoet pairs, but I am not sure this is a major drawback for MX crystals. If you can adjust the orientation so that Bijvoet pairs are on the same image, this can help here. I recomend you take a look a Zbigniew Dauter's article Data-collection strategies, Acta Cryst D55 (1999) p. 1703-1717 doi:10.1107/S0907444999008367 This is of course excellent advice. Regards, Peter. Best, Tim On 10/27/2012 07:58 AM, Vijayakumar.B wrote: Dear CCP4BB users, I have some basic questions in the data collection. Please give me some ideas to get clear in this part. 1)Why orientation of the crystal is importance? 2)If we mounted the crystal in arbitrary, what it leads? 3)How to find out crystal misseting angels in the data collection if we mounted arbitrary? 4)What should we make clear before collecting anomalous signal data ? Thanks in advance. With regards B. Vijay -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom -- *B.Vijayakumar Research Scholar, CAS in Crystallography and Biophysics, University of Madras, Guindy campus,Chennai-25 INDIA Mobile: +919791929209*
Re: [ccp4bb] how to find and add water molecules in electron density map in coot??
Read the manual? !! There is a menu under Other modelling tools with a task - Add waters. That will scan the map and add waters conservatively. Or you can use the validation tool. Find difference map peaks, and decide for yourseld whether they are waters. If you like the peak click Add atom at pointrer and assign it atom type water. Eleanor On 29 October 2012 11:29, saleem raza mysaleemr...@hotmail.com wrote: I have a question regarding model building. can anyone guide how to find and add water molecules in electron density map in coot. regards Saleem Date: Mon, 29 Oct 2012 19:23:00 +0900 From: robie0...@gmail.com Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? To: CCP4BB@JISCMAIL.AC.UK Hi, everyone Now I can get collect result after setting ORGX and ORGY to 1024. Thank Manfred for his help. Thank everyone who helped me. Best regard Chang 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de: The same is true for the third data. I would suggest the following. Examine the images and try to see where the origin is. If you cannot figure this out, set ORGX and ORGY both to 1024, which is the exact center of the detector. And then try again and send me the IDXREF.LP Best wishes Manfred On 29.10.2012 08:35, Chang Qing wrote: 2012/10/29 Chang Qing robie0...@gmail.com: 2012/10/29 Chang Qing robie0...@gmail.com: Thank you very much. I will send you the files through three mail. 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de: Thank you very much. I think this is a trivial error, but I will have to investigate a little bit. Can you also send me the files IDXREF.LP and FRAME.cbf for the three data sets processed with XDS? Of course I will treat your data in confidence. With best wishes Manfred On 29.10.2012 07:54, Chang Qing wrote: 2012/10/29 Chang Qing robie0...@gmail.com: 2012/10/29 Chang Qing robie0...@gmail.com: Dear Manfred Thank you very much. I think I cannot answer your questions in detail. As I am a clinical doctor indeed, I don't know some principles in detail. I will send you all log file. Mail will be separated in three. First letter, data is collected in spring8(41xu), and can get correct result. Second and third letter, date is collected in KEK(nw12a), and space group are wrong. As my data is not publication yet, would you please keep it secret? Thank you very much. As I use macbook, XDSAPP cannot be installed on it. 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de : Dear Chang, there is something seriously wrong with this data. It is possible that the lattice is mis-indexed. Which images did you use for indexing. In contrast to HKL2000, which indexes based on a Fourier analysis of just one images, XDS indexes based on differences vector and needs at least a few (10) images, better would be two slices of 10 images 90 degrees apart. Which XDS tutorial have you followed? Have you tried any of the automatic versions of XDS, such as XDSAPP which we are developing in our lab? Where were the data collected? If you send me some more information about your data I will help you process them using XDS. With best regards Manfred On 29.10.2012 06:03, Chang Qing wrote: And CORRECT file 2012/10/29 Chang Qing robie0...@gmail.com: Here, I show some information about my data and input files of XDS. Wavelength (A) 1. Raster size (mm) 0.10240 (default) Raster size (mm) 0.10240 (default) Film width (mm) 209.72 (default) Film length (mm) 209.72 (default) Record length (pixels) 2048 (default) Number of records 2048 (default) Top limit of useful data 0. (default) Left limit of useful data 0. (default) spots rejected when pixel overflow at value : 65500.0 pixels rejected at value: 0 Oscillation starts at 0. Oscillation range 1. Lattice type: primitive Orientation axis 1 (vertical plane) 1*h 0*k 0*l (default) Orientation axis 2 (spindle) 0*h 0*k 1*l (default) Mosaicity 0.3 CrysZ (beam) axis 0. (default) CrysY (vertical) axis 0. (default) CrysX (spindle) axis 0. (default) unit cell parameters not entered Detector (mis)orientation angles: CassZ (beam) axis 0. CassY (vertical) axis 0. CassX (spindle) axis 0. Detector 2 theta 0. Detector rotation 90.000 (default) Flat detector (default) Detector to crystal distance 166.20 X beam 104.80 Y beam 105.10 Beam polarization 0.99000 Detector absorption 100.00 (default) Air absorption length 860.00 (default) Crossfire y 0. Crossfire x 0. Crossfire xy 0. Horizontal box size 3.6864 Vertical box size 3.6864
Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
There is a big difference between reading does not discriminate on the basis of race, color, religion, sex, age, sexual orientation, marital status, national origin, disability, or status as a disabled, Vietnam-era, or other eligible veteran and below 35 years. Then regarding Prof. Chitta's reply, comparing 35 years (india) and 45 years (US) extends it not just to the age, but also to the origin maybe :) toufic On Mon, Oct 29, 2012 at 7:21 PM, James Stroud xtald...@gmail.com wrote: The agism in the advertisement doesn't do the institute much credit. I'm inclined to believe Sham, given the Institutes stated policies: Applicants, preferably below 35 years James On Oct 29, 2012, at 11:28 AM, Narayana VL Sthanam wrote: Sham, who so ever you are, if you have such a long list of complaints, why don’t you put your name clearly and complain openly, instead of hiding behind some anonymous ‘SHAM’ name. What you write about IISc may be all true or it may be reflection of your frustration for not getting a job at IISc!*** * How do we know? So, grow a ‘spine’, if you have a complaint, say it like a man and do not hide behind and bad mouth others anonymously like spoiled child. You are not only throwing dirt on such a prestigious Indian institution, and also on many decent and capable scientists who do outstanding work and produce brilliant graduate students, some of which I was fortunate to have in my lab. ** ** Best Narayana Sthanam ** ** *--* *Narayana Sthanam,Ph D* *Professor of Structural Biology* *244 CBSE 1025 18th Street South* *Center for Biophysical Sciences and Engineering* *University of Alabama at Birmingham* *Birmingham, Al 35294* *Phone: 205 934 0119* *URL: **http://www.opt.uab.edu/narayanalab*https://mail.ad.uab.edu/owa/redir.aspx?C=80a7a9ef03ea46b58d648b78f13d4272URL=http%3a%2f%2fwww.opt.uab.edu%2fnarayanalab “Never let success go to your head, nor failure to your heart ” ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *U US *Sent:* Monday, October 29, 2012 12:03 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore ** ** Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham ** ** -- Date: Mon, 29 Oct 2012 11:47:06 +0530 From: vikasnavra...@gmail.com Subject: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore To: CCP4BB@JISCMAIL.AC.UK Dear all Kindly make a note. Indian Institute of Science, Bangalore. ** ** Molecular Biophysics Unit (http://mbu.iisc.ernet.in/) ** ** Opening for Assistant Professor Positions. ** ** Applicants, preferably below 35 years, should have a Ph.D. with postdoctoral experience with an excellent publication record. ** ** We seek candidates in the general area of structural biology with an emphasis on understanding macromolecular systems at the molecular level. ** ** Applications with a detailed CV, research plan (not exceeding 3 pages) and names of at least 4 referees should be sent to chair...@mbu.iisc.ernet.in Best
Re: [ccp4bb] Phaser MR with partial solution, 8 molecules/ASU
if you are sure about it's position, why not put the 8th molecule by hand? why believe what a program does more than you can see by eye? (this is nothing against Phaser, it is a great program) Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 30 Oct 2012, at 15:44, Jacob Wong wrote: Dear all, I have this (3.0 A) structure that has 8 molecules per ASU - Phaser was able to find 7 molecules correctly, but not the last one, as indicated by the .sol file (TFZ=5.1) below and the resultant density map. I tried to delete the entry of the last molecule and give the truncated .sol file for another round of MR but Phaser returned with the same solution that has the 8th molecule misplaced. I am tempted to place the 8th molecule by hand but before that would like to learn from you a better way of handling it. One thing I could think of is to refine/rebuild the partial structure with the 7 molecules so as to resolve any potential packing clashes due to model/structure variations and then let Phaser find/position the 8th one for me, but it appears that Phaser doesn't accept .pdb file for a MR with partial solution routine? Thank you, Jacob # [No title given] SPACEGROUP P 21 21 21 SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248 TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0 LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1 PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0 TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0 SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985 -0.12420 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107 -0.12591 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927 -0.27514 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096 -0.17121 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711 -0.09462 -0.07282 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754 -0.02533 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041 -0.17986 BFAC 0.0 SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915 -0.05760 BFAC 0.0
[ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
[ccp4bb] Fwd: email received from Nick Keep...
With permission from Nick Keep to forward to the bb which I am doing right now :-) If I may add: an organization advertising for a rigged job but not reimbursing the candidate's expenses is, in my opinion, wrong doing. I have never seen this happen in the UK but this has happened elsewhere... With this I think we can close the discussion (I do not favour ccp4bb wars). And I am in favour of job ads being posted to the bb. Fred. Original Message Subject:Re: Date: Tue, 30 Oct 2012 10:55:18 + From: Nicholas Keep n.k...@mail.cryst.bbk.ac.uk To: vellieux frederic.velli...@ibs.fr CC: n.k...@mail.cryst.bbk.ac.uk Dear Fred, Sorry did not mean to send a personal post, it was meant to go to the list which it has now. I think some discussion of career issues is not a bad thing for ccp4bb particularly as we allow job adverts. The discussion was starting to be a bit negative about recruitment. What you recount is a truly dreadful story. Like the original posting I think one of the major problems was being made to pick up your own expenses. Not something that I have come across in the UK. Perhaps a point that should be made on the list, except I think there is a desire to shut this line down. Institutions should at least pay the costs of attendance; they have the balance of power. There are as I said people who come for interview with little intention of taking the job, but the faculty at least get a seminar for the travel costs. Feel free to post this or a summary if you think it is helpful. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Eike - This unfortunately, is a well-known feature of coot on OS X - something to do with Apple's implementation of X11. Perhaps Paul knows if this happens on Mountain Lion, now that you need to use Quartz X11? Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 30, 2012, at 3:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Yes, it's still happening on Mountain Lion. Cheers, Ronnie -- Dr. Ronnie Berntsson PostDoctoral Fellow Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University 10691 Stockholm Sweden On Oct 30, 2012, at 16:51 , Antony Oliver antony.oli...@sussex.ac.uk wrote: Eike - This unfortunately, is a well-known feature of coot on OS X - something to do with Apple's implementation of X11. Perhaps Paul knows if this happens on Mountain Lion, now that you need to use Quartz X11? Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 30, 2012, at 3:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
I do not think prof Chitta Das understands the meaning of Equal Employment Opportunity (EEO) in US. If Purdue which is an EEO institute had followed the criteria of below 35 years age to select assistant profs then he would not have served as an Assistant Prof today. On Tue, Oct 30, 2012 at 5:56 AM, Toufic El Arnaout tou...@inmesolabs.netwrote: There is a big difference between reading does not discriminate on the basis of race, color, religion, sex, age, sexual orientation, marital status, national origin, disability, or status as a disabled, Vietnam-era, or other eligible veteran and below 35 years. Then regarding Prof. Chitta's reply, comparing 35 years (india) and 45 years (US) extends it not just to the age, but also to the origin maybe :) toufic On Mon, Oct 29, 2012 at 7:21 PM, James Stroud xtald...@gmail.com wrote: The agism in the advertisement doesn't do the institute much credit. I'm inclined to believe Sham, given the Institutes stated policies: Applicants, preferably below 35 years James On Oct 29, 2012, at 11:28 AM, Narayana VL Sthanam wrote: Sham, who so ever you are, if you have such a long list of complaints, why don’t you put your name clearly and complain openly, instead of hiding behind some anonymous ‘SHAM’ name. What you write about IISc may be all true or it may be reflection of your frustration for not getting a job at IISc!** ** How do we know? So, grow a ‘spine’, if you have a complaint, say it like a man and do not hide behind and bad mouth others anonymously like spoiled child. You are not only throwing dirt on such a prestigious Indian institution, and also on many decent and capable scientists who do outstanding work and produce brilliant graduate students, some of which I was fortunate to have in my lab. ** ** Best Narayana Sthanam ** ** *--* *Narayana Sthanam,Ph D* *Professor of Structural Biology* *244 CBSE 1025 18th Street South* *Center for Biophysical Sciences and Engineering* *University of Alabama at Birmingham* *Birmingham, Al 35294* *Phone: 205 934 0119* *URL: **http://www.opt.uab.edu/narayanalab*https://mail.ad.uab.edu/owa/redir.aspx?C=80a7a9ef03ea46b58d648b78f13d4272URL=http%3a%2f%2fwww.opt.uab.edu%2fnarayanalab “Never let success go to your head, nor failure to your heart” ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *U US *Sent:* Monday, October 29, 2012 12:03 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore ** ** Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham ** ** -- Date: Mon, 29 Oct 2012 11:47:06 +0530 From: vikasnavra...@gmail.com Subject: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore To: CCP4BB@JISCMAIL.AC.UK Dear all Kindly make a note. Indian Institute of Science, Bangalore. ** ** Molecular Biophysics Unit (http://mbu.iisc.ernet.in/) ** ** Opening for Assistant Professor Positions. ** ** Applicants, preferably below 35 years, should have a Ph.D. with postdoctoral experience with an excellent publication record. ** ** We seek candidates in the general area of structural biology with an emphasis on understanding macromolecular systems at the molecular level. ** ** Applications with a detailed CV, research plan (not exceeding 3 pages) and names of at least 4 referees should be sent to chair...@mbu.iisc.ernet.in Best
[ccp4bb] ResearchGate?
Hi, At the risk of starting another series of rants, and somewhat off-topic, is anyone actively using ResearchGate? It is bombarding me with email messages, but I am uncertain as to whether people are really using it or whether it is just scientific spam. Adrian Goldman Adrian Goldman Institute of Biotechnology, University of Helsinki, Finland
[ccp4bb] oof topic: pH effect on substrate analog
Hi all, I'm working on a protein that I recently got crystals of. My functional studies show that the protein has optimal activity at lower pHs, while losing 90% activity at about pH8. I've been trying to soak/cocrystallize a substrate analog (small molecule) into my crystals (grown at ~pH8) with no real luck. I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Thanks for any insights Peter
Re: [ccp4bb] oof topic: pH effect on substrate analog
Dear Peter, You could check your putative binding site to see if there are charged groups which need to be protonated for your substrate analog to bind (or whether the substrate analog needs to be protonated). In order to draw physiologically relevant conclusions, you would need a crystal structure at a pH where the protein is active. Try if you can transfer your crystals to lower pH, perhaps by significantly increasing the precipitant concentration. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Hsu Sent: Tuesday, October 30, 2012 5:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] oof topic: pH effect on substrate analog Hi all, I'm working on a protein that I recently got crystals of. My functional studies show that the protein has optimal activity at lower pHs, while losing 90% activity at about pH8. I've been trying to soak/cocrystallize a substrate analog (small molecule) into my crystals (grown at ~pH8) with no real luck. I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Thanks for any insights Peter
Re: [ccp4bb] ResearchGate?
Hello Adrian, I use Research Gate and there are a few occasions where I have found it useful, particularly the questions feature. HTH, Dave David C. Briggs PhD http://about.me/david_briggs On 30 October 2012 16:13, Adrian Goldman adrian.gold...@helsinki.fi wrote: Hi, At the risk of starting another series of rants, and somewhat off-topic, is anyone actively using ResearchGate? It is bombarding me with email messages, but I am uncertain as to whether people are really using it or whether it is just scientific spam. Adrian Goldman Adrian Goldman Institute of Biotechnology, University of Helsinki, Finland
[ccp4bb]
I agree with Garib that we should stop this, because nothing productive seems to be coming out of this discussion. I however like to clarify one thing about the comment I made about agism. I merely intended to interpret what the age limit preference means in the context of Government of India's policy (therefore, I used the quotation mark). I DO NOT endorse the policy. The government stipulates an age limit for any government job, including the job at MBU, IISC (last time I knew, it used to be controlled by the Government, at least in the recruitment and retirement part). Clearly, it does not confirm to the Equal Employment Opportunity (EEO) in the US, very much like many regulations in China or in Europe do not mean anything in the US. What works for US does not necessarily work for India. I always wondered what the age limit means. Why should there be one? Maybe the answer lies in the socio-economic structure of the country. Here is a country with nearly a billion people with much less opportunity (the GDP is nowhere comparable to that of US). The question for the law makers is how to distribute a very few job among the most qualified people. If we are looking at two candidates that have very similar credentials, maybe the one who accomplished them at an earlier age is better?. I think that's what the word 'preferably' signifies. I also think that it is somehow related to some grant agencies in the US determining who is a 'young investigator'. Again, because the opportunities are so few. Am I wrong? Once again, I love the Equal Employment Opportunity (EEO) in US and that's one of the reasons I came to US. But, do I think a discussion over CCP4bb can change government of India' policy and India's socio-economic status? I think not, but then, I may be a pessimist. Best Chitta - Original Message - From: Garib N Murshudov ga...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 5:40:23 AM Subject: [ccp4bb] Dear all Could we stop at this point. regards Garib On 30 Oct 2012, at 18:35, Kavyashree Manjunath wrote: Dear Sir, I agree to that. But I presume that this is a platform to discuss scientific problems and not a forum to discuss or pour out personal frustrations. There may be other channels for such grievances but not this. I was just hoping this does not become a social network wherein everyone are free to express anything. Thank you kavya -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, given the test is written in proper English with proper grammer etc., I think you are actually asking for censorship. I am happy ccp4bb does not censor such emails, be they in accordance with one's opinion or not! Best, Tim On 10/30/2012 06:15 AM, Kavyashree Manjunath wrote: Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQj5K5UxlJ7aRr7hoRAum6AKDzlXQSoX827+OrPJOiWy1zF24pVgCgymMq Hgv5aAxCqVjSnONml1GSfx0= =KVPK -END PGP SIGNATURE- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed
Re: [ccp4bb] oof topic: pH effect on substrate analog
Peter, I think it would depend if the substrate analog have ionizable groups? If the analog does not have ionizable groups, it is hard to imagine how the the titration of ionizable groups on the protein would impair the binding. Chitta - Original Message - From: Peter Hsu hsuu...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 12:12:58 PM Subject: [ccp4bb] oof topic: pH effect on substrate analog Hi all, I'm working on a protein that I recently got crystals of. My functional studies show that the protein has optimal activity at lower pHs, while losing 90% activity at about pH8. I've been trying to soak/cocrystallize a substrate analog (small molecule) into my crystals (grown at ~pH8) with no real luck. I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Thanks for any insights Peter
Re: [ccp4bb] oof topic: pH effect on substrate analog
As for most questions in science, the answer is unfortunately it depends. A substrate analog may bind just peachy at a pH in which the enzyme is inactive, depending on what interactions are involved in stabilizing the analog compared to the substrate transition state. Such a complex may still be structurally informative. Changing the ionization states of active site groups may or may not have a significant effect on binding. One must consider not only electrostatic interactions, but also hydrogen bonding donor-acceptor interactions. Lowering pH, for example, may turn H-bonding acceptors into obligate donors, or in the case of metalloenzymes, make metal-bound water/hydroxide labile for exchange. In any event, I'd be willing to bet that a substrate analog structure at a non-optimal pH is more informative than no structure at the optimal pH! :) Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 10/30/2012 1:39 PM, Chittaranjan Das wrote: Peter, I think it would depend if the substrate analog have ionizable groups? If the analog does not have ionizable groups, it is hard to imagine how the the titration of ionizable groups on the protein would impair the binding. Chitta - Original Message - From: Peter Hsu hsuu...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 12:12:58 PM Subject: [ccp4bb] oof topic: pH effect on substrate analog Hi all, I'm working on a protein that I recently got crystals of. My functional studies show that the protein has optimal activity at lower pHs, while losing 90% activity at about pH8. I've been trying to soak/cocrystallize a substrate analog (small molecule) into my crystals (grown at ~pH8) with no real luck. I'm wondering, since I lack activity at this pH point, would it lead to no binding of a substrate analog? Thanks for any insights Peter
[ccp4bb] Ca or Zn
Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Ca or Zn
calculate an anomalous map, you should see the Zn signal even if you collected at the SeMet peak. Jürgen .. 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://lupo.jhsph.edu On Oct 30, 2012, at 2:55 PM, Kumar, Veerendra wrote: Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Ca or Zn
How would you distinguish between a mixture of Ca and Zn in the same locations? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kumar, Veerendra [veerendra.ku...@uconn.edu] Sent: Tuesday, October 30, 2012 1:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Ca or Zn
On Tue, Oct 30, 2012 at 12:12 PM, Jim Pflugrath jim.pflugr...@rigaku.com wrote: How would you distinguish between a mixture of Ca and Zn in the same locations? How often would they be likely to bind in the same place? Some of the other transition metals are difficult to tell apart, but Ca and Zn have very different coordination preferences. -Nat
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
Re: [ccp4bb] Ca or Zn
On 10/30/12 15:02, Bosch, Juergen wrote: calculate an anomalous map, you should see the Zn signal even if you collected at the SeMet peak. Jürgen .. Ca can have a noticeable anomalous signal of its own, if your data are good. If the possibility to collect new data exists, collecting above and below the Zn edge should be informative. (Zn K edge 1.28 A = 9.6586 keV) -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Ca or Zn
If you calculate an edgeplot via Ethan's server: http://skuld.bmsc.washington.edu/scatter/AS_form.html you'll see that Zn @1Å has about 3 anomalous electrons whereas Ca less than 1, so assuming occupancy of 1 the stronger anomalous signal should give you a hint, second looking at the refined B-values if you placed the wrong metal should also coincide with your correct choice of metal. The question with the mixture, well lets wave some hands and bring in biological relevance. If the protein is supposed to do something with Ca then I would say so, even if Zn is bound. If the anomalous signal is comparable to the SeMet sites then I would model Zn there but say it's likely not physiological as Ca is required by this enzyme. Jürgen On Oct 30, 2012, at 3:12 PM, Jim Pflugrath wrote: How would you distinguish between a mixture of Ca and Zn in the same locations? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kumar, Veerendra [veerendra.ku...@uconn.edu] Sent: Tuesday, October 30, 2012 1:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra .. 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://lupo.jhsph.edu
Re: [ccp4bb] Ca or Zn
Do occupancy refinement. Especially if you use the new anomalous refinement option available in refmac, phenix.refine and other packages as well, you should be able to get a pretty reliable number for how many real electrons as well as anomalous electrons are at each site. At almost any reasonable B-factor a Ca+2 looks a LOT like a Zn+2 at 64% occupancy, and the f will also be very different (depends on your wavelength). If the results are not abundantly clear, then you can get a kinda-sorta error bar by starting refinement with different occupancies, and perhaps kicking the starting model coordinates around (to remove bias). If the occupancy keeps refining back to the same value, then you can be reasonably confident that it is well-determined by your data. If the occupancy doesn't appear to stably return to the same value, or at least values different enough to say it is Zn vs Ca, then the identity of your metal sites is NOT well-determined by your data. -James Holton MAD Scientist On 10/30/2012 7:55 PM, Kumar, Veerendra wrote: Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
[ccp4bb]
Chita, I disagree that the age limitation for an entry level job does anything good to a society. It gives a clear advantage to graduates from a few prestigious universities, because less fortunate students would need more time to develop their careers, no matter how talented they are. So, a competition for those positions shifts to a younger age of application to colleges, where social inequity defines a success even stronger. Moreover, it creates conditions for a corruption, because people will try to place their children in those colleges at any cost. Very poor countries cannot copy free market models from the West. Their governments should develop special programs giving an opportunity to talented kids from socially disadvantageous families to compete for good jobs. I hope your government does not require a proof of birth in a city where an institute is located? There were countries with such preconditions. Best regards, Alex On Oct 30, 2012, at 10:25 AM, Chittaranjan Das wrote: I agree with Garib that we should stop this, because nothing productive seems to be coming out of this discussion. I however like to clarify one thing about the comment I made about agism. I merely intended to interpret what the age limit preference means in the context of Government of India's policy (therefore, I used the quotation mark). I DO NOT endorse the policy. The government stipulates an age limit for any government job, including the job at MBU, IISC (last time I knew, it used to be controlled by the Government, at least in the recruitment and retirement part). Clearly, it does not confirm to the Equal Employment Opportunity (EEO) in the US, very much like many regulations in China or in Europe do not mean anything in the US. What works for US does not necessarily work for India. I always wondered what the age limit means. Why should there be one? Maybe the answer lies in the socio-economic structure of the country. Here is a country with nearly a billion people with much less opportunity (the GDP is nowhere comparable to that of US). The question for the law makers is how to distribute a very few job among the most qualified people. If we are looking at two candidates that have very similar credentials, maybe the one who accomplished them at an earlier age is better?. I think that's what the word 'preferably' signifies. I also think that it is somehow related to some grant agencies in the US determining who is a 'young investigator'. Again, because the opportunities are so few. Am I wrong? Once again, I love the Equal Employment Opportunity (EEO) in US and that's one of the reasons I came to US. But, do I think a discussion over CCP4bb can change government of India' policy and India's socio-economic status? I think not, but then, I may be a pessimist. Best Chitta - Original Message - From: Garib N Murshudov ga...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 5:40:23 AM Subject: [ccp4bb] Dear all Could we stop at this point. regards Garib On 30 Oct 2012, at 18:35, Kavyashree Manjunath wrote: Dear Sir, I agree to that. But I presume that this is a platform to discuss scientific problems and not a forum to discuss or pour out personal frustrations. There may be other channels for such grievances but not this. I was just hoping this does not become a social network wherein everyone are free to express anything. Thank you kavya -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, given the test is written in proper English with proper grammer etc., I think you are actually asking for censorship. I am happy ccp4bb does not censor such emails, be they in accordance with one's opinion or not! Best, Tim On 10/30/2012 06:15 AM, Kavyashree Manjunath wrote: Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of
Re: [ccp4bb] Ca or Zn
Veerendra, You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. Best Chitta - Original Message - From: Veerendra Kumar veerendra.ku...@uconn.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 2:55:33 PM Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Ca or Zn
This doesn't really give a useful answer. It tells you the overall composition, but there is no means of knowing whether the metal ions are equally present at all sites: some sites can favour Zn over Ca and vice versa. Flame spectroscopy also works but has the same issue - and both have the problem that you don't really know whether you have got rid of all metal ions bound weakly to the surface of the protein/crystal and most crystals, being small, have a humongous surface-to-volume ratio. The coordination is indicative but not conclusive but, as I responded to the original poster, I think the best approach is to use anomalous scattering. You can measure just below and above the Ca edge, and similarly with the Zn, and those maps will be _highly_ indicative of the relative amounts of metal ion present. In fact, you can deconvolute so that you know the occupancy of the metals at the various sites. Adrian On 30 Oct 2012, at 22:37, Chittaranjan Das wrote: Veerendra, You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. Best Chitta - Original Message - From: Veerendra Kumar veerendra.ku...@uconn.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 2:55:33 PM Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
Re: [ccp4bb] Ca or Zn
On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: The coordination is indicative but not conclusive but, as I responded to the original poster, I think the best approach is to use anomalous scattering. You can measure just below and above the Ca edge, Actually, you can't. The Ca K-edge is at 3.07Å, which is not a wavelength amenable to macromolecular data collection. cheers, Ethan and similarly with the Zn, and those maps will be _highly_ indicative of the relative amounts of metal ion present. In fact, you can deconvolute so that you know the occupancy of the metals at the various sites. Adrian On 30 Oct 2012, at 22:37, Chittaranjan Das wrote: Veerendra, You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. Best Chitta - Original Message - From: Veerendra Kumar veerendra.ku...@uconn.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 2:55:33 PM Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] refmac
hi, i have a large pdb file and i keep getting this error with refmac ERROR: number of chains 1500 i suspect something needs to be done to my pdb any suggestions ? thanks jpd
Re: [ccp4bb] refmac
hi, answering my own question, but maybe this will save some searching in the future, the error was related to 3 letter RNA codes refmac doesn't like that. jpd --- On Tue, 10/30/12, jp d yo...@yahoo.com wrote: From: jp d yo...@yahoo.com Subject: [ccp4bb] refmac To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 30, 2012, 3:43 PM hi, i have a large pdb file and i keep getting this error with refmac ERROR: number of chains 1500 i suspect something needs to be done to my pdb any suggestions ? thanks jpd
Re: [ccp4bb] refmac
Hi Refmac use one letter code for RNA and two letter for DNA. Otherwise each residue is considered as one chain (if there is no link between them). I hope it helps. regards Garib On 31 Oct 2012, at 08:05, jp d wrote: hi, answering my own question, but maybe this will save some searching in the future, the error was related to 3 letter RNA codes refmac doesn't like that. jpd --- On Tue, 10/30/12, jp d yo...@yahoo.com wrote: From: jp d yo...@yahoo.com Subject: [ccp4bb] refmac To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 30, 2012, 3:43 PM hi, i have a large pdb file and i keep getting this error with refmac ERROR: number of chains 1500 i suspect something needs to be done to my pdb any suggestions ? thanks jpd Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] Ca or Zn
On Tuesday, 30 October 2012, Jrh wrote: This paper describes use of data either side of the calcium edge:- http://dx.doi.org/10.1107/S0907444905002556 I think that counts as not amenable (which is not quite the same as impossible. From the Methods section of that paper: Measurements in the vicinity of the K absorption edge of calcium (3.07 Å) are close to or beyond the physical limit of most beamlines typically used for X-ray crystallography [...] It was not possible to observe interpretable diffraction patterns at λ = 3 Å with the weakly diffracting furin crystals using the MAR CCD detector and exposure times up to 20 min per degree of rotation. They did soldier on and managed to collect extremely weak data below the Ca edge and stronger but still very weak data above the edge where the Ca f term was appreciable. But this is far from a routine experiment. Another approach dating back to work in 1972 by Peter Coleman and Brian Matthews http://dx.doi.org/10.1016/0006-291X(72)90750-4 is to replace the Ca with a rare earth having similar chemistry (e.g. La, whose L-1 edge is at 1.98Å). This next paper describes a case of gallium and zinc mix at one site with occupancy AND sigmas estimated with different software. This example is however much better diffraction resolution than that you may have. But hopefully will still be of interest:- http://dx.doi.org/10.1107/S0108768110011237 Ga and Zn, sure. That's an easy one. The Ga edge is at 1.196Å and the Zn edge is at 1.284Å, both edges are nicely in range for data collection and they are close enough together that little or no beamline readjustment is needed when jumping from one to the other. Ethan Prof John R Helliwell DSc On 31 Oct 2012, at 04:53, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote: The coordination is indicative but not conclusive but, as I responded to the original poster, I think the best approach is to use anomalous scattering. You can measure just below and above the Ca edge, Actually, you can't. The Ca K-edge is at 3.07Å, which is not a wavelength amenable to macromolecular data collection. cheers, Ethan and similarly with the Zn, and those maps will be _highly_ indicative of the relative amounts of metal ion present. In fact, you can deconvolute so that you know the occupancy of the metals at the various sites. Adrian On 30 Oct 2012, at 22:37, Chittaranjan Das wrote: Veerendra, You can rule out if zinc has replaced calcium ions (although I agree with Nat and others that looking at the coordination sphere should give a big clue) by taking a few crystals, washing them a couple of times and subjecting them to ICP-MS analysis, if you have access to this technique. You can learn how many zinc, if any, have bound per one protein molecule in the dissolved crystal. Best Chitta - Original Message - From: Veerendra Kumar veerendra.ku...@uconn.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, October 30, 2012 2:55:33 PM Subject: [ccp4bb] Ca or Zn Dear CCP4bb users, I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I purified the protein in presence of Ca2+ and crystallized the Ca2+ bound protein. I got crystal and solved the structure by SAD phasing at 2.1A resolution. I can see the clear density in the difference map for metals at the expected binding sites. However I had ZnCl2 in the crystallization conditions. Now i am not sure whether the observed density is for Ca or Zn or how many of them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value difference can be used to make a guess about different ions? is there any way we can find the electron density value at different peaks? Thank you Veerendra
