[ccp4bb] Positions available - Photon Factory, Japan
Dear all The Structural Biology Research Center at the Photon Factory (Japan) is advertising for several PostDoc positions in structural biology. Notably, one position will link methodology in structural biology applied to XFEL by comparison with 'classical' x-ray sources at synchrotrons. Further details available below. You can also contact me directly, and have a look at the Structural Biology Research Center webpage for detailed information on our diverse activities: http://pfweis.kek.jp/eng/index.html Kind regards. Leo CHAVAS ###DETAILS BELOW### Title : Postdoctoral Fellow Number of Job Opening : 1 Inst/Lab : Structural Biology Research Center Term : The contract is for 1 year, but may be renewed at the end of the term until March 2017 at the longest Start of the term : Successful candidate is expected to take the position as soon as possible Job Description : In 2012, the Ministry of Education, Culture, Sports, Science Technology in Japan (MEXT) launched a five-year program Key Strategic Research Projects Using X-ray Free Electron Laser, SACLA (XFEL). As a co-leader of one of its projects, for the Development of Rapid Structural Analysis Methodologies for Protein Drug Targets directed by Prof. So Iwata, KEK will pursue structural biology research on human proteins of medical interest. The KEK team will be responsible for developing new methodologies applicable to in vivo crystal growth and nano-crystallography using the XFEL. The successful candidate is expected to play a central role in the development of these methodologies, as well as directly applying them to the structural analysis of human protein crystals grown in vivo at the Japanese XFEL SACLA. The candidate is expected to have experiences in protein crystallography research including protein production, X-ray crystallography and relevant software developments. Method of Selection : We will first make a selection by submitted documents and interview. Interview will take place on a first-come first-served policy. (We will inform of the interview date the candidates who passed our documentary screening.) Documents to submit : A4 size paper - 29.5 cm x 21 cm or similar including 1) Curriculum vitae: please write the possible date you would be able to start the job at the Synchrotron Radiation Science Division II. Please also write your birth date in the application form. 2) Research and job experience related to this application. 3) Publication list 4) Research and development plan at the SBRC if employed (should cover areas corresponding to the whole job description) 5) Reprints of major publications (fewer than 6) 6) Other reference materials (list of invited talks, awards etc.) 7) Recommendation of reference letter(s): recommendation of reference letter(s) must be addressed to Dr. Kazuyoshi Yamada, Director, IMSS, attention to Personnel Affairs Unit 1 of KEK. For more information : Please contact Assist. Prof. Leo Chavas, Synchrotron Radiation Science Division ll, Institute of Materials Structure Science. Tel: +81 29-864-5200 (ext: 4901) Fax: +81 29-864-2801 E-mail: leonard.cha...@kek.jp Application to be mailed to: Personnel Affairs Unit 1 KEK 1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan (We accept recommendation or reference letter(s) by email) Others : - KEK is an equal-opportunity employer and encourages applications from women. - This program will be evaluated in the third year. --- Chavas Leonard M.G., Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Accelerator Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan --- Phone : +81(0)29-864-5642 (4901) Fax : +81(0)29-864-2801 E-mail : leonard.cha...@kek.jp ---
[ccp4bb] the FCCC license
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, the FCCC license for the program scwrl4 (http://dunbrack.fccc.edu/scwrl4/license/index.html) says that Licensee will take all reasonable precautions to avoid any unauthorized disclosure of SCWRL4.0. I may misunderstand the meaning of the word 'disclosure', but to me this statement excludes putting the program on any computer accessible by anybody except me. I would like to install scwrl4 on our group's network for general use, but with my current understanding and interpretation this would make me violate this license. Would anyone kindly let me know whether I understand this license correctly, or whether I can install scwrl4 on a networked computer and allow access to other group members? The could copy it easily unless I fiddle around with access permissions, probably at the level of ACL's which I am not familiar with. Thanks for comments, Tim - -- - -- 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/ iD8DBQFQM1r3UxlJ7aRr7hoRAgi6AJ9zmVlOuafCLrcGiLAMfH2MvLz09gCcC8dl KgmOrlk6/XPLqwRa6fqwpG8= =zUsq -END PGP SIGNATURE-
Re: [ccp4bb] the FCCC license
Tim, doesn't para 12 of the Agreement cover that: If SCWRL4.0 is installed on computers owned by a corporation or other legal entity, then this agreement is formed by and between FCCC and such entity (Licensee). You represent and warrant to FCCC that you have the authority to bind Licensee to this Agreement.. Cheers -- Ian On 21 August 2012 10:55, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, the FCCC license for the program scwrl4 (http://dunbrack.fccc.edu/scwrl4/license/index.html) says that Licensee will take all reasonable precautions to avoid any unauthorized disclosure of SCWRL4.0. I may misunderstand the meaning of the word 'disclosure', but to me this statement excludes putting the program on any computer accessible by anybody except me. I would like to install scwrl4 on our group's network for general use, but with my current understanding and interpretation this would make me violate this license. Would anyone kindly let me know whether I understand this license correctly, or whether I can install scwrl4 on a networked computer and allow access to other group members? The could copy it easily unless I fiddle around with access permissions, probably at the level of ACL's which I am not familiar with. Thanks for comments, Tim - -- - -- 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/ iD8DBQFQM1r3UxlJ7aRr7hoRAgi6AJ9zmVlOuafCLrcGiLAMfH2MvLz09gCcC8dl KgmOrlk6/XPLqwRa6fqwpG8= =zUsq -END PGP SIGNATURE-
Re: [ccp4bb] the FCCC license
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, it depends whether George Sheldrick's group can be considered a 'legal entity', or whether the next available legal entity would be the Inorganic Chemistry Dpt. - in the latter case I would not think I have the authority to bind the Dpt. to the FCCC license. I'll assume the former - FCCC will probably not behave like SCO... But I am not happy with this license. E.g. it does not explicitly allow me to install the program on computers of the group, the quoted paragraph only seems to imply it. Best, Tim On 08/21/12 12:06, Ian Tickle wrote: Tim, doesn't para 12 of the Agreement cover that: If SCWRL4.0 is installed on computers owned by a corporation or other legal entity, then this agreement is formed by and between FCCC and such entity (Licensee). You represent and warrant to FCCC that you have the authority to bind Licensee to this Agreement.. Cheers -- Ian On 21 August 2012 10:55, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear all, the FCCC license for the program scwrl4 (http://dunbrack.fccc.edu/scwrl4/license/index.html) says that Licensee will take all reasonable precautions to avoid any unauthorized disclosure of SCWRL4.0. I may misunderstand the meaning of the word 'disclosure', but to me this statement excludes putting the program on any computer accessible by anybody except me. I would like to install scwrl4 on our group's network for general use, but with my current understanding and interpretation this would make me violate this license. Would anyone kindly let me know whether I understand this license correctly, or whether I can install scwrl4 on a networked computer and allow access to other group members? The could copy it easily unless I fiddle around with access permissions, probably at the level of ACL's which I am not familiar with. Thanks for comments, Tim - -- - -- 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/ iD8DBQFQM2DAUxlJ7aRr7hoRAtixAKCHVT7xEsJgzIPbfbGvm2o6lg5CnwCfZYlL e4j1vVfD39vzOOft82pO7AE= =B+83 -END PGP SIGNATURE-
[ccp4bb] predicting membrane-association domain
Sorry for the off-topic post… Does anyone know of software that predicts the membrane-association domain of peripheral membrane proteins using sequence and/or atomic coordinates? Thanks. John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tanne...@missouri.edumailto:tanne...@missouri.edu phone: 573-884-1280 fax: 573-882-2754 web: http://www.chem.missouri.edu/tannergroup/tanner.html
[ccp4bb] IUCr checkCIF server.
Dear Collegues, Does anybody know how to use the server http://checkcif.iucr.org/? I have downloaded structure factor and structure model cif files of a structure from PDB. However it looks this server only accept one single file, it does not work if these two files are uploaded separately. My question is: do I need to combine these two cif files into one? How to do that? Thanks! Niu
Re: [ccp4bb] IUCr checkCIF server.
Hi, The interface for uploading both structure factor and model files can be found here: http://journals.iucr.org/services/cif/checking/checkfull.html Checkcif is mainly intended for checking the structural details of small molecule CIF files - I have no idea what it will make of mmcif-format PDB files (the mmcif dictionary differs significantly from the core CIF dictionary which is used for small molecules), or indeed whether any checkcif output would be meaningful for a macromolecule. Cheers, Richard -- Richard Gildea Software Developer Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd Mail Stop 64R0121 Berkeley CA 94720-8118 On 21 August 2012 11:02, Niu Tou niutou2...@gmail.com wrote: Dear Collegues, Does anybody know how to use the server http://checkcif.iucr.org/? I have downloaded structure factor and structure model cif files of a structure from PDB. However it looks this server only accept one single file, it does not work if these two files are uploaded separately. My question is: do I need to combine these two cif files into one? How to do that? Thanks! Niu
Re: [ccp4bb] Problem with Coot on Mountain Lion
On 15 août 2012, at 02:23, Wataru Kagawa wakag...@mac.com wrote: Hi Jinyi, Do you have two versions of python installed? Maybe executing fink remove python will solve the problem (?) Hi, After updating to Mountain Lion, coot crashed when launched from the phenix GUI. But launching coot from the terminal did work. which python told me that the first python in the path was an old 2.6.1 from python.org that I had installed a couple of years ago. I guessed that my Coot/Phenix issue was related to this version. So I uninstalled it. But then I got the very same crash described by Jinyi when launching coot either from the terminal or from the Phenix GUI. I knew it was still a python issue but could not find the right thing to do (rebuilding coot was not enough), until I found your message. fink remove python did the trick! Thank you, you saved my day! Florian.
[ccp4bb] Purify non-stable protein
Dear all I made deletion mutation of a stretch of 20 amino acids on my protein. I can purify and crystallize wild type protein but not the mutated. Mass spec on gel separated protein shows degradation of mutant losing about another 150 amino acids. Is there any way of purifying this non-stable protein? I know nature has designed proteins to be stable. All steps are done at 4 C and protease inhibitor added during cell lysis for both proteins. Thank you.
Re: [ccp4bb] Purify non-stable protein
Hi Theresa, The deletion probably led to a folding problem, making it susceptible to residual proteases. You might try the following: -Lysis and purification in the presence of 1mM EDTA, which can help to neutralize proteases in addition to the protease inhibitor, without significant leaching of metal in a metal-affinity column (assuming your protein does not have natively-bound metal at an active site required for stability) -Try cocktails of different protease inhibitors -Denature the target completely with urea of GuHCl and then try refolding after purification efforts -In case your target of interest is from a thermostable organism and expressed in E. coli, you can try heating the sample to denature contaminating proteins/proteases. Best, Debanu. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Tuesday, August 21, 2012 1:15 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Purify non-stable protein Dear all I made deletion mutation of a stretch of 20 amino acids on my protein. I can purify and crystallize wild type protein but not the mutated. Mass spec on gel separated protein shows degradation of mutant losing about another 150 amino acids. Is there any way of purifying this non-stable protein? I know nature has designed proteins to be stable. All steps are done at 4 C and protease inhibitor added during cell lysis for both proteins. Thank you.
Re: [ccp4bb] Purify non-stable protein
In addition I would try expressing very late and short. Growing up your cells to the maximum OD600 and then inducing for as short as you can at lower temperature e.g. 16-20 ˚C Your protein might be degraded while expressed. Jürgen On Aug 21, 2012, at 4:28 PM, Das, Debanu wrote: Hi Theresa, The deletion probably led to a folding problem, making it susceptible to residual proteases. You might try the following: -Lysis and purification in the presence of 1mM EDTA, which can help to neutralize proteases in addition to the protease inhibitor, without significant leaching of metal in a metal-affinity column (assuming your protein does not have natively-bound metal at an active site required for stability) -Try cocktails of different protease inhibitors -Denature the target completely with urea of GuHCl and then try refolding after purification efforts -In case your target of interest is from a thermostable organism and expressed in E. coli, you can try heating the sample to denature contaminating proteins/proteases. Best, Debanu. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Tuesday, August 21, 2012 1:15 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Purify non-stable protein Dear all I made deletion mutation of a stretch of 20 amino acids on my protein. I can purify and crystallize wild type protein but not the mutated. Mass spec on gel separated protein shows degradation of mutant losing about another 150 amino acids. Is there any way of purifying this non-stable protein? I know nature has designed proteins to be stable. All steps are done at 4 C and protease inhibitor added during cell lysis for both proteins. Thank you. .. 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] Purify non-stable protein
Need more information: 1. Do you actually know the smaller protein is actually your target protein, or is it an impurity protein present in host cells? It could be that your truncation simply does not express well, and the darkest band in your crude lysate is something else. 2. Are you doing tag purification or are you purifying native protein? Purification conditions for truncated proteins may likely be very different than the native protein. Purification tags may stabilize your truncated protein (or not). 3. It is possible that the protein is being degraded in E. coli, but on the other hand I have made dozens of native N-terminal truncation variants without degradation. This is probably highly protein-dependent. 4. Does your truncation make chemical sense for protein stability? Is the N-terminus possibly required for the protein fold? Maybe another truncation site is appropriate, assuming you have a wild-type structure or homolog to go by. 5. It is possible to express your truncation variant as a protein-tagged (e.g. MBP or NusA, etc.) chimera, where you can control generation of the truncated variant after purification? 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 8/21/2012 4:15 PM, Theresa Hsu wrote: Dear all I made deletion mutation of a stretch of 20 amino acids on my protein. I can purify and crystallize wild type protein but not the mutated. Mass spec on gel separated protein shows degradation of mutant losing about another 150 amino acids. Is there any way of purifying this non-stable protein? I know nature has designed proteins to be stable. All steps are done at 4 C and protease inhibitor added during cell lysis for both proteins. Thank you.
Re: [ccp4bb] IUCr checkCIF server.
On 21/08/12 19:02, Niu Tou wrote: Does anybody know how to use the server http://checkcif.iucr.org/? I have downloaded structure factor and structure model cif files of a structure from PDB. However it looks this server only accept one single file, it does not work if these two files are uploaded separately. My question is: do I need to combine these two cif files into one? How to do that? One can't help but imagine that that is something of a mismatch (checkcif, AFAIK, is only to validate (small molecule) structures from cif files (not the same things as macromolecular (mm)cif/PDBx files)). So it's somewhat unclear what you want to do. I'm going to imagine that you want to look at a model and map for a particular accession code from the PDB. Perhaps the easiest ways to do that is using the Electron Density Server: http://eds.bmc.uu.se/eds/ (Presumably you are not using Coot pre-release, if you were you could you Extensions - Get From PDBe) HTH, Paul.
Re: [ccp4bb] Purify non-stable protein
In addition to the other very good suggestions, you could consider using a purification tag at both the N- and C-termini of your protein to only pull out full length protein. I've had success with Flag+His and MBP+His. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu On Tue, Aug 21, 2012 at 1:00 PM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Date:Tue, 21 Aug 2012 21:15:15 +0100 From:Theresa Hsu theresah...@live.com Subject: Purify non-stable protein Dear all I made deletion mutation of a stretch of 20 amino acids on my protein. I can purify and crystallize wild type protein but not the mutated. Mass spec on gel separated protein shows degradation of mutant losing about another 150 amino acids. Is there any way of purifying this non-stable protein? I know nature has designed proteins to be stable. All steps are done at 4 C and protease inhibitor added during cell lysis for both proteins. Thank you.
[ccp4bb] protein sequence database with conservation score annotation
Hi,everyone, Does anyone here could recommend such a database for me? I've searched the web and only find tools like 'consurf'. Databases like 'consurf' are important for the analysis of the current known structures. However, for the original discoveries of new domains, sequence databases with such conservation score annotation could be as important as the secondary structure prediction. Although the 'conservation score' maynot be as accurate as that from the 'consurf database' which is based on the 3-D alignment. The information of such database could be much more helpful, especially for some new proteins, or proteins regions without any structure available. Best regards, Yuan SHANG HKUST
