[ccp4bb] X-ray crystallography software developer position at Astex
Dear All, We have an opening for a skilled software developer with crystallographic computing background at our Cambridge (UK) site. For more information about the position, please see the full advert: https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSearch=True==30 To apply, please follow the link in the advert. For informal enquiries, please feel free to contact me. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] reminder - postdoc position at Astex
Dear All, Just a quick reminder that Astex has an opening for a skilled post-doctoral researcher with an interest in software development. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-advert.pdf Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] postdoc position, automated ligand placement
Dear All, We have an opening for skilled post-doctoral researcher with an interest in software development at our Cambridge (UK) site. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-advert.pdf Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] open positions at Astex
Dear All, Astex has multiple positions open within the Molecular Sciences group based in Cambridge, UK. Software developer/X-ray crystallography: http://astx.com/wp-content/uploads/2019/12/Xray-Software-Developer.pdf Structural biologist/protein scientist: http://astx.com/wp-content/uploads/2019/12/Structural-Biologst-MAT-cover.pdf Software developer/X-ray crystallography (sustaining innovation PDRA): http://astx.com/wp-content/uploads/2019/10/SI-Post-Doc-2019-Mol-Sci.pdf Interested candidates should liaise with the HR department (email address can be found in the adverts). For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] X-ray crystallography software developer position at Astex
Dear All, Astex is seeking to recruit a software developer to join the Molecular Sciences group. Interested candidates should liaise with the HR department (please see email address below). For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK ### Job Description: X-ray Crystallography Software Developer (Ref: XS/0519) Location: Cambridge, UK Astex Pharmaceuticals is a world leader in innovative drug discovery and development. The company has successfully applied its proprietary Fragment-Based Drug Discovery (FBDD) platform to generate multiple new drug candidates that are progressing in clinical development. Successful collaborations have led to two launched oncology drugs (Kisqali(r) partnered with Novartis and BalversaTM partnered with Janssen). Astex continues to grow and focuses on oncology and neurological disorders. CURIOSITY, CREATIVITY AND INNOVATIVE SCIENCE FOR DRUG DISCOVERY ...UNLOCK YOUR POTENTIAL Astex has a strong culture of developing bespoke software to support our fragment-based drug discovery platform, in particular our high throughput X-ray crystallography pipeline. As part of Astex's ongoing commitment to extending its existing computational crystallography infrastructure, the Molecular Sciences Group has an opportunity for a highly motivated scientist to join the X-ray Technology Team. The ideal candidate will be a crystallographer with an aptitude for software development, or a computer scientist with experience of working in macromolecular crystallography. Principal Responsibilities: * Design and implement computational crystallography tools and web applications * Maintain and improve the existing computational crystallography platform * Keep abreast of the latest developments in crystallography to identify new opportunities * Collaborate with and work alongside structural biologists and software developers at Astex Skills and Experience Required: * Degree in physics, chemistry, biology, computer science or related field * Background in crystallographic computing * Proven software development experience working in industry or an equivalent academic setting * Expert knowledge in Python and/or JavaScript * Knowledge of Perl, C++, Fortran and experience with relational databases is a plus * Familiarity with common software development tools and practices (version control, testing, etc.) * Excellent team working, written and verbal communication skills We offer excellent training and career development opportunities as well as a highly competitive salary and benefits package. Closing date: 31st July 2019 To apply, please send your CV and a cover letter quoting the job reference: XS/0519 to hr...@astx.com We are recruiting into permanent and 2-3-year fixed term contract positions depending on qualifications and experience For information on Astex Pharmaceuticals please visit: www.astx.com<http://www.astx.com> and for information on Otsuka Pharmaceuticals please visit: www.otsuka.co.jp<http://www.otsuka.co.jp> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
Hi Ivan, you need to tell Phaser which ensemble to use for searching. Open the Search parameters tab, and select the ensemble you defined. HTH, Gabor On 2015-06-29 16:48, xaravich ivan wrote: Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the error that is poping up indicating I have not set an ensamble. How can I set an ensamble if I have only one PDB? Or do I have to make some changes in the input. (I just put an arbitrary name for ensmale that sounds similar to the single PDB input (search model) file Thanks, Ivan On Mon, Jun 29, 2015 at 1:01 AM, herman.schreu...@sanofi.com wrote: Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON xaravich ivan GESENDET: Montag, 29. Juni 2015 09:43 AN: CCP4BB@JISCMAIL.AC.UK BETREFF: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan -- ## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##
Re: [ccp4bb] Resolve Domain Sequence Ambiguities
Hi Jacob, I would superpose domain B onto each domain A in turn, and run refinement in Phaser. If the LLG goes up, exchange that domain A for a domain B, otherwise keep. This requires 14 refinement calculations. This procedure may not give you what you are hoping for if your models are distant, since in this case domain A may be a better model for both domains. However, you could still improve your solution this way, and is therefore probably worth it. BW, Gabor On 2015-02-05 15:20, Keller, Jacob wrote: Hi All, I have 14 identical domains placed in my ASU with reasonable MR scores, but the problem is that there should really be 7+7 or 8+8 of domains A and B (which are structurally similar). Can anyone think of a great and easy way of resolving the ambiguity? I was thinking potentially: -change one domain to polyAla -SA omit map of that one -rebuild/refine -iterate through all domains, noting scores Seems it might be pretty low reliability and a fair amount of work though. Otherwise, could try to go back to a small SAD signal, use partial model phases to find HAs, then phase without the model, rebuild from there. Any thoughts or similar experiences? JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- ## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##
Re: [ccp4bb] How to Run ensembler:CCP4
Hi Yogesh, you need to change the extension to .aln, and then it will recognize it as a ClustalW file. Perhaps this is something that could be improved in Ensembler. As a separate note, with your current settings, the alignment will not be used, so you can just run it without the alignment. BTW, I am assuming that your input PDB contain multiple identical copies. Best wishes, Gabor On 2014-11-14 14:13, yogesh khandokar wrote: Dear ALL, I am trying to use ensembler program to generate MR ensembler, available in CCP4 Suit. I am getting a error and not getting results. The report is attached herewith please suggest corrections.. Thanks in Advance Regards -- Yogesh Khandokar PhD Student School of Biomedical Sciences Charles Sturt University Wagga Wagga, NSW, Australia http://www.csu.edu.au/faculty/science/biomed/ [1] Links: -- [1] http://www.csu.edu.au/faculty/science/biomed/
Re: [ccp4bb] new phaser and threads
Hi Francois, add the keyword JOBS N to your scripts. If it still uses more than N threads, this is possibly a bug. BW, Gabor On Apr 4 2013, Francois Berenger wrote: Hello, Is there a way to tell the new phaser to not use more than N threads when running? I have a problem with it overloading some cluster nodes. Thanks a lot, F.
Re: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit
This seems to be very a common scenario in MR and recently we have added some code to phaser.MRage that would handle it automatically. Each partial solution is analysed for the presence of (complete of incomplete) assemblies that obey local point group symmetry. After such an assembly is identified, the program can either fill in molecules where they should be (provided the obey the previously identified local symmetry), and can also search with the full assembly. This greatly enhances the signal (since the model comprises a larger fraction of the asymmetric unit), and also speeds up the search. (MRage is not yet included in the current CCP4 release, but available as alpha-test in recent Phenix nightly builds.) BW, Gabor On Apr 30 2012, Roger Rowlett wrote: A partial solution can potentially lead you to an appropriate MR solution. With many protein chains in the ASU, there will be several reasonable possibilities by Matthews analysis. When I originally solved 2A8D, cell content analysis suggested 8 monomers per ASU, but it was clear after a few MR runs that was not going to work. Inspecting the packing of a partial solution with 4 monomers, which formed a nice, biological-looking tetramer, clearly suggested that another dimer would fit into the lattice just nicely. A search with 3 such dimers produced an excellent MR solution starting point for the final refinement. I used a similar procedure for 3UAO. The Matthews analysis suggested 10-12 chains per ASU, but it was clearly 8 based on packing of partial solutions. A 4-dimer search was immediately successful. 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 4/30/2012 5:20 PM, mjvdwo...@netscape.net wrote: Provided that you guess the number of copies and your guess is reasonably close, my experience is that Phaser will do the job. But you have to tell it how many copies you expect, or it will never make sense of the data. When I did my structure with 6(?) copies some years ago, I guessed a number that was close enough and then when I inspected the electron density I could see that there were more copies than I had told the software and all was fine after that. It was surprising to see that good solutions were obvious from a packing consideration, while inadequate solutions were obviously wrong. Mark -Original Message- From: Ke, Jiyuan jiyuan...@vai.org To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Mon, Apr 30, 2012 2:28 pm Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit Dear All, I have a question regarding solving a crystal structure by molecular replacement. It is a single protein with a molecular weight of 25.5 kDa. The cell dimension is rather big from the diffraction data ( 90.9 Å, 143.9 Å, 216.3Å, 90°, 90°, 90°). The possible space group is P212121. With such a big unit cell, we predicted that there are 8-10 molecules per asymmetric unit. We have a decent model with sequence similarity of 49%. I tried several times with Phaser search with the current model and had difficulty to find any clear solution. Has anyone seen such cases and any suggestions to solve the structure? Thanks! Jiyuan Ke, Ph.D. Research Scientist Van Andel Research Institute 333 Bostwick Ave NE Grand Rapids, MI 49503 -- ## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##
