Re: [ccp4bb] seeing if this list can be put on gmane
Here is an example: http://news.gmane.org/gmane.editors.textmate.general Charles Ballard wrote: Dear Mark gmane has an obscure e-mail address function. We would use that. Charles On 26 Feb 2008, at 16:58, Mark J. van Raaij wrote: Dear Charles, it would perhaps be good to make sure email addresses are not publicly visible on gmane, to avoid spamming. greetings, Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 26 Feb 2008, at 17:25, Charles Ballard wrote: Right, if CCP4BB is to be archived on gmane, the list owner must agree (and as that is me, it seems OK), and the list users must be informed. If there is any reason not to gmane this list, please let me know. Note, I do not plan to allow posting from gmane, as this defeats the purpose of having to get people to register. Charles Ballard CCP4
Re: [ccp4bb] SC program in CCP4 - No radius found for residue G atom P
Hi Rosemary SC has stopped because P is not in its list of atomic radii. This list is located at $CCP4/lib/data/sc_radii.lib You will need to edit this file to add a value for P ( and possibly some of the other atoms in your RNA fragment). The format is fairly self-explanatory, with asterisks being used for wildcards. Alternatively you can use your own dictionary of atomic radii, and specify its location using the SCRADII command e.g. SC XYZIN .pdb SCRADII mydictionary.lib Norman Stein CCP4 Daresbury Laboratory From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rosemary Harrison Sent: 27 February 2008 06:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] SC program in CCP4 - No radius found for residue G atom P Hi, I have been trying to run SC on a pdb file with an RNA fragment. I get the answer below. There appears to be a problem with the P in the RNA backbone. Has anyone else had this problem and/or suggestions to fix it Thanks in advance, Rose Harrison Parameter values Dot density :15.00 per square Angstrom Interface separation : 8.00 Angstroms Trim width : 1.50 Angstroms Probe radius : 1.70 Angstroms Weight factor: 0.50 per square Angstrom No radius found for Residue G Atom P BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: S/r assign_r: no radius for residue/atom SC: S/r assign_r: no radius for residue/atom
[ccp4bb] Structural Biologist - permanent position in Central London
Structural Biologist - permanent position Central London (Reference SB0308) Cancer Research Technology (CRT) is a specialist oncology company, which advances discoveries arising from Cancer Research UK and other prestigious oncology focused organisations' research activities into potential therapies and diagnostics for the benefit of cancer patients. CRT is seeking to recruit a highly motivated structural biologist to join our X-ray structure determination team responsible for all aspects of crystallography, including protein expression, purification, characterization, crystallization, data collection and structure determination of pharmaceutically important protein-ligand complexes. The team is based within the School of Crystallography, Birkbeck College, adjacent to CRT's laboratories within the Wolfson Institute of Biomedical Research, University College London. The successful candidate will have at least three years postdoctoral experience within either academic or biopharmaceutical settings and will have a track record of accomplishments demonstrating technical excellence. Previous involvement in projects relating to oncology would also be advantageous. This is a permanent position with significant opportunity to influence the development of new cancer therapeutics and will suit a highly talented individual with strong interpersonal skills. To apply for this position, please send two copies of your CV and a covering letter, quoting the relevant reference number, to the HR Manager, CRT, Sardinia House, Sardinia Street, London, WC2A 3NL or by email to [EMAIL PROTECTED] No Agencies Closing Date: Thursday 20th March 2008 We have a no smoking policy CRT is an equal opportunities employer -- Andrew Turnbull, PhD Structural Biologist Cancer Research Technology Ltd Birkbeck College University of London Malet Street London WC1E 7HX UK Tel: +44 (0)20 7631 6837 Fax: +44 (0)20 7631 6803 www.CancerTechnology.com http://www.cancertechnology.com/ This email is from Cancer Research Technology Limited, registered in England Wales under no 1626049, registered office Sardinia House, Sardinia Street, London, WC2A 3NL., a wholly-owned subsidiary of Cancer Research UK, registered charity no. 1089464. CONFIDENTIALITY: The information contained in this communication may be privileged and confidential and is intended for the exclusive use of the addressee designated above. If you are not the addressee, any disclosure, reproduction, distribution or other dissemination or use of this communication is strictly prohibited. If you have received this transmission in error please would you be kind enough to inform us.
Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
Donghui, We have several membrane proteins crystallized in salt-based conditions, actually in high sodium citrate. Yes, LiCl or lithium formate are good alternatives, but also try lithium citrate, as citrate also depresses the freezing point quite well. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: [EMAIL PROTECTED] On Feb 27, 2008, at 12:36 AM, wu donghui wrote: Dear Lokesh, Actually I have tried to dip my crytal directly into mineral oil, no ice ring, but also no diffraction, which might indicate crystal packing under mineral oil is not stable. Anyway, thanks a lot for your valuable information. Other friends mention the use of LiCl or Lithium formate as cryoprotectant, I will try these immediately and will let you know if it works. Best regards, Donghui On 2/27/08, Lokesh Gakhar [EMAIL PROTECTED] wrote: Hi Donghui, Have you tried mineral oil? That has sometimes worked for us when other cryoprotectants have given problems. -Lokesh On Tue, Feb 26, 2008 at 9:30 PM, wu donghui [EMAIL PROTECTED] wrote: Dear all, Recently, I got a crystallization condition as 0.1 M Bis tris ph 6.5, 1.3M lithium sulfate, 0.1M NaCl, the shape of crystals is needle cluster, very difficult to grow bigger, microseeding does not work, then I tried macroseeding, and found crystal can grow bigger and rod like. However as for the cryoprotectant, crystal will dissolve in glycerol, ethylene glycol, MPD and PEG, even in the very low concentration about 5%. I found my crystal can grow under the additive 2-propanol in addition to the above mentioned crystallization condition. I also noticed that Hampton cryoprotectant kit has the 2-propanol as cryoprotectant. I want to know if anyone have ever used 2-propanol as the cryoprotectant and what effect it might be. By the way Hampton also mention lithium sulfate can be used as cryoprotectant, the recommended maxium concentration is 2M, I tried and found ice ring is severe and it is very easily to form lithium sulfate salt crystal at this high concentration, I also tried sodium malonate, the diffraction gave me few spots, resolution is only about 6--7 angstrom. Does anyone encounter such problem by lithium sulfate? Welcome to any replies. Thanks a lot in advance. Donghui
Re: [ccp4bb] torsion restraints COOT
Hi Brenda, Brenda Patterson wrote: I am doing molecular replacement with a model of sequence identity 42%. If you used a CCP4 automated MR tool to generate your model, then the [Post MR] Fill Partial Residues can conveniently restore side-chains that have been Schwarzenbachered. Have been trying numerous combinations of weighting in refmac of CCP4. However the geometry of the model is not being maintained. Geometry in the sense of things that are restrainted or those that are not? I am then trying manual fitting of the model in COOT. However when torsion restraints are applied in the refine/regularisation option the model comes out of the density. Regularize and Real Space Refinement (RSR) are not the quite the same thing. how would you tackle this please? If, when using the RSR, you think that not enough emphasis is being placed on the map, then you can change the weight (Set Matrix). i also have developed CIS peptides in places and have found that trying to revert these to trans is again causing the model to come out of the density severely. Oh dear. Olden Coot? There is a trick for even the wary, Refmac will add a CISPEP card to its output where there are unlabelled CISPEPs (from the output of Coot). If there are labelled CISPEPs (but not actually in the structure) Refmac will make the peptide CISPEP. Coot and Refmac are out of step (Coot is behind, it should catch up at some stage). Currently you would have to hand-edit the output of Coot/input to refmac to remove CISPEP cards that are inappropriate. Does anyone think it's ok not to use the torsion restraints in COOT Yes, I do. Torsion restraints are not (yet) applied across peptide linkages. and simply use real space refine/regularisation as it is in COOT? As long as your traffic lights are green[1], you should be OK. [1] http://www.ysbl.york.ac.uk/~emsley/coot/screenshots/traffic-lights-example.png Paul.
Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
There are many excellent review articles about cryocrystallography and cryoprotectants. Do labs generally have these articles handy in a methods folder? Do lab heads help their colleagues by making them read them? Mineral oil is generally not a good oil to use because it changes volume too much upon freezing. Have you tried other oils like Paratone-N, perfluoropolyether oil (also known as fomblin or turbomolecular pump oil), olive oil, etc? Also have you tried sugars? Have you tried growing the crystals in the presence of a little cryoprotectant? Even a little bit in the growth may help your crystals to survive a transfer or swish into a higher concentration for flash-cooling. Jim On Wed, 27 Feb 2008, wu donghui wrote: Dear Lokesh, Actually I have tried to dip my crytal directly into mineral oil, no ice ring, but also no diffraction, which might indicate crystal packing under mineral oil is not stable. Anyway, thanks a lot for your valuable information. Other friends mention the use of LiCl or Lithium formate as cryoprotectant, I will try these immediately and will let you know if it works. Best regards, Donghui On 2/27/08, Lokesh Gakhar [EMAIL PROTECTED] wrote: Hi Donghui, Have you tried mineral oil? That has sometimes worked for us when other cryoprotectants have given problems. -Lokesh On Tue, Feb 26, 2008 at 9:30 PM, wu donghui [EMAIL PROTECTED] wrote: Dear all, Recently, I got a crystallization condition as 0.1 M Bis tris ph 6.5, 1.3M lithium sulfate, 0.1M NaCl, the shape of crystals is needle cluster, very difficult to grow bigger, microseeding does not work, then I tried macroseeding, and found crystal can grow bigger and rod like. However as for the cryoprotectant, crystal will dissolve in glycerol, ethylene glycol, MPD and PEG, even in the very low concentration about 5%. I found my crystal can grow under the additive 2-propanol in addition to the above mentioned crystallization condition. I also noticed that Hampton cryoprotectant kit has the 2-propanol as cryoprotectant. I want to know if anyone have ever used 2-propanol as the cryoprotectant and what effect it might be. By the way Hampton also mention lithium sulfate can be used as cryoprotectant, the recommended maxium concentration is 2M, I tried and found ice ring is severe and it is very easily to form lithium sulfate salt crystal at this high concentration, I also tried sodium malonate, the diffraction gave me few spots, resolution is only about 6--7 angstrom. Does anyone encounter such problem by lithium sulfate? Welcome to any replies. Thanks a lot in advance. Donghui
[ccp4bb] opening Marketing Structural Biology Solutions
Dear group members, I'd like to bring following opening to your attention: - Bruker AXS designs and manufactures analytical X-ray systems for elemental analysis, materials research and structural investigations. Our innovative solutions enable a wide range of customers in heavy industry, chemistry, pharmacy, semiconductor, life science and nanotechnology to make technological advancements and to accelerate their progress. During the recent years Bruker AXS' solutions in Single-Crystal Structural-Biology have convinced an increasing number of scientists. Bruker AXS B.V., Delft (The Netherlands) has an immediate opening for a full or part-time position Marketing Structural Biology Solutions A strong background in scientific instrumentation will help the qualified applicant to promote Bruker AXS' solutions for Single-Crystal Structural-Biology. The successful candidate will be responsible for short term and long term marketing activities. This includes the continuous update of the internet presence, the release of brochures and the coordination of Bruker's activities at exhibitions and major trade-shows. Based on an excellent knowledge of the analytical market the applicant will like an involvement in setting up specifications for future instruments. Market developments will be carefully monitored and innovative suggestions derived from these activities. This is a position with international contacts to Bruker AXS' facilities in Central Europe and the US. Excellent communication skills will help to work within the international, interdisciplinary environment. The position calls for the ability to travel since the applicant will have to join conferences, Bruker AXS seminars or workshops, actively. Bruker AXS offers a competitive salary and comprehensive benefits package. Applicants are invited to submit their application with resume in confidence to: Bruker AXS B.V. Attn: Eric Hovestreydt, Managing Director Oostsingel 209 2612 HL Delft Tel: +31.15.2152.501 E-mail: [EMAIL PROTECTED] - Kind Regards, Martin ___ Dr. Martin Adam Bruker AXS B.V. International Sales Manager Oostsingel 209 2612 HL Delft, the Netherlands Tel.:+31 152 152 509 Mobil: +49 172 2917807 Fax: +31 152 152 500 Email: [EMAIL PROTECTED] WWW: http://www.bruker-axs.com http://www.bruker-axs.com/ ___ ** Der Inhalt dieser E-Mail ist vertraulich und ausschliesslich fuer den bezeichneten Adressaten bestimmt. Wenn Sie nicht der vorgesehene Adressat dieser E-Mail oder dessen Vertreter sein sollten, so beachten Sie bitte, dass jede Form der Kenntnisnahme, Veroeffentlichung, Vervielfaeltigung oder Weitergabe des Inhalts dieser E-Mail unzulaessig ist. Wir bitten Sie, sich in diesem Fall mit dem Absender der E-Mail in Verbindung zu setzen. The information contained in this email is confidential. It is intended solely for the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. **
[ccp4bb] opening Junior Application Scientist - Structural Biology
Dear group members, I'd like to bring following opening to your attention: - Bruker AXS designs and manufactures analytical X-ray systems for elemental analysis, materials research and structural investigations. Our innovative solutions enable a wide range of customers in heavy industry, chemistry, pharmacy, semiconductor, life science and nanotechnology to make technological advancements and to accelerate their progress. During the recent years Bruker AXS' solutions in Single-Crystal Structural-Biology have convinced an increasing number of scientists. To further strengthen the capacities of the application laboratories Bruker AXS B.V, Delft (the Netherlands) has an immediate opening for a Junior Application Scientist Structural Biology (full or part-time) The qualified applicant will help promote Bruker AXS' solutions for Single-Crystal Structural-Biology. Supported by experienced Senior application scientists the successful candidate will advise prospective users on the most appropriate analytical solutions. Experience gained towards an advanced degree in macro-molecular sciences will enable the applicant to measure and process test samples provided by our prospects or point out the equipment's superior features to potential customers. A strong background in the use of scientific instrumentation - preferably in X-ray structural biology - is a pre-request. It will help to always operate the systems at their high-end specifications. This is a position with international contacts to Bruker AXS' facilities in Central Europe and the US. The position calls for the ability to travel a fair amount of time since the applicant will have to join conferences, Bruker AXS seminars or workshops, actively. Explicitly, Bruker AXS encourages young, dynamic scientists at the begin of a career outside of the university to submit their application. Bruker AXS offers a competitive salary and comprehensive benefits package. Applicants are invited to submit their application with resume in confidence to: Bruker AXS B.V. Attn: Eric Hovestreydt, Managing Director Oostsingel 209 2612 HL Delft Tel: +31.15.2152.501 E-mail: [EMAIL PROTECTED] - Kind Regards, Martin ___ Dr. Martin Adam Bruker AXS B.V. International Sales Manager Oostsingel 209 2612 HL Delft, the Netherlands Tel.:+31 152 152 509 Mobil: +49 172 2917807 Fax: +31 152 152 500 Email: [EMAIL PROTECTED] WWW: http://www.bruker-axs.com http://www.bruker-axs.com/ ___ ** Der Inhalt dieser E-Mail ist vertraulich und ausschliesslich fuer den bezeichneten Adressaten bestimmt. Wenn Sie nicht der vorgesehene Adressat dieser E-Mail oder dessen Vertreter sein sollten, so beachten Sie bitte, dass jede Form der Kenntnisnahme, Veroeffentlichung, Vervielfaeltigung oder Weitergabe des Inhalts dieser E-Mail unzulaessig ist. Wir bitten Sie, sich in diesem Fall mit dem Absender der E-Mail in Verbindung zu setzen. The information contained in this email is confidential. It is intended solely for the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. **
Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
Hi Donghui, I just want to draw your attention to the following article. It sums up suggestions which were already made by others for using concentrated (lithium) salt solutions for cryoprotection: Rubinson, K.; Ladner, J.; Tordova, M. Gilliland, G. Cryosalts: suppression of ice formation in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr, 2000, 56 ( Pt 8), 996-1001 Good luck, christian wu donghui wrote: Dear all, Recently, I got a crystallization condition as 0.1 M Bis tris ph 6.5, 1.3M lithium sulfate, 0.1M NaCl, the shape of crystals is needle cluster, very difficult to grow bigger, microseeding does not work, then I tried macroseeding, and found crystal can grow bigger and rod like. However as for the cryoprotectant, crystal will dissolve in glycerol, ethylene glycol, MPD and PEG, even in the very low concentration about 5%. I found my crystal can grow under the additive 2-propanol in addition to the above mentioned crystallization condition. I also noticed that Hampton cryoprotectant kit has the 2-propanol as cryoprotectant. I want to know if anyone have ever used 2-propanol as the cryoprotectant and what effect it might be. By the way Hampton also mention lithium sulfate can be used as cryoprotectant, the recommended maxium concentration is 2M, I tried and found ice ring is severe and it is very easily to form lithium sulfate salt crystal at this high concentration, I also tried sodium malonate, the diffraction gave me few spots, resolution is only about 6--7 angstrom. Does anyone encounter such problem by lithium sulfate? Welcome to any replies. Thanks a lot in advance. Donghui ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
Hi everyone, I received a lot of positive e-mails about my post on cryo methods. One theme was, Well, what are the papers I should read? Blatant self-promotion I know of one such paper published in Methods. I have made the PDF of it downloadable from our web site at http://www.rigaku.com/cryo/ Cheers, Jim
