[ccp4bb] calculation of the orientation angles between helices
Hello, I am using Qhelix, for the calculation of the orientation angles between helices. when am running the demo its working,but when am uploading my pdb file it is not working, can someone help me to resolve the problem.suggest me the other softwares for the same. Thank you. Regards, Gajanan __ Gajanan K Arbade Research Scholar Defence Institute of Advanced Technology (DIAT) Pune Maharashtra, India Pin Code-411025 Contact No. Lab.+ 91-20-24304377 Mob: 08698198016
Re: [ccp4bb] calculation of the orientation angles between helices
Hi Gajanan, i never try Qhelix, but i use Chimera to do that. It's possible to mesure angle, distance etc between helix. Hope to help. Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gajanan Arbade [gajanan_pbi...@diat.ac.in] Envoyé : mercredi 17 septembre 2014 09:31 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] calculation of the orientation angles between helices Hello, I am using Qhelix, for the calculation of the orientation angles between helices. when am running the demo its working,but when am uploading my pdb file it is not working, can someone help me to resolve the problem.suggest me the other softwares for the same. Thank you. Regards, Gajanan __ Gajanan K Arbade Research Scholar Defence Institute of Advanced Technology (DIAT) Pune Maharashtra, India Pin Code-411025 Contact No. Lab.+ 91-20-24304377 Mob: 08698198016
[ccp4bb] Protein Crystallography course via the web at Birkbeck College
Dear all, registration is currently open for the postgraduate certificate course in Protein Crystallography via the web at Birkbeck that begins on Monday, October the 6th. It is for the duration of 1 year during which all aspects of protein crystallography will be covered from the fundamentals of protein structure to validation. The emphasis is very much on techniques and the underlying principles so is ideally suited to students currently enroled on PhD programs or those who wish to expand their skills in structural biology. Information on registration and course content can be found at: http://px14.cryst.bbk.ac.uk/px/course/course.htm under General information or contact the course director (Tracey Barrett) at p...@mail.cryst.bbk.ac.uk for further details. Although a stand-alone course, the postgraduate certificate in protein crystallography can also be taken as part of the MSc in Structural Molecular Biology. For more details, please see http://www.bbk.ac.uk/study/2014/postgraduate/programmes/TMSBISCL_C/ Dr Tracey Barrett, Crystallography, Senior Lecturer in Structural Biology, Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX Tel: 020 7631 6822 Fax: 020 7631 6803
[ccp4bb] REFMAC - TWIN OPTION
Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
[ccp4bb] Immediately available: Postdoctoral position in Computational Structural Biology
Dear colleagues, This fall I start my own research group in the Physics Department at Simon Fraser University in Vancouver, British Columbia. In the near future, I hope to hire an exceptional, highly-motivated postdoctoral fellow to work on computational structural biology. Please forward this announcement to any interested parties. My group combines approaches from physics, information theory, and statistics to study the fundamental principles of biomolecular function under strong fluctuations. The postdoctoral position will focus on the development of model comparison methods to understand the conformational heterogeneity revealed by structural biology experiments, especially X-ray crystallography. Within this broad research thrust there is ample freedom to pursue particular areas of personal scientific interest. Our theoretical flights of fancy are tethered to reality through a close collaboration with the experimental group of Jaime Fraser at UC San Francisco. Postdoctoral fellows in my group will work in the intellectually-stimulating and interactive biophysics community within SFU Physics, with close ties to the Molecular Biology/Biochemistry department, home to several top-notch structural biology groups. In my own (possibly biased) opinion, the endless all-season outdoors opportunities, mind-blowing food from all ethnicities, and mild weather make Vancouver an enviable place to call home; slightly more objectively, it makes every official top 5 list of most livable cities in the world. The ideal candidate would have experience with computer programming, biomolecular modeling and statistics, and a PhD in a relevant field (broadly construed: physics, biophysics, chemistry, bio- or chemical-engineering, molecular biology, or relevant areas of statistics, computer science, applied math, etc). But most important is intellectual curiosity, enthusiasm for research in this area, and an excellent track record in whatever field they have pursued. Interested candidates should send me a cover letter and CV (including publication list and contact information for 2-3 references). Further information is available at: http://davidsivak.com/ Thank you in advance! David -- David Sivak Asst. Prof., Dept. of Physics, Simon Fraser U david.si...@gmail.com davidsivak.com 778-928-7995
[ccp4bb] AW: [ccp4bb] REFMAC - TWIN OPTION
Dear Berni, DETWIN will detwin your Fobs, which can be done if the twin fraction is sufficiently far from 0.5. However, as you discovered, you need to know the twin fraction, which is by convention specified by the smaller fraction. Once your data is detwinned, it should just be that, a file with regular fobs and not twinned anymore, so in Refmac you should not use any TWIN keywords. However, this is not the best way to proceed. The best way is to provide Refmac with your twinned dataset and let Refmac figure it all out for you! As you mentioned, Refmac will test the different possible twinning operators and will refine the twinning fraction. In my hands it works very well and is extremely easy even for crystals with multiple twinning operators. Good luck! Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Santarsiero, Bernard D. Gesendet: Mittwoch, 17. September 2014 14:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] REFMAC - TWIN OPTION Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] REFMAC - TWIN OPTION
Hi Bernie, I agree with Herman. I think you will be all set if you simply change the no twin refinement option near the top of the Refmac interface to intensity based or amplitude based twin refinement. Refmac will determine the appropriate twin operators/fractions and refine. Best, Chris On Sep 17, 2014, at 14:19, Santarsiero, Bernard D. b...@uic.edu wrote: Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to estimate the twin fraction and select various twin laws. 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, but does it matter what the twin factor you assign is? (It seems to get refined, or just estimated, in refinement?) 4. There are potentially 3 twin laws, so do you run DETWIN three times? You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run it once and three times, and seems to give the same result in REFMAC refinement. 5. Select the Free R subset. Will uniqueify choose correctly? 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. Then it seems to select and test three twin laws, even if you only ran DETWIN once, with one selected twin law. It tests if the twin laws give low R(merge). If not, it tosses them out. It seems like the R(merge) calculation depends on the starting model, and not just on the modified Fobs data. It also seems like it tries to calculate the twin fraction, and then refine the structure. Or, is it just giving an estimate, and I need to go back to original data and rerun DETWIN? 7. I tried to work with intensities instead of amplitudes, and it can blow up. I've also refined, got a good refinement (3 twin laws, each with twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and it blows up, suggesting no twinning, but Rs around 35%. Does REFMAC refine the twin fraction? Do I have to assign a twin fraction in DETWIN, or does it just set up the relationships between reflections and amplitudes? Should I try to work with intensities or amplitudes. The calculation is presumably done on intensities, but seems to be more unstable using that option. I haven't tried the PHENIX option. Just a quick step-by-step guide on what to do would be useful. Thanks, Bernie -- Bernard D. Santarsiero Research Professor Center for Structural Biology University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
[ccp4bb] Post Doc Postion in Oklahoma
I am posting this position announcement on the behalf of Dr. Rakhi Rajan, please direct any questions to her. A Post-doctoral Research position is available in the laboratory of Dr. Rakhi Rajan in the Department of Chemistry and Biochemistry at the University of Oklahoma. The research is focused on characterizing an RNA-mediated immune system in bacteria and archaea. The successful applicant will join a team that employs molecular biology, biochemistry, structural biology, and microbiology approaches to characterize the recently discovered CRISPR-Cas system. The ideal candidate should have a recent Ph.D. degree in biochemistry, structural biology, biophysics or another related area, and a strong publication record. Experience in molecular biology, protein expression and purification is essential. Prior experience in macromolecular X-ray crystallography and/or bioinformatics is desired. The successful applicant will perform research in all aspects of structural and functional characterization of protein-nucleic acid complexes belonging to RNA-mediated immune systems, specifically the CRISPR-Cas system. Applications and informal inquiries should be addressed to Dr. Rakhi Rajan by email at r-ra...@ou.edu. Applicants should submit a single PDF document containing: (1) a CV stating your career goals, and highlighting your important contributions to research and professional activities, and (2) name and contact details of three professional references. Applications will be accepted until the position is filled. The University of Oklahoma is an Equal Opportunity Employer. Protected veterans and individuals with disabilities are encouraged to apply.
[ccp4bb] Two PhD position are available at The Hamburg Centre for Ultrafast Imaging (Germany)
Two PhD position are available at The Hamburg Centre for Ultrafast Imaging to work on the following topics: 1. Structure-Function Relationship of bacterial protein translocation machines and their effectors (Supervisor Prof.Martin Aepfelbacher) link to the announcement: http://www.uni-hamburg.de/uhh/stellenangebote/exzellenzcluster-cui/CUI-B-2-1.pdf 2. Nucleation, growth, and characterisation of 2D and 3D proteinnanocrystals (Supervisor Prof. Christian Betzel) link to the announcement: http://www.uni-hamburg.de/uhh/stellenangebote/exzellenzcluster-cui/CUIB-3-1-Betzel.pdf Applications are invited from candidates with proven expertise inmolecular microbiology, biochemistry, biotechnology such as large-scaleproduction of proteins by mammalian cell cultures, insect cells, orother recombinant hosts. The candidates must be extremely self-motivatedand dedicated, be able to work very hard independently but also tosynergistically interact with other lab- and group members. Thetentative starting date would be in November, 2014. Interested persons should apply exclusively per e-mail and send adetailed CV, as well as a covering letter including motivation, detailson their expertise in protein production, and contact details of threereferees.
Re: [ccp4bb] calculation of the orientation angles between helices
Hi Gajanan, I am using Qhelix, for the calculation of the orientation angles between helices. when am running the demo its working,but when am uploading my pdb file it is not working, can someone help me to resolve the problem. can't help with Qhelix, but... suggest me the other softwares for the same. ... phenix.angle can do it. Pavel
[ccp4bb] binding surface
I am looking for a program that will map out the binding surface of a dimer interface. For example if you have a PDB can you draw a colored surface for the contact sites. Specifically what I want to do is look at the interface for multiple dimer parteners and show how they overlap. Is that a program that will do this easily?
Re: [ccp4bb] binding surface
On 9/17/2014 11:51 AM, brian walker wrote: I am looking for a program that will map out the binding surface of a dimer interface. For example if you have a PDB can you draw a colored surface for the contact sites. Specifically what I want to do is look at the interface for multiple dimer parteners and show how they overlap. Is that a program that will do this easily? This can be undertaken using ICM-Browser - a free download from here: http://www.molsoft.com/icm_browser.html The option you need is molskin - see the documentation here: http://www.molsoft.com/gui/meshes-surfaces-grobs.html#molskin Andrew -- Andrew Orry Ph.D. Senior Research Scientist MolSoft LLC 11199 Sorrento Valley Road San Diego, CA 92121 Tel: 858-625-2000 x108 Fax: 858-625-2888 www.molsoft.com www.twitter.com/MolSoft
[ccp4bb] Assistant Professor – Structural Biology/Natural Products-U of Oklahoma
Faculty position open at the University of Oklahoma. Assistant Professor – Structural Biology/Natural Products. The Department of Chemistry and Biochemistry (http://chem.ou.edu) at the University of Oklahoma invites applications for a tenure-track faculty position at the rank of Assistant Professor with a start date of August 16, 2015. We are especially interested in applicants who have expertise in macromolecular X-ray crystallography with research interests that fall within the broad area of natural products drug discovery/drug development. Research areas of particular interest include the structural biology of natural product biosynthesis and structural biology studies of small molecule ligand/protein binding interactions. The successful candidate will become an active member in the Oklahoma Center of Biomedical Research Excellence (COBRE) in Structural Biology (http://structuralbiology.ou.edu) and the Institute for Natural Products Applications and Research Technologies (INPART) (http://inpart.ou.edu). Both units are located in the Stephenson Life Sciences Research Center on the University of Oklahoma Research Campus. The successful candidate is expected to establish a productive and externally funded research program that involves collaborations among the COBRE and INPART teams, as well as contribute to the department’s graduate and undergraduate teaching missions; normal teaching expectation is one major course per semester. Applicants must have completed a Ph.D. degree in chemistry, biochemistry, or a closely related field (postdoctoral experience preferred) by the appointment start date. Interested individuals should submit a single PDF file to biochems...@ou.edu containing the following: a cover letter describing their interest in this position, a curriculum vita, a description of research accomplishments and future research plans (6 page limit), and a statement of teaching experience and interests. Candidates should also request three letters of recommendation and have them sent directly to biochems...@ou.edu. To ensure full consideration, all application materials should be submitted as soon as possible, application review will begin on October 15, 2014. This position will remain open until filled. The University of Oklahoma is an Equal Opportunity Employer. Protected veterans and individuals with disabilities are encouraged to apply. http://www.ou.edu/eoo Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019 405-325-1126 lmtho...@ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu
Re: [ccp4bb] Guard columns from FPLC
Dear Anita, As has been stated in another post I think, it is not a good idea to use a guard column in front of a Superdex column or any gel filtration column. It will dilute the sample and decrease the resolution and depending on the nature of the aggregate and guard column it might just clog. If you have aggregates, or suspect you have, installing an in-line filter will not help you in any other way than protecting the column. You need to remove the aggregates by ultracentrifugation beforehand and then make sure your sample volume is within the recommended load volume for the column (read the documentation that comes with column or get it from the GE Healthcare Lifesciences website) in order to get the resolution you paid GE for. If you do not have any inline filters and you have a bunch of users with varied experience it might be a very good idea to install them and make sure that people run proper methods where the column has been selected to get the right max pressure settings. Compression of the matrix will also kill you column pretty nicely. Good Luck and Happy Hunting KM - Original Message - From: Anita P crystals...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, September 16, 2014 1:29:44 AM Subject: [ccp4bb] Guard columns from FPLC Hi All, Sorry for this off topic. I have heard that there are these little columns called guard columns which can be attached to AKTA purifiers. These columns prevent the incoming huge aggregates to be deposited and blocking of the gel filtration columns. Can any one advice me regarding where to purchase these columns. I could not find them in GE website. We have Superdex 16/60 on AKTA purifier. Thanks in advance. Have a good day Anita -- -- Karl-Magnus Larsson, Ph.D. Mail: Department of Structural Biology Fairchild Bldg D100 299 Campus Drive West Stanford University School of Medicine Stanford, CA 94305-5126 U.S.A - Visit: Beckman Center, Room B137 Stanford University School of Medicine 279 Campus Drive West Stanford, CA 94305 --- Phone: +1-650-391-7408 (Cell)
Re: [ccp4bb] Guard columns from FPLC
I have two small points to add to what has been amply said already. First, those columns (like the pre-filter 6000) are nice to use with ion-exchange or metal affinity columns on FPLCs, attached right after a superloop. Not gel filtration columns. Second, for small samples loaded on gel filtration columns, a hard spin is advised; what I prefer is actually using 0.5-ml spin cups (with 0.4 um filters) from Millipore. There is practically no hold-up volume, and I have been lucky enough to not lose protein over them yet. http://www.emdmillipore.com/US/en/product/Ultrafree-MC-HV-Centrifugal-Filter,MM_NF-UFC30HVNB Engin On 9/17/14 3:10 PM, Karl-Magnus Larsson wrote: Dear Anita, As has been stated in another post I think, it is not a good idea to use a guard column in front of a Superdex column or any gel filtration column. It will dilute the sample and decrease the resolution and depending on the nature of the aggregate and guard column it might just clog. If you have aggregates, or suspect you have, installing an in-line filter will not help you in any other way than protecting the column. You need to remove the aggregates by ultracentrifugation beforehand and then make sure your sample volume is within the recommended load volume for the column (read the documentation that comes with column or get it from the GE Healthcare Lifesciences website) in order to get the resolution you paid GE for. If you do not have any inline filters and you have a bunch of users with varied experience it might be a very good idea to install them and make sure that people run proper methods where the column has been selected to get the right max pressure settings. Compression of the matrix will also kill you column pretty nicely. Good Luck and Happy Hunting KM - Original Message - From: Anita P crystals...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, September 16, 2014 1:29:44 AM Subject: [ccp4bb] Guard columns from FPLC Hi All, Sorry for this off topic. I have heard that there are these little columns called guard columns which can be attached to AKTA purifiers. These columns prevent the incoming huge aggregates to be deposited and blocking of the gel filtration columns. Can any one advice me regarding where to purchase these columns. I could not find them in GE website. We have Superdex 16/60 on AKTA purifier. Thanks in advance. Have a good day Anita -- Engin Özkan, Ph.D. Assistant Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu
