Re: [ccp4bb] How to fix sidechain rotamers for Refmac?
It is hard to believe that REFMAC is being driven by rotamer conformations - REFMAC weighting scheme gives a low priority to fitting a preferred rotamer - quite rightly since the SD on rotamer angles is high. The ideal is only ideal for a residue in a near vacuum - the interactions with other nearby atoms often distort rotamers a lot. So the question is more about why the positive /negative peaks are persisting. One possibility is that there are alternate conformations and the occupancies you are assigning are too high. Another that you have created an ideal rotamer using neighbouring water sites as say the OE1 OE2 for a GLU, and actually the side chain IS in the wrong place.. This is extremelyy easy to do I find! When you are worried it is a good idea to set the occupancies of the side chains and nearby HOH to 0.00 - leave them in the pdb file - then do a few cycles of refinement and check the maps again. Eleanor Peter J Stogios wrote: Hi, I'm working with a 1.8 A structure with Coot and Refmac, and there are many sidechain rotamers that show very clear difference density peaks for setting their correct positions. However, Refmac continuously moves the rotamers back into negative density peaks. It's really quite silly because often there is an obvious positive density peak near to a negative density peak. I have tried using automatic geometry weighting and manually setting the weighting term to a very tight 0.025, but each has no effect. I have also tried increasing the torsion angle restraint term to 2.0 but this also has no effect. Does anyone have any suggestions? Is there any way to fix atom positions for Refmac? Thanks in advance, ~ Peter J Stogios, Ph.D. Postdoctoral Research Fellow e: p.stog...@utoronto.ca p: 416-978-4033 w: http://www.uhnres.utoronto.ca/centres/proteomics/ Structural Proteomics in Toronto Research Group, University Health Network C.H. Best Institute 112 College Street, Room 70 Toronto, Ontario, Canada M5G 1L6
Re: [ccp4bb] MOLREP
How can that be! Are you also providing a sequence? Eleanor Tommi Kajander wrote: Hi, I have been using a dimer as a search model in MOLREP (there will be several in AU), for some reason the program tends to break the dimer into monomers wihtout asking me.. how is this determined in the program... a more detailed manual would be nice, also on the output as the different contrasts and their meaning appear bit cryptic to me. (i am beginning to get the hang of it but its still bit fuzzy..) Also if i am searching for number of say these dimers and there is a speudo-translation vector should it be used all the time? (i would assume not all the searched unit are related necessarily by the translational NCS) (to make it even merrier, there is both proper speudo centering and just translational NCS .. and you can only specify one vector... if we are lucky its also twinned... thanks for comments, Tommi
Re: [ccp4bb] ACORN2 in ccp4
Mea culpa I am (slowly) getting it from Michael Woolfson form to a CCP4 compatible version. If you like I can send you the old version but you will have to reformat mtz etc. Thank you for the reminder -0 I wll move the job to a higher personal priority! Eleanor Dodson José Manuel Otero Casas wrote: Hi all, Someone knows if ACORN2 (Acta D 2009, 881) is implemented in ccp4? If no, where is possible to find a copy or when it is going to be implemented? Thanks Jose Otero
Re: [ccp4bb] MOLREP
Then I suspect the sequence is overriding the model. My preferred approach. Get a sequence alignment from somewhere and use CHAINSAW to edit the model you want to use. That is documented! And it will edit both monomers in turn I believe.. Then you will have a dimer with the appropriate sequence editing done for you. Now give that toMOLREP without any sequence. Now I am pretty sure it will use your whole model. It will determine the non-cryst tramslation and apply it automatically to all copies I guess but if you have strong NCT then it usually more or less relates allmolecules.. . Pseudo centring - what do you mean by that? Twinning - Aaagh Eleanor tommi kajander wrote: yes i am, i haven't got a clue, it always seems to be doing somethig other than i want it to.. to be honest the manual is prety obsolete and non-existent, would be nice if the authors provided more info on current vresion. tommi On 1.10.2009, at 11.10, Eleanor Dodson wrote: How can that be! Are you also providing a sequence? Eleanor Tommi Kajander wrote: Hi, I have been using a dimer as a search model in MOLREP (there will be several in AU), for some reason the program tends to break the dimer into monomers wihtout asking me.. how is this determined in the program... a more detailed manual would be nice, also on the output as the different contrasts and their meaning appear bit cryptic to me. (i am beginning to get the hang of it but its still bit fuzzy..) Also if i am searching for number of say these dimers and there is a speudo-translation vector should it be used all the time? (i would assume not all the searched unit are related necessarily by the translational NCS) (to make it even merrier, there is both proper speudo centering and just translational NCS .. and you can only specify one vector... if we are lucky its also twinned... thanks for comments, Tommi Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
[ccp4bb] Postdoctoral Fellow for the Structural Biology group at ESRF
Dear all, Another job advertisement :-) We have an opening at the ESRF Macromolecular crystallography group ( http://www.esrf.fr/UsersAndScience/Experiments/MX) for a Post-Doc to study proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray crystallography and complementary spectroscopic techniques. Please follow the instructions below to apply. The deadline to apply is the 15th of October. Thank you, Daniele. Post-doctoral fellow (m/f) for the Structural Biology group - Ref: PDID29-2 in the Experiments Division *THE FUNCTION:* You will work on *the study of proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray crystallography and complementary spectroscopic techniques.* Electronic or vibrational spectroscopic data obtained directly on protein crystals (from UV-visible light, fluorescence or Raman spectroscopies) have become instrumental in corroborating structural data. Complementary spectroscopic techniques during crystallographic data collection can also serve as a tool to monitor X-ray induced radical formation and damage to metal and sulphur centres. The use of specific sensitizers and optical markers will help to define rigorously the experimental procedures. This project will be carried out primarily at the off-line spectroscopy facility Cryobench ( http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench/), but also in the state-of-the-art C.I. Branden building (Partnership for Structural Biology, http://www.psb-grenoble.eu/). The project will benefit from interactions with the ‘Protein Dynamics’ group at the nearby Institut de Biologie Structurale (http://www.ibs.fr). You will also participate in support activities for external users on MX beamlines using complementary spectroscopies. *QUALIFICATIONS AND EXPERIENCE:* You hold a PhD in Biophysics, Protein Crystallography or Biochemistry with a strong background in structural biology. Additional skills in molecular biology, recombinant protein expression and purification and biochemical characterization of proteins are desirable. *ADDITIONAL INFORMATION:* The ESRF shares a site with several other major European scientific institutes; it offers an exciting opportunity in an international atmosphere. New staff coming from outside the Grenoble area benefit from installation allowances to move and settle in the area. An expatriation allowance may be payable in accordance with specific regulations. Only candidates holding a Ph.D. obtained less than 3 years ago are eligible for Post-doctoral positions. *Post-doctoral fellows are employed for an eighteen-month period with a possibility of extension of another six to eighteen months. *The* *contract should start as soon as possible. Further information on the post can be obtained from Antoine Royant ( antoine.roy...@ibs.fr), Martin Weik (martin.w...@ibs.fr), Daniele de Sanctis (daniele.de_sanc...@esrf.fr) or Sean McSweeney (mcswee...@esrf.fr). The ESRF is an equal opportunity employer and encourages applications from disabled persons. *If you are interested, please send us a fax (+33 (0)4 76 88 24 60) or an e-mail (recru...@esrf.fr) with your address, and we will provide you with an application form. Or print out an application form on the World Wide Web http://www.esrf.fr/Jobs/Applying http://www.esrf.fr/Applying. In addition to the application form, you should provide us with a detailed CV and the names of two referees.* *Deadline:* 15-10-2009 *Contract type:* Non-permanent contract (CDD) * Please send your application (form, covering letter and CV) to: * Louise Peritore-Niang -- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869
[ccp4bb] Postdoctoral Fellow for the Structural Biology group at ESRF
Dear all, Another job advertisement :-) We have an opening at the ESRF Macromolecular crystallography group ( http://www.esrf.fr/UsersAndScience/Experiments/MX) for a Post-Doc to study proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray crystallography and complementary spectroscopic techniques. Please follow the instructions below to apply. The deadline to apply is the 15th of October. Thank you, Daniele. Post-doctoral fellow (m/f) for the Structural Biology group - Ref: PDID29-2 in the Experiments Division *THE FUNCTION:* You will work on *the study of proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray crystallography and complementary spectroscopic techniques.* Electronic or vibrational spectroscopic data obtained directly on protein crystals (from UV-visible light, fluorescence or Raman spectroscopies) have become instrumental in corroborating structural data. Complementary spectroscopic techniques during crystallographic data collection can also serve as a tool to monitor X-ray induced radical formation and damage to metal and sulphur centres. The use of specific sensitizers and optical markers will help to define rigorously the experimental procedures. This project will be carried out primarily at the off-line spectroscopy facility Cryobench ( http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench/), but also in the state-of-the-art C.I. Branden building (Partnership for Structural Biology, http://www.psb-grenoble.eu/). The project will benefit from interactions with the ‘Protein Dynamics’ group at the nearby Institut de Biologie Structurale (http://www.ibs.fr). You will also participate in support activities for external users on MX beamlines using complementary spectroscopies. *QUALIFICATIONS AND EXPERIENCE:* You hold a PhD in Biophysics, Protein Crystallography or Biochemistry with a strong background in structural biology. Additional skills in molecular biology, recombinant protein expression and purification and biochemical characterization of proteins are desirable. *ADDITIONAL INFORMATION:* The ESRF shares a site with several other major European scientific institutes; it offers an exciting opportunity in an international atmosphere. New staff coming from outside the Grenoble area benefit from installation allowances to move and settle in the area. An expatriation allowance may be payable in accordance with specific regulations. Only candidates holding a Ph.D. obtained less than 3 years ago are eligible for Post-doctoral positions. *Post-doctoral fellows are employed for an eighteen-month period with a possibility of extension of another six to eighteen months. *The* *contract should start as soon as possible. Further information on the post can be obtained from Antoine Royant ( antoine.roy...@ibs.fr), Martin Weik (martin.w...@ibs.fr), Daniele de Sanctis (daniele.de_sanc...@esrf.fr) or Sean McSweeney (mcswee...@esrf.fr). The ESRF is an equal opportunity employer and encourages applications from disabled persons. *If you are interested, please send us a fax (+33 (0)4 76 88 24 60) or an e-mail (recru...@esrf.fr) with your address, and we will provide you with an application form. Or print out an application form on the World Wide Web http://www.esrf.fr/Jobs/Applying http://www.esrf.fr/Applying. In addition to the application form, you should provide us with a detailed CV and the names of two referees.* *Deadline:* 15-10-2009 *Contract type:* Non-permanent contract (CDD) * Please send your application (form, covering letter and CV) to: * Louise Peritore-Niang -- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869
[ccp4bb] BEAMTIME @ SLS X06DA
MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE X06DA AT SLS Deadline: Thursday, October 15, 2009 Periods: January 1, 2010 - April 30, 2010 ( Normal / Test proposals) January 1, 2010 - December 31, 2011 ( Long-term proposals) Beamline features: (http://sls.web.psi.ch/view.php/beamlines/px3/index.html ) - Fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - 4x10¹¹ photons/sec at sample position - 90x70 microns focused beam - MAR225 CCD detector - Mini-hutch design for fast manual mounting - Automatic sample changer (IRELEC CATS) with SPINE pucks and Molecular Dimension vials and caps - In-situ diffraction screening (test your initial crystals directly in the crystallization plate) Proposal submission: Users are encouraged to combine beamtime application for X06DA and X06SA http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Travel support: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html Best regards, Meitian Wang Vincent Olieric __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
[ccp4bb] Saint into Scala
Does anyone know how to convert data in Saint format into a format that is recognized by Scala? Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za mailto:sylvia.fanuc...@wits.ac.za htmlpfont face = verdana size = 0.8 color = navyThis communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html image001.jpg
[ccp4bb] force display of sheet in PYMOL
Dear Friends, Sorry for the off topic question. How I can force PYMOL to display a portion of the molecule as beta sheet? PYMOL is displaying this part as a loop by default, but I like to see this as beta sheet. Is there any way? Thanking you in advance... Raja Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew
Re: [ccp4bb] force display of sheet in PYMOL
On Thu, Oct 1, 2009 at 2:11 PM, Raja Dey deyra...@yahoo.co.in wrote: Dear Friends, Sorry for the off topic question. How I can force PYMOL to display a portion of the molecule as beta sheet? PYMOL is displaying this part as a loop by default, but I like to see this as beta sheet. Is there any way? Thanking you in advance... alter atom selection, ss='S' then hide/show the cartoon representation and it should come up with the new sheet. Also: https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [ccp4bb] force display of sheet in PYMOL
Raja Here is a snippet from one of my PML scripts. # beta sheets: alter A/447-451/, ss='S' ; rebuild alter A/447:451/ and MyModel, ss='S' rebuild Hope this helps, Mark On Thu, 2009-10-01 at 16:11 -0500, Raja Dey wrote: Dear Friends, Sorry for the off topic question. How I can force PYMOL to display a portion of the molecule as beta sheet? PYMOL is displaying this part as a loop by default, but I like to see this as beta sheet. Is there any way? Thanking you in advance... Raja __ Try the new Yahoo! India Homepage. Click here. Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] force display of sheet in PYMOL
Dear Raja, A note of caution: if a program doesn't show something as a beta strand that must mean that that part of the molecule doesn't have the attributes for strand. Rather than cosmetically fix it by changing it in pymol, it might be a good idea to look closely at the structure/density and see if the model can be improved. Cheers, Charlie Raja Dey wrote: Dear Friends, Sorry for the off topic question. How I can force PYMOL to display a portion of the molecule as beta sheet? PYMOL is displaying this part as a loop by default, but I like to see this as beta sheet. Is there any way? Thanking you in advance... Raja Try the new Yahoo! India Homepage. Click here http://in.rd.yahoo.com/tagline_metro_1/*http://in.yahoo.com/trynew. -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] force display of sheet in PYMOL
On Oct 1, 2009, at 7:51 PM, Charlie Bond wrote: A note of caution: if a program doesn't show something as a beta strand that must mean that that part of the molecule doesn't have the attributes for strand. Rather than cosmetically fix it by changing it in pymol, it might be a good idea to look closely at the structure/density and see if the model can be improved. This is good general advice, but in the specific case of pymol, the manual says: 'It is recommended that you read in PDB files which already have correct secondary structure assignments from a program like DSSP. However, PyMOL does have a reasonably fast secondary structure alignment algorithm called dss. Please be aware that due to the subjective nature of secondary structure assignment in borderline cases, dss results will differ somewhat from DSSP.' http://pymol.sourceforge.net/newman/user/S0260cartoons.html This may help: http://structure.usc.edu/dssp2pdb/ James
