Re: [ccp4bb] Unknown density
Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of noise around these regions - and it may not, in fact, be possible to model this satisfactorily. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Feb 25, 2013, at 10:03 AM, Natashin Pavel wrote: Hello everyone, I’m working on a structure with a 1.72Å resolution data and almost finished it. But there is a piece of unknown density between two protein molecules. The following pictures show this density from two sides: http://www.4sync.com/photo/WHewU7Ek/Density_1.html http://www.4sync.com/photo/RM3IEesw/Density_-_2.html This density is located between two protein molecules and is not connected to either of them. I have tried to fit several small organic molecules from crystallization conditions and protein sample buffer, also tried ligand database search using “Phenix ligand identification” software, but no satisfactory results. Crystallization condition: DL-Malic acid Sample Buffer: Bis-Tris, EDTA Reagents from protein purification step (also checked): Tris, Urea, Triton-X100, DTT. I will very much appreciate to hear any suggestions and ideas on what to do. Best regerds, Pavel V. Natashin PhD student Photobiology Laboratory Institute of Biophysics Russian Academy of Sciences Siberian Branch Krasnoyarsk 660036, Russia National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101, China
Re: [ccp4bb] Unknown density
Dear Pavel, you should also always consider your cryoprotectant molecules, so let's say if you used PEG for cryoprotection, there's a very high probability you may see it in your structure. It's very hard to say from the snapshots, but for the patch of density depicted in fig.2 I would try PEG (of course only if you had it). All the best, Albert 2013/2/25 Antony Oliver antony.oli...@sussex.ac.uk Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of noise around these regions - and it may not, in fact, be possible to model this satisfactorily. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Feb 25, 2013, at 10:03 AM, Natashin Pavel wrote: Hello everyone, I’m working on a structure with a 1.72Å resolution data and almost finished it. But there is a piece of unknown density between two protein molecules. The following pictures show this density from two sides: http://www.4sync.com/photo/WHewU7Ek/Density_1.html http://www.4sync.com/photo/RM3IEesw/Density_-_2.html This density is located between two protein molecules and is not connected to either of them. I have tried to fit several small organic molecules from crystallization conditions and protein sample buffer, also tried ligand database search using “Phenix ligand identification” software, but no satisfactory results. Crystallization condition: DL-Malic acid Sample Buffer: Bis-Tris, EDTA Reagents from protein purification step (also checked): Tris, Urea, Triton-X100, DTT. I will very much appreciate to hear any suggestions and ideas on what to do. Best regerds, Pavel V. Natashin PhD student Photobiology Laboratory Institute of Biophysics Russian Academy of Sciences Siberian Branch Krasnoyarsk 660036, Russia National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101, China
[ccp4bb] Pseudo-translation?
Dear all, I have an orthorhombic crystal (pointless suggests most likely space groups P 2 21 21 or P 2 21 2) with two molecules expected in the asymmetric unit. Analyzing the native Patterson map I found the following peaks (in fractional coordinates): CELL 63.0400 117.2500 133.6500 90. 90. 90. ATOM1 Ano 0. 0. 0. 111.03 0.0 BFAC 20.0 ATOM2 Ano 0.0102 0.0416 0. 15.98 0.0 BFAC 20.0 ATOM3 Ano 0. 0.5000 0.00376.21 0.0 BFAC 20.0 ATOM4 Ano 0.0669 0.0850 0.5.86 0.0 BFAC 20.0 ATOM5 Ano 0.0772 0.4168 0.5.78 0.0 BFAC 20.0 ATOM6 Ano 0.1139 0.1196 0.00495.10 0.0 BFAC 20.0 The third and fifth are far enough from the origin to represent tranlations. Is the third due to an alternative origin? Could the fifth represent a pseudo-translation? Thanks, Michele
[ccp4bb] Measure Cell option in imosflm
Does anyone know how to access the 'Measure Cell' function in iMosflm? This function in ipmosflm allowed you to click on a pair of spots, then input the number of diffraction orders, to output a rough measure of the cell length. Any help appreciated! Thanks Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester
Re: [ccp4bb] Pseudo-translation?
The general rule is that a Patterson peak should be ~ 20% of the origin before considering it significant so none of those would really need to be considered. Eleanor On 25 February 2013 12:48, Michele Lunelli efu...@yahoo.it wrote: Dear all, I have an orthorhombic crystal (pointless suggests most likely space groups P 2 21 21 or P 2 21 2) with two molecules expected in the asymmetric unit. Analyzing the native Patterson map I found the following peaks (in fractional coordinates): CELL 63.0400 117.2500 133.6500 90. 90. 90. ATOM1 Ano 0. 0. 0. 111.03 0.0 BFAC 20.0 ATOM2 Ano 0.0102 0.0416 0. 15.98 0.0 BFAC 20.0 ATOM3 Ano 0. 0.5000 0.00376.21 0.0 BFAC 20.0 ATOM4 Ano 0.0669 0.0850 0.5.86 0.0 BFAC 20.0 ATOM5 Ano 0.0772 0.4168 0.5.78 0.0 BFAC 20.0 ATOM6 Ano 0.1139 0.1196 0.00495.10 0.0 BFAC 20.0 The third and fifth are far enough from the origin to represent tranlations. Is the third due to an alternative origin? Could the fifth represent a pseudo-translation? Thanks, Michele
Re: [ccp4bb] Measure Cell option in imosflm
Hi Richard I'm afraid it doesn't exist at the moment. It could be added if there's sufficient demand for it. On 25 Feb 2013, at 12:57, Bayliss, Richard (Dr.) wrote: Does anyone know how to access the 'Measure Cell' function in iMosflm? This function in ipmosflm allowed you to click on a pair of spots, then input the number of diffraction orders, to output a rough measure of the cell length. Any help appreciated! Thanks Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] the matrix format
Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai
Re: [ccp4bb] the matrix format
Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
[ccp4bb] Post Doctoral Position at Imperial College London in Structural Biology
Imperial College London Department of Life Sciences Faculty of Natural Sciences Research Associate Salary: £32,100 - £35,620 per annum We wish to recruit a Research Associate for up to 24 months in the first instance with possible extension to up to five years to work in the research group of Professor Paul Freemont and Professor Xiaodong Zhang (http://www.msf.bio.ic.ac.uk/index.php) in the Centre for Structural Biology, Department of Life Sciences at the South Kensington Campus of Imperial College London. Our research group comprise research fellows, research associates and PhD students from a diverse range of background including molecular biology, biochemistry, X-ray crystallography, electron microscopy, physics and engineering. We employ a multi-disciplinary approach to study the structures and mechanisms of large macromolecular complexes. Funded by a CRUK programme grant to Professor Paul Freemont and Professor Xiaodong Zhang, you will join a multi-disciplinary group to investigate the structure and mechanism of the AAA ATPase p97. p97 is a versatile participant of the ubiquitin proteasome system, interacting with a larger network of adaptor proteins to mediate a variety of cellular processes including ER associated degradation, autophagy and DNA damage repair. Successful candidates must hold a PhD in a structural biology or biochemistry discipline or an equivalent level of research, industrial or commercial experience and have demonstrated capacity for innovative high quality structural biological research. Previous research experience in a structural biological laboratory environment covering X-ray crystallography or electron microscopy single particle analysis is essential. The successful candidate must also have an advanced knowledge of protein biochemistry and structural biology. Experience in supervision and training of junior research staff and students and in writing scientific research papers would be advantageous. The successful candidate must be able to work effectively within a team, have the ability to develop and apply new concepts, and have a creative approach to problem-solving. They will also be expected to demonstrate excellent verbal and written communication skills, and be able to write clearly and succinctly for publication. For informal enquiries please contact Professor Paul Freemont (p.freem...@imperial.ac.uk) or Professor Xiaodong Zhang (xiaodong.zh...@imperial.ac.uk) Our preferred method of application is online via our website http://www3.imperial.ac.uk/employment (please select “Job Search” then enter the job title or vacancy reference number – NS 2012 047 IL - including spaces into “Keywords”). Please complete and upload an application form as directed. *** Professor Paul Freemont Co-director of Macromolecular Structure and Function Group Department of Life Sciences Sir Ernst Chain Building - Wolfson Laboratories South Kensington Campus London SW7 2AZ, UK www.msf.bio.ic.ac.uk Tel: 02075945327 Email: p.freem...@imperial.ac.uk ***
Re: [ccp4bb] the matrix format
Dear Jon, Thanks for your reply. The matrix format in the REMARK 290 section of the pdb file (download from rcsb.org) is : r11r12r13tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file REMARK 290 section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre jon.agi...@gmail.com Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] Measure Cell option in imosflm
Dear Harry, It's a useful function. Could you please added it? Thanks. Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Harry Powell ha...@mrc-lmb.cam.ac.uk Hi Richard I'm afraid it doesn't exist at the moment. It could be added if there's sufficient demand for it. On 25 Feb 2013, at 12:57, Bayliss, Richard (Dr.) wrote: Does anyone know how to access the 'Measure Cell' function in iMosflm? This function in ipmosflm allowed you to click on a pair of spots, then input the number of diffraction orders, to output a rough measure of the cell length. Any help appreciated! Thanks Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] the matrix format
Hi, Emacs, vi, any (text file) editor ? I wouldn't advise a word processing program (Word and the likes). Unless you want to do this on many pdb files in which case writing a small program or shell script would be required. Fred. On 25/02/13 14:24, Qixu Cai wrote: Dear Jon, Thanks for your reply. The matrix format in the REMARK 290 section of the pdb file (download from rcsb.org http://rcsb.org) is : r11r12r13tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file REMARK 290 section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com mailto:caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre jon.agi...@gmail.com mailto:jon.agi...@gmail.com Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com mailto:caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] the matrix format
If you just want to generate symm mates from MTRIX records, you may want to give GK's 'xpand' a go: http://xray.bmc.uu.se/usf/xpand_man.html Otherwise, I would follow Fred's advice. Jon 2013/2/25 vellieux frederic.velli...@ibs.fr: Hi, Emacs, vi, any (text file) editor ? I wouldn't advise a word processing program (Word and the likes). Unless you want to do this on many pdb files in which case writing a small program or shell script would be required. Fred. On 25/02/13 14:24, Qixu Cai wrote: Dear Jon, Thanks for your reply. The matrix format in the REMARK 290 section of the pdb file (download from rcsb.org) is : r11r12r13tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file REMARK 290 section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre jon.agi...@gmail.com Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
[ccp4bb] Postdoctoral position available : Crystallization of CFTR
Nanobody-aided crystallization and structure determination of CFTR Start date : march 1st 2013 The project: Cystic Fibrosis (CF or mucoviscidosis), is a fatal genetic disorder affecting one in 2500 newborn. It is caused by mutation in the CFTR, a chloride channel, leading to destabilization, degradation and malfunctioning of the protein. Obtaining the molecular structure of CFTR will represent a major breakthrough both for our understanding of the protein function /dysfunction but also to provide new avenues for therapeutic strategies. The project aims at obtaining the crystal structure of CFTR by combining cutting edge methodologies such as Lipidic Cubic Phase-based crystallography and nanobody stabilization of CFTR. Host laboratories: As a joint effort between 3 laboratories, the project is coordinated by Dr C. Govaerts at the Structure and Function of Membrane Biology Laboratory (SFMB,) affiliated with the Université Libre de Bruxelles and is located in Brussels, Belgium, the capital of Europe. A large part of the training and of the crystallization work will take place in the laboratory of Prof Martin Caffrey, Trinity College Dublin, Ireland, a pioneer in the LCP methodology. Finally, part of the work will be performed in the laboratory of Prof John Riordan, a discoverer of CFTR, located at University of North Carolina in Chappell Hill, USA. Profile: Candidates should have a PhD and have a background in biochemistry, protein expression and purification, preferably with membrane proteins. Experience with structural biology, specifically protein crystallization is a plus. The successful candidate must be creative, self-motivated, persistent, resourceful and be willing to travel between the different labs and enjoy working both independently and in a collaborative setting. Applications: Send a CV, a list of publications, a short overview of research activities and the name of two or more references to cedric.govae...@ulb.ac.be. Preselected applicants will be requested to travel to Brussels for a lecture and an interview.
[ccp4bb] Teaching and Research Postdoctoral Fellowship-COLGATE UNIVERSITY
The following position may be of interest for individuals thinking of pursuing a career in teaching and scholarship at a predominantly undergraduate institution: * Colgate University -- TEACHING RESEARCH POSTDOCTORAL FELLOWSHIP IN BIOCHEMISTRY. *Colgate University seeks applications for a teaching research postdoctoral fellowship in biochemistry starting in Fall 2013. The fellowship is intended for a recent Ph.D. recipient in chemistry, biochemistry or a related field who has expertise in protein X-ray crystallography, enzyme kinetics, and/or protein expression and purification, or is looking to gain additional training in one or more of these research methodologies. This is a full-time, two-year position with duties divided between teaching (one course equivalent per semester) and research during the academic year, and full-time research during the summer months. The teaching component will include a mentored experience in teaching general chemistry and advanced courses in biochemistry. Research will be conducted in association with Prof. Roger Rowlett on an NSF-sponsored project to study a novel allosteric regulatory mechanism of beta-carbonic anhydrase, and will involve supervision of undergraduate research students during both the summer and academic year. Fellows will also receive mentorship in grant proposal writing. Colgate and the Rowlett laboratory are well-equipped for research and training, including an Agilent/Oxford Diffraction Gemini R system for protein X-ray diffraction studies. For more information see http://capsicum.colgate.edu/chwiki. Annual compensation is $42,840 plus benefits. Colgate is a highly selective liberal arts college in the beautiful Chenango Valley of central New York. Application materials should include a curriculum vitae, a description of teaching and research objectives, and three letters of recommendation. All application materials should be submitted to https://academicjobsonline.org/ajo/jobs/2537. Evaluation of applications will begin March 15 and will continue until the position is filled.Applicants with dual-career considerations can find postings of other employment opportunities at Colgate and at other institutions of higher education in upstate New York at www.upstatenyherc.org./Developing and sustaining a diverse faculty, staff, and student body further the University's educational mission. Colgate University is an Equal Opportunity/Affirmative Action Employer; women and minorities are especially encouraged to apply. /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
Re: [ccp4bb] the matrix format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Qixu Cai, cut and paste is yet another option and probably quickest if it is only for a few PDB files. Best, Tim On 02/25/2013 02:30 PM, vellieux wrote: Hi, Emacs, vi, any (text file) editor ? I wouldn't advise a word processing program (Word and the likes). Unless you want to do this on many pdb files in which case writing a small program or shell script would be required. Fred. On 25/02/13 14:24, Qixu Cai wrote: Dear Jon, Thanks for your reply. The matrix format in the REMARK 290 section of the pdb file (download from rcsb.org http://rcsb.org) is : r11r12r13 tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file REMARK 290 section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21 r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com mailto:caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre jon.agi...@gmail.com mailto:jon.agi...@gmail.com Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com mailto:caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32 r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 - -- - -- 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/ iD8DBQFRK4KtUxlJ7aRr7hoRAmmHAJ98bjTECrsRsoksaeZku2BmEPF9WACeK1CE wyvRASnup1qIwPYjlbNeKDY= =7S0m -END PGP SIGNATURE-
[ccp4bb] How to slow down crystallization? Need hep!
Hello everyone, I need your suggestion for slowing down crystallization for my proteinmy protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions
Re: [ccp4bb] How to slow down crystallization? Need hep!
On Mon, Feb 25, 2013 at 8:02 AM, lei feng spartanfeng...@hotmail.com wrote: I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Sometimes you can do this by adding a tiny amount of glycerol to your protein solution - I've seen 0.5% make the difference between awful plate clusters and nice individual crystals. I think it's also possible to use a combination of low concentrations and micro-seeding, but I've never done this personally. -Nat
Re: [ccp4bb] How to slow down crystallization? Need hep!
Feng Lei, I would personally recommend slowing down the process of nucleation either by lowering the temperature of crystallization or by utilizing Al's oil. These are two powerful ways to slow the overall kinetics of crystallization. Here is a relevant reference for you: http://scripts.iucr.org/cgi-bin/paper?he0181 Sincerely, lorenzo Lorenzo Ihsan Finci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityCollege of Life SciencesBeijing, China Date: Mon, 25 Feb 2013 11:02:03 -0500 From: spartanfeng...@hotmail.com Subject: [ccp4bb] How to slow down crystallization? Need hep! To: CCP4BB@JISCMAIL.AC.UK Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions
Re: [ccp4bb] How to slow down crystallization? Need hep!
Le 25/02/13 17:02, lei feng a écrit : Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions you can run crystallization at 4°C, or add agarose gel to your crystallization drop. -- Philippe Leone AFMB-UMR7257 Team 'Structural Immunology' Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33 491 82 55 81 Fax: +33 491 26 67 20 e-mail: philippe.le...@afmb.univ-mrs.fr
Re: [ccp4bb] How to slow down crystallization? Need hep!
a. Go with phase diagram gradually changing concentrations of protein, precipitant, salt concentrations and pH. Find where you are going out of crystallisation. Define region for streak seeding. b. Screen for ratios of precipitant to protein from 1:9 to 9:1. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Feb 25, 2013, at 18:02 , lei feng spartanfeng...@hotmail.com wrote: Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions
Re: [ccp4bb] How to slow down crystallization? Need hep!
Hi Lei Fang, I cannot tell what technique you are using for crystallization. Also, many details like protein concentration, temperature of crystallization etc. are missing in your email so it's hard to guess what's going on. In any case, here are my thoughts. I used to get a shower of needles from hanging drops at 19C but a lot fewer and bigger crystals when I set up sitting drops under mineral oil at 19C. The crystals took lot longer to grow (two weeks as opposed to four days using hanging drop) so bear that in mind. My guess is that you may be able to find protocols if you just do a quick web search. There are many other ways to optimize crystal growth and size including playing with temperature of crystallization (lowering to 4C), amount of precipitant vs protein, drop size, crystallization technique, seeding by dilution etc. Hope that helps. Raji On Mon, Feb 25, 2013 at 11:02 AM, lei feng spartanfeng...@hotmail.comwrote: Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Measure Cell option in imosflm
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Richard, adxv has this functionality and you do not even need to put in the diffraction orders, just drag the mouse pointer through two adjacent reflections (or more and do the maths yourself). Cheers, Tim On 02/25/2013 01:57 PM, Bayliss, Richard (Dr.) wrote: Does anyone know how to access the 'Measure Cell' function in iMosflm? This function in ipmosflm allowed you to click on a pair of spots, then input the number of diffraction orders, to output a rough measure of the cell length. Any help appreciated! Thanks Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester - -- - -- 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/ iD8DBQFRK5JRUxlJ7aRr7hoRAl49AJ99JbwtmWXjq9mOMN2VEwTTSW5f4ACgxZJ+ fv8xyYa0UGmUX8CYbQy7GAA= =8Dgb -END PGP SIGNATURE-
Re: [ccp4bb] How to slow down crystallization? Need hep!
Try using dioxane as an additive. I'd suggest adding 5- 15% dioxane into your well solution. This should inhibit nucleation resulting in fewer, larger crystals. On 25/02/13, Felix Frolow mbfro...@post.tau.ac.il wrote: a. Go with phase diagram gradually changing concentrations of protein, precipitant, salt concentrations and pH. Find where you are going out of crystallisation. Define region for streak seeding. b. Screen for ratios of precipitant to protein from 1:9 to 9:1. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Feb 25, 2013, at 18:02 , lei feng spartanfeng...@hotmail.com wrote: Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions -- Roksana OgrodowiczDivision of Molecular Structure MRC National Institute for Medical Research The Ridgeway, Mill Hill London, NW7 1AA
[ccp4bb] How to compare B-factors between structures?
Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] How to compare B-factors between structures?
Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] How to compare B-factors between structures?
Why not normalize each to its average b-factor? And...maybe they are not significantly different in the first place? JPK On Mon, Feb 25, 2013 at 3:08 PM, Yarrow Madrona amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
Re: [ccp4bb] How to compare B-factors between structures?
Thanks Nat, I was planning on plotting B-factors vs. residue anyway, so maybe this will save me time. I will take a look. -Yarrow Not a CCP4 solution, but the structure comparison program in the Phenix GUI will plot B-factors for different structures of the same protein. (I am happy to make additions or modifications to this, but so far I haven't received much feedback.) -Nat On Mon, Feb 25, 2013 at 12:08 PM, Yarrow Madrona amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] How to compare B-factors between structures?
Thank you Manfred, To be honest I have tried to understand the Pearson linear CC since reading the nature crystallography methods paper by Karplus and diederichs, but I am having trouble. I do not clearly understand what it represents. Do you know any good resources that could help me out? -Yarrow If you have two sets of numbers which correspond ideally, you should calculate a correlation coefficient, to be precise a Pearson linear CC. This is independent of scaling. If you want to compare mutant vs native, you probably have to calculate residue average B-factors, because you won't have the exact same number of atoms. Best, Manfred On 25.02.2013 21:08, Yarrow Madrona wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Re: [ccp4bb] How to compare B-factors between structures?
Hi Yarrow, I'm sure other visualizing tools can do this, but I just wanted to share that our free Discovery Studio Visualizerhttp://accelrys.com/products/discovery-studio/visualization-download.php can do this quite easily. Contact me off the list and we can set up a time when I can show you how to do this. I could also send you some instructions as well. Cheers, Francisco Sr. Product Manager Accelrys Software, Inc -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yarrow Madrona Sent: Monday, February 25, 2013 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to compare B-factors between structures? Thanks Nat, I was planning on plotting B-factors vs. residue anyway, so maybe this will save me time. I will take a look. -Yarrow Not a CCP4 solution, but the structure comparison program in the Phenix GUI will plot B-factors for different structures of the same protein. (I am happy to make additions or modifications to this, but so far I haven't received much feedback.) -Nat On Mon, Feb 25, 2013 at 12:08 PM, Yarrow Madrona amadr...@uci.edumailto:amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this is significant if the average B-factor is also higher? Thank you for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
[ccp4bb] Autodock Vina output files
Hi All, I am sure that some of you have used AutoDock Vina so I thought I would give it a go and ask two questions. I performed a round of docking and obtained an output file containing 9 different models. The affinity (kcal/mol) ranged from -4.5 to -3.0. My first question is what is considered high binding affinity i.e. what range is considered high affinity, moderate affinity etc. My second question is about the output file. The output file is in pdbqt format and can be viewed in Pymol just fine, but the problem is that I cannot separate out the individual orientations of the output file. I want to change the format to pdb so that I can change the depiction of the models in PyMol, but PyMol treats the file as one file and will not allow me to read out the models as separate pdb files. Does anybody know how to separate out the different models contained in one output file provided by AutoDock Vina. Thanks for any advice. Take care, Christine
[ccp4bb] CCPBioSim workshop on MD and Annual Conference
Dear All, CCPBioSim are once again running a 1-day workshop covering the basics of setting up Molecular Dynamics simulations for biological systems. The workshop is on Wednesday 20th March 2013 at the Unilever Centre for Molecular Informatics, University of Cambridge. The deadline for applications is Friday 8th March. Further details at: http://www.ccpbiosim.ac.uk/?q=workshops/2ndSetupSimulation Also, a reminder that the closing date for registrations for the Annual Conference of CCPBioSim is today. If there are any last minute registrations, please register asap and/or let me know. Further details at: http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2013 Cheers Martyn * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
Re: [ccp4bb] the matrix format
Thanks. That's what I need. Qixu Cai Email: caiq...@gmail.com 在 2013-2-25，下午9:38，Jon Agirre jon.agi...@gmail.com 写道： If you just want to generate symm mates from MTRIX records, you may want to give GK's 'xpand' a go: http://xray.bmc.uu.se/usf/xpand_man.html Otherwise, I would follow Fred's advice. Jon 2013/2/25 vellieux frederic.velli...@ibs.fr: Hi, Emacs, vi, any (text file) editor ? I wouldn't advise a word processing program (Word and the likes). Unless you want to do this on many pdb files in which case writing a small program or shell script would be required. Fred. On 25/02/13 14:24, Qixu Cai wrote: Dear Jon, Thanks for your reply. The matrix format in the REMARK 290 section of the pdb file (download from rcsb.org) is : r11r12r13tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file REMARK 290 section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre jon.agi...@gmail.com Dear Qixu, here's an excerpt from the pdbset manual: TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz I'm not sure what you mean by covert from the pdb file format to the pdbset format. Please elaborate on this. Jon 2013/2/25 Qixu Cai caiq...@gmail.com: Dear all, The matrix formats in different program always confuse me. The matrix format of the REMARK 290 SMTRY section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the transform file keywords of the pdbset program? is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz? And how to covert from the pdb file format to the pdbset format? What's the matrix format of apply NCS operators in phenix GUI? Thanks a lot! Qixu Cai -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] Unknown density
Dear all, Thank you very much for help! The problem was solved very easy (thanks Dominik A. Herbs). I just used another program for refinement (Refmac5 instead Phenix.refine) and this noisy density almost disappeared. http://www.4sync.com/photo/--e2gHrG/Density-Refmac5.html Thanks a lot for help again! Best regards, Pavel V. Natashin PhD student Photobiology Laboratory Institute of Biophysics Russian Academy of Sciences Siberian Branch Krasnoyarsk 660036, Russia National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101, China
[ccp4bb] How to split a dataset with PST?
Dear all, currently, I have a data set scaled in P22121 which containing a PST of (0.5,0.5,0.111). The structure were successfully solved by molecular replacement. However, the R free factors remained as high as ~33% in the refinement. I search the literature and found that it was common to have such high R free factors in case of PST (Felix F.Vajdos,etc.,protein science,1997;Arthur H.Robbins,etc.,Acta D,2010;Florence Poy,etc,NSMB,2001;Cory L.Brooks etc,Acta D,2008;). In the 2001 NSMB paper( doi:10.1038/nsb720), the authors split the dataset into 'weak,medium and strong' reflections, and showed good refinement statistcs in the 'medium reflection dataset'. Although I had good electron density maps to show my solution is correct. To further convince the reviewers, I also want to split my data set into such sub-datasets according to the symmetry. Did anyone know how to split the data set in this case? Best regards, Yuan
Re: [ccp4bb] Autodock Vina output files
Dear Christine, Your fist question is regarding range of energy in high affinity. In Autodock Vina high affinity energy varies from -9 to -11 Kcal/mol. In my opinion -4.5 to -3.0 Kcal/mol is moderate affinity for ligand. Second question is how to save individual orientation of Vina output in pymol. generally i used to open vina output(.pdbqt) in pymol, which contain 9 orientations. I clicked in each orientation and go to filesave molecule in pymol and save our interest of orientation. so you can save 9 orientation in .pdb format. Good luck Chandan --- On Mon, 25/2/13, Harman, Christine christine.har...@fda.hhs.gov wrote: From: Harman, Christine christine.har...@fda.hhs.gov Subject: [ccp4bb] Autodock Vina output files To: CCP4BB@JISCMAIL.AC.UK Date: Monday, 25 February, 2013, 3:46 PM Hi All, I am sure that some of you have used AutoDock Vina so I thought I would give it a go and ask two questions. I performed a round of docking and obtained an output file containing 9 different models. The affinity (kcal/mol) ranged from -4.5 to -3.0. My first question is what is considered high binding affinity i.e. what range is considered high affinity, moderate affinity etc. My second question is about the output file. The output file is in pdbqt format and can be viewed in Pymol just fine, but the problem is that I cannot separate out the individual orientations of the output file. I want to change the format to pdb so that I can change the depiction of the models in PyMol, but PyMol treats the file as one file and will not allow me to read out the models as separate pdb files. Does anybody know how to separate out the different models contained in one output file provided by AutoDock Vina. Thanks for any advice. Take care, Christine
Re: [ccp4bb] Autodock Vina output files
Hi Christine, You can split outputs by this way (vina site) : Separate models All predicted binding modes, including the positions of the flexible side chains are placed into one multimodel PDBQT file specified by the out parameter or chosen by default, based on the ligand file name. If needed, this file can be split into individual models using a separate program called vina_split, included in the distribution. Le 25/02/2013 23:46, Harman, Christine a écrit : Hi All, I am sure that some of you have used AutoDock Vina so I thought I would give it a go and ask two questions. I performed a round of docking and obtained an output file containing 9 different models. The affinity (kcal/mol) ranged from -4.5 to -3.0. My first question is what is considered high binding affinity i.e. what range is considered high affinity, moderate affinity etc. My second question is about the output file. The output file is in pdbqt format and can be viewed in Pymol just fine, but the problem is that I cannot separate out the individual orientations of the output file. I want to change the format to pdb so that I can change the depiction of the models in PyMol, but PyMol treats the file as one file and will not allow me to read out the models as separate pdb files. Does anybody know how to separate out the different models contained in one output file provided by AutoDock Vina. Thanks for any advice. Take care, Christine
