Re: [ccp4bb] R-Rfree vs resolution
Hi All, Many thanks for replying to my request on R-Rfree vs resolution. Your wonderful advices are very helpful. 2010-08-05 joybeiyang
[ccp4bb] Postdoctoral position in adhesin structural biology
There is an immediate opening for a postdoctoral position in the Goldman group in the Institute of Biotechnology at the University of Helsinki (http://www.biocenter.helsinki.fi/bi/xray/goldman/Home_.html). My group focusses on proteins in or near the cell membrane. In particular, we have a series of projects aimed at understanding the structure and function of bacterial trimeric autotransporter adhesins (TAAs) (eg: Nummelin et al., EMBO J, 23, 701-771, 2004; Leo et al., Infect Immun, 78, 3226-3236, 2010; Leo et al., Mol. Immunol., 46, 2860-6, 2009). Our current goals are to solve the structure of TAA-ligand complexes, and to understand the mechanism of TAA folding. The Goldman group is well-equipped, with several GE Healthcare Akta systems for protein purification, a robotic crystallisation and visualisation unit (Cartesian, Oryx, Mosquito LCP coming), as well as standard x-ray crystallography and molecular biology equipment. I head the Finnish crystallography BAG at the ESRF, and we have access to the ESRF on a monthly basis. The successful candidate will have a strong background either in protein structural work or in protein production and characterisation, with a desire to learn the other field. Experience in automation will be a great plus, as the candidate will also have responsibility for the management of the robot crystallisation facility, in conjunction with the programmer and technicians who run it. The Institute of Biotechnology at UH provides a richly collaborative environment for studying problems at the interfaces between cell, molecular, developmental and structural biology. For further information, please contact Professor Adrian Goldman, Institute of Biotechnology, University of Helsinki. Email: adrian.gold...@helsinki.fi or phone: +358 (0)9 191 58923. Applications: please send a complete c.v., publication list and the names and addresses of two referees to me by email. The University of Helsinki is an equal opportunity employer and salary will be on the standard University payscale, depending on experience.
[ccp4bb] Fwd: molecule name from pdb id and chain identifier
Apologies if this has been posted already but I couldn't see it yet! Hi, Sorry for the off topic question! I'm looking at Dali search results and find the molecule names are not always the same as the ones for the chain identifier from the pdb entry (maybe the molecule names are always of chain A of the entries???). I'm wondering if there is a way/tool to extract the proper molecule names of the corresponding chains for the dali hits giving multiple hits at the same time. So far I've found only Uniprot ID mapping that might be useful but it doesn't allow using chain id's. My googling skills have failed me. So any help would be very much appreciated. Many thanks. Kind regards, Sid.
[ccp4bb]
Dear Changyi, If refmac distorts the ring to fit INTO the density, the first question I would ask myself is whether the sugar ring has been fitted correctly. Sugars can be a pain in the neck with different puckers, chair/boat conformations, different anomers etc. If the sugar is somewhat disordered, or the resolution of your data is low, it is even possible that the sugar ring needs to be rotated 180 degrees. Also make sure that you use the right anomer. Only after you are sure the ring has been fitted correctly and you merely need cosmetic corrections because of low resolution data and/or a disordered binding mode, I would try to restrain the ring more tightly. For this, you need to locate the cif file with the parameters of your ligand and increase the weight on the angle restraints. Good luck! Herman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Changyi Xue Sent: Wednesday, August 04, 2010 10:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Dear all, In my structure, there is a ligand, which contains a sugar ring. In the process of refinement, refmac always tried to distort the sugar ring to fit into the density. Is there any way to fix or restrain the ring conformation more tightly? I know CNS has such function, just wandering if refmac could do it also. all suggestions are welcome. changyi
[ccp4bb] FW: [ccp4bb]
Dear Changyi, If refmac distorts the ring to fit INTO the density, the first question I would ask myself is whether the sugar ring has been fitted correctly. Sugars can be a pain in the neck with different puckers, chair/boat conformations, different anomers etc. If the sugar is somewhat disordered, or the resolution of your data is low, it is even possible that the sugar ring needs to be rotated 180 degrees. Also make sure that you use the right anomer. Only after you are sure the ring has been fitted correctly and you merely need cosmetic corrections because of low resolution data and/or a disordered binding mode, I would try to restrain the ring more tightly. For this, you need to locate the cif file with the parameters of your ligand and increase the weight on the angle restraints. Good luck! Herman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Changyi Xue Sent: Wednesday, August 04, 2010 10:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Dear all, In my structure, there is a ligand, which contains a sugar ring. In the process of refinement, refmac always tried to distort the sugar ring to fit into the density. Is there any way to fix or restrain the ring conformation more tightly? I know CNS has such function, just wandering if refmac could do it also. all suggestions are welcome. changyi
[ccp4bb] XSCALE
Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna
Re: [ccp4bb] XSCALE
Dear Anna, Something I find useful is to convert the output of XSCALE (unmerged) to MTZ format using pointless (pointless -c xdsin SCALED.XDS hklout sorted.mtz) then to merge the reflections with Scala: scala hklin sorted.mtz hklout scaled.mtz eof run 1 all scales constant anomalous on # or off eof This will write out the merging statistics in the usual scala way - very helpful. You also get all the loggraphs etc. Best wishes, Graeme On 5 August 2010 15:07, anna delprato del_...@yahoo.com wrote: Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna
Re: [ccp4bb] XSCALE
anna delprato wrote: Hello All; I've just started using XDS and have scaled three data sets from the same crystal - unmerged. It was a SAD experiment My question is concerning which R values to use as data processing statistics. I don't find any Rsymm or even Redundancy values in the LP files. I came across an exmple where Rr.i.m / Rmeas was reported but I don't understand the distinction between these values. Thank you in advance. Anna Dear Anna, The classical R-sym (on intensities) in the files XCALE.LP and CORRECT.LP is called R-FACTOR observed. There is another R-sym value called R-meas, plus something called Rmrgd-F defined in Diederichs Karplus (1997), Nature Struct. Biol. 4, 269-275 (this is all given above the tables in the .LP files). In case of anomalous diffraction, there is no R-ano as such but other values are provided. WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? Fred.
[ccp4bb] Postdoctoral Position in Membrane Protein Crystallography
Postdoctoral Position in Membrane Protein Crystallography A postdoctoral position in membrane protein crystallography is available at the Center of Membrane Biology at the University of Virginia. The position is available in the laboratory of Dr. Jochen Zimmer who studies the membrane translocation of biopolymers, with a special interest in polysaccharide biosynthesis. Polysaccharides are among nature's most abundant and hydrophilic polymers and are essential for numerous cellular functions, such as energy storage, cell adhesion and migration, and cellular stability. Extracellular polysaccharides are generally synthesized inside the cell and are translocated to the outside during their synthesis. The position available is part of a group studying the biosynthesis of hyaluronan. The successful candidate will join a dynamic group that uses the tools of molecular biology to study fundamental processes in biology. The available project has already been established in terms of protein expression and purification, functional reconstitution in vitro, and preliminary crystallization. Initially, the project will focus on optimization of expression and purification of integral membrane proteins and protein-complexes for structural studies, which will be followed by crystallization experiments and electron microscopy analysis. Our laboratory is part of the Centre of Membrane Biology at the University of Virginia which serves as a site for state-of-the-art expertise in electron microscopy, x-ray crystallography, single molecule fluorescence spectroscopy, SAXS, and NMR EPR spectroscopy, all of which are readily accessible to the highly motivated fellow. The competitive candidate must have a Ph.D. or equivalent, have extensive experience in cloning and protein expression purification, and should have a basic knowledge of protein crystallography. The ability to function independently yet work well with a diverse group of scientists and students is a must. For further information please visit http://people.virginia.edu/~jz3x/. Applications, including a current CV, a cover letter stating why you are qualified for this position, and the names and contact information of 3 references, can be sent directly to jochen_zim...@virginia.edu. The University of Virginia is an Equal Opportunity/Affirmative Action Employer. UVa is one of the best public Universities in the US. It is located in Charlottesville/Virginia which offers reasonable housing cost and a vibrant cultural life. Charlottesville is conveniently located close to the Blue Ridge Mountains and Washington DC and Baltimore. Visit http://www.charlottesvilletourism.org/ for further information. Jochen Zimmer, D.Phil Assistant Professor Dept. of Mol. Physiology Biol. Physics University of Virginia Snyder Bldg. #360 / 362 480 Ray C Hunt Dr. Charlottesville, VA 22908 jochen_zim...@virginia.edu Phone: 434 243 6506
[ccp4bb] Fwd: [ccp4bb] XSCALE
WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? No need to do that - you can use the xdspub command within XDSi: http://cc.oulu.fi/~pkursula/xdsi.html http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSi which gives this kind of output: Final data processing statistics SPACE_GROUP_NUMBER= 197 UNIT_CELL_CONSTANTS=78.0978.0978.09 90.000 90.000 90.000 INPUT_FILE= ./XDS_ASCII.HKL XDS_ASCII Unique reflections 11084. High res. shell 1.65-1.50 Redundancy 4.3( 1.9) R(sym) 3.1( 53.1) R(meas) 3.5( 70.7) R(mergd-F) 7.8(106.0) I/s(I) 25.1( 1.5) completeness 86.2( 57.3) Best, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
[ccp4bb] Fwd: [ccp4bb] XSCALE (II)
Apologies for the repetition, but only the first link: http://cc.oulu.fi/~pkursula/xdsi.html is for the xdspub program that produces the output I attached. The other one has the same name, but does something else! Luca
[ccp4bb] Handy shortcuts to information on the PDBe website
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe (PDBe) website, we acquired the domain name pdbe.org and have used it to implement a number of shortcuts to many of our services etc. - http://pdbe.org/ - the new PDBe website - http://pdbe.org/1cbs - go directly to the PDBe atlas pages for PDB entry 1cbs (replace by the PDB code of your favourite entry) - http://pdbe.org/download/1cbs - download the PDB file for entry 1cbs - http://pdbe.org/random - go to the summary page for a random PDB entry - http://pdbe.org/wizard - the PDBe Wizard that helps you find information on the website - http://pdbe.org/help - help pages - http://pdbe.org/deposit http://pdbe.org/nmrdeposit http://pdbe.org/emdeposit - deposit structures and data in the PDB and/or EMDB - http://pdbe.org/search - search the PDBe database - http://pdbe.org/fold - use the PDBeFold service (which runs SSM) to find structures with similar folds or do (multiple) structure superposition - http://pdbe.org/pisa - use the PDBePISA service (assemblies, interfaces, quaternary structure) - http://pdbe.org/motif - use the PDBeMotif service (analysis of ligands and their binding properties, sequence motifs, structure motifs, etc._ - http://pdbe.org/browse - use the PDBeXplore structure browser or one of its modules: - http://pdbe.org/ec - enzyme classification browser - http://pdbe.org/cath - CATH classification browser - http://pdbe.org/pfam - Pfam classification browser - http://pdbe.org/fasta - compare your protein sequence to all proteins in the PDB and analyse the results with the browser - http://pdbe.org/chem - search the ligands in the PDB - http://pdbe.org/analysis - use one of the PDBe data analysis servers - http://pdbe.org/pdbprints - read about PDBprints (graphical representation of key information about PDB entries) - http://pdbe.org/emdb - go to the EMDB page at PDBe - http://pdbe.org/nmr - go to the NMR pages at PDBe - http://pdbe.org/sifts - go to the SIFTS page - http://pdbe.org/capri - go to the CAPRI site - http://pdbe.org/eurocarb - go to the EUROCarbDB site - http://pdbe.org/resources - more information about some PDBe resources - http://pdbe.org/teaching - more information about PDBe tutorials - http://pdbe.org/training - more information about PDBe roadshows - http://pdbe.org/about - more information about PDBe - http://pdbe.org/contact - contact information As always, we welcome comments and suggestions on new features (preferably using the big, fat FEEDBACK button on the PDBe web pages). --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Fwd: [ccp4bb] XSCALE
Another very nice script to run and collect statistics from XDS is xdsme from Pierre Legrand http://code.google.com/p/xdsme/ Daniel Le 05/08/2010 16:55, Jovine Luca a écrit : WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observations and number of unique reflections (this is what I do all the time). I suppose one could always write a jiffy program to compute the correct values using both files INTEGRATE.HKL and XDS_ASCII.HKL, but I haven't done it myself... Yet ? No need to do that - you can use the xdspub command within XDSi: http://cc.oulu.fi/~pkursula/xdsi.html http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSi which gives this kind of output: Final data processing statistics SPACE_GROUP_NUMBER= 197 UNIT_CELL_CONSTANTS=78.0978.0978.09 90.000 90.000 90.000 INPUT_FILE= ./XDS_ASCII.HKL XDS_ASCII Unique reflections 11084. High res. shell 1.65-1.50 Redundancy 4.3( 1.9) R(sym) 3.1( 53.1) R(meas) 3.5( 70.7) R(mergd-F) 7.8(106.0) I/s(I) 25.1( 1.5) completeness 86.2( 57.3) Best, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
[ccp4bb] Post-doctoral Position in Membrane Protein Crystallography
The Stroud Lab at UCSF (http://www.msg.ucsf.edu/stroud/index.htm) is looking to fill a post-doctoral position in membrane protein crystallography. Applicants should have background in biochemistry, molecular biology, and/or crystallography. The position in membrane proteins will be in close affiliation with Membrane Protein Expression Center (MPEC) (http://mpec.ucsf.edu/index.htm) and Center for the Structures of Membrane Proteins (CSMP) (http://csmp.ucsf.edu/index.htm). Candidates with experience with membrane proteins is highly preferred for this position. If interested, please email your cover letter and CV to: beth...@msg.ucsf.edu Thank you
[ccp4bb] Protein + DNA volume calculation
Hi, I would like to measure the volume of a protein-DNA complex. I'm using VOIDOO but it only gives me the volume of the protein. Does anybody know of a software that allows calculation of DNA volume too? thanks a lot vincent -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Re: [ccp4bb] Protein + DNA volume calculation (solved)
I got VOIDOO to work by editing the library file, mine was only reading protein. To make it read the bases, I added this lines to the file: RESI 'THR' (example) RESI ' DA' RESI ' DT' RESI ' DC' RESI ' DG' Thank you Eric for the web site. vincent Eric Pettersen wrote: Hi, I would like to measure the volume of a protein-DNA complex. I'm using VOIDOO but it only gives me the volume of the protein. Does anybody know of a software that allows calculation of DNA volume too? The StrucTools server (http://helixweb.nih.gov/structbio/basic.html) can calculate the Voronoi volume of a molecule. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
