Re: [ccp4bb] PDB deposition ADIT without frames?
Dear Dirk, Not a remedy, but how about iyour colleague trying a different browser or deposition site (e.g. www.pdbe.org)? Cheers, Tim On Tue, Feb 15, 2011 at 05:00:00PM +0100, Dirk Kostrewa wrote: Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump between the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone:+49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de *** -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Liquid nitrogen resistant flooring
Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] Off Topic: Web or e-tools for booking instrument time
Hello, Since we are now part of the Facebook Generation (or at least 10% of the planet is), it seems there must be a better way of distributing time on our various Aktas to an institute of scientists than our current system which involves a race for the paper booking sheet every Thursday morning. Inevitably people book in a speculative manner and time slots are not always used due to problems in preparative steps etc. Bits of paper in different buildings make it difficult to see who booked what and when. Has anyone successfully implemented an electronic system, perhaps shared through the cloud, that allows real time booking in a manner that can be revised easily and has worked well? An electronic calendar (Google..) would partially address this, but it seems some sort of social networking site/tool might be better for negotiating instrument time, swapping timeslots, reallocating unused time if the sample prep fails. Any suggestions would be greatly appreciated. If governments can be toppled through Facebook, I'm sure we can book our Aktas in a better way! Darren -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** www.embl.fr/research/unit/hart/index.html For funded access to ESPRIT construct screening via EU FP7 PCUBE: http://tinyurl.com/ydnrwg4 Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] Liquid nitrogen resistant flooring
This has been a problem for us too. Sorry, I don't have a solution to offer except, recently, we have provided metal buckets filled with a layer of aquarium gravel at each station and encouraged users to dump their excess nitrogen there instead of on the floor. Richard On Feb 16, 2011, at 7:20 AM, Nicholas Keep wrote: Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick --
[ccp4bb] PhD studentship in enzyme engineering at University of Reading
3-year PhD studentship available from October 2011 Department of Food and Nutritional Sciences and School of Biological Sciences University of Reading Project title: Optimisation of prebiotic galactooligosaccharide production through enzyme engineering Project overview: Prebiotic oligosaccharides are compounds with potential health benefits, and as such have found various commercial applications as nutraceutical supplements or food ingredients. The aim of this project is to substantially improve the current process for the production of galactooligosaccharides (GOS), which involves the enzymatic synthesis of it from lactose using a b-galactosidase from Bifidobacterium, expressed in E. coli. The specific objectives of the project are to engineer the enzyme through site-directed mutagenesis and rational design in order to increase the production yields and the ratio of oligosaccharides with a high degree of polymerisation in the product mixture, and to optimise the fermentation and purification process for its production. The PhD candidate will develop expertise in a range of techniques and methodologies including enzymology, protein engineering, protein expression, fermentation, purification, preparative and analytical chromatography. Supervisors: Dr Dimitris Charalampopoulos (Department of Food and Nutritional Sciences), Dr Kim Watson (School of Biological Sciences) Funding Details: Studentship will cover Home/EU Fees and pay the Research Council minimum stipend (£13,590 for 2010/11) per year for a period of up to 3 years. Eligibility: Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent. Please note that due to restrictions on the funding, this studentship is for UK/EU applicants only. How to apply: Eligible candidates should complete a University of Reading postgraduate application form available from http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx. This should be submitted with supporting documents either to sc...@rdg.ac.uk or to: Postgraduate Office Joint Faculty Office for Science and Life Sciences Geography Building University of Reading, PO Box 227 Reading, RG6 6AB Application Deadline: Thursday, 31 March 2011 Further Enquiries: Informal enquiries may be addressed to Dr Dimitris Charalampopoulos d.charalampopou...@reading.ac.uk or Dr Kim Watson k.a.wat...@reading.ac.uk. For application enquiries please contact Jonathan Lloyd j.d.ll...@reading.ac.uk http://www.reading.ac.uk/research/res-pgr-degrees/FundingOpportunities/res-pgstudlife
Re: [ccp4bb] Liquid nitrogen resistant flooring
We went through a building renovation and this has been a problem for us too. In the old days, our building was simply sealed concrete - and you could do anything with it with no issues. Now, it's an epoxy floor, but really what happens is the liquid nitrogen cools it down and breaks the seal between the epoxy and the concrete - causing cracks and ugliness. We use a series of throw rugs and large containment pans to hold the nitrogen. It doesn't really work - so every now and then we simply repaint the floor. It's only in a few places that we use this, so it's not too bad. I do have 1 room that they put the wrong floor down first. It's a spongy floor - designed to not carry a static charge. Instead of removing the covering (which they can't do), they just went over that floor with an epoxy coating. Oddly enough - that room doesn't crack when I pour liquid nitrogen on the floor. So maybe that's the trick - put a cushion between the concrete and the epoxy. They wouldn't leave sealed concrete because it looked bad (we did a renovation, not a new building). Too bad Dave On 2/16/2011 7:32 AM, Richard Edward Gillilan wrote: This has been a problem for us too. Sorry, I don't have a solution to offer except, recently, we have provided metal buckets filled with a layer of aquarium gravel at each station and encouraged users to dump their excess nitrogen there instead of on the floor. Richard On Feb 16, 2011, at 7:20 AM, Nicholas Keep wrote: Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick --
Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time
We use Google Calendar for booking our X-ray facility. Klaus === Klaus Fütterer, Ph.D. Reader in Structural Biology Undergraduate Admissions School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab === On 16 Feb 2011, at 12:25, Darren Hart wrote: Hello, Since we are now part of the Facebook Generation (or at least 10% of the planet is), it seems there must be a better way of distributing time on our various Aktas to an institute of scientists than our current system which involves a race for the paper booking sheet every Thursday morning. Inevitably people book in a speculative manner and time slots are not always used due to problems in preparative steps etc. Bits of paper in different buildings make it difficult to see who booked what and when. Has anyone successfully implemented an electronic system, perhaps shared through the cloud, that allows real time booking in a manner that can be revised easily and has worked well? An electronic calendar (Google..) would partially address this, but it seems some sort of social networking site/tool might be better for negotiating instrument time, swapping timeslots, reallocating unused time if the sample prep fails. Any suggestions would be greatly appreciated. If governments can be toppled through Facebook, I'm sure we can book our Aktas in a better way! Darren -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** www.embl.fr/research/unit/hart/index.html For funded access to ESPRIT construct screening via EU FP7 PCUBE: http://tinyurl.com/ydnrwg4 Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] Liquid nitrogen resistant flooring
BSD Dear Nicholas, Three possible solutions that I have seen: 1. A sheet of stainless steel under the filling area over concrete (I think I saw that at the ESRF). 2. A throw-away layer of linolium that you replace every few months. Sort of like an ablation layer on a heat shield (that's what we have here in our building, but I'm not sure how well it works; the lino underneath is also cracked, but that may be due to infrequent replacement). 3. Hard flooring tiles (ceramic, granite), or just plain concrete. We have ceramic tiles under a storage dewar in our Proteomics unit, but I'm not sure how often it's refilled, so it may not get the same punishment that the area around a filling station would get. If you find a solution I'd like to hear about it Harry Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
Re: [ccp4bb] Liquid nitrogen resistant flooring
We have linoleum floor in the x-ray room which of course cracks under LN2. We put wood panel under the large container of the Oxford Cryo to prevent this. We have tiled floor in the corridor outside the room and that's where we empty the containers used for freezing crystals and other containers of LN2. It's always fun to watch. No cracks have appeared on the floor for nearly 10 years. I'm not sure what the tiles are made of. Cheers, Boaz - Original Message - From: David Roberts drobe...@depauw.edu Date: Wednesday, February 16, 2011 15:00 Subject: Re: [ccp4bb] Liquid nitrogen resistant flooring To: CCP4BB@JISCMAIL.AC.UK We went through a building renovation and this has been a problem for us too. In the old days, our building was simply sealed concrete - and you could do anything with it with no issues. Now, it's an epoxy floor, but really what happens is the liquid nitrogen cools it down and breaks the seal between the epoxy and the concrete - causing cracks and ugliness. We use a series of throw rugs and large containment pans to hold the nitrogen. It doesn't really work - so every now and then we simply repaint the floor. It's only in a few places that we use this, so it's not too bad. I do have 1 room that they put the wrong floor down first. It's a spongy floor - designed to not carry a static charge. Instead of removing the covering (which they can't do), they just went over that floor with an epoxy coating. Oddly enough - that room doesn't crack when I pour liquid nitrogen on the floor. So maybe that's the trick - put a cushion between the concrete and the epoxy. They wouldn't leave sealed concrete because it looked bad (we did a renovation, not a new building). Too bad Dave On 2/16/2011 7:32 AM, Richard Edward Gillilan wrote: This has been a problem for us too. Sorry, I don't have a solution to offer except, recently, we have provided metal buckets filled with a layer of aquarium gravel at each station and encouraged users to dump their excess nitrogen there instead of on the floor. Richard On Feb 16, 2011, at 7:20 AM, Nicholas Keep wrote: Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
[ccp4bb] CNS and protein structure refinement
Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement? Rex Palmer Birkbeck College
Re: [ccp4bb] Liquid nitrogen resistant flooring
Dear Nick, We start have the same sort of problem here at MPL. However, we have already a few solutions to put in practice. 1-The research complex at Harwell has a excellent floor on the Liquid Nitrogen Room. The name of the floor tiles are Matlocker and you can find it from this site www.jaymart.co.uk/search.php 2-Imperial College has solved the problem by acquiring a similar type of floor : Medium Rib Matting thickness 5 from the following supplier: Key Industrial Equipment Ltd 35 Black Moor Road Verwood Wimborne, BH31 6AT United Kingdom Fax: 0800 37303 In the case you are around Diamond you are welcome to have a look. Regards, Isabel - Dr. Isabel De Moraes, MRSC Membrane Protein Laboratory Facilities Co-ordinator/Group Leader Membrane Protein Laboratory, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire, OX11 ODE, UK Tel: 01235 778664 email: isabel.de-mor...@diamond.ac.uk http://www.diamond.ac.uk/Science/MPL/default.htm http://www.rc-harwell.ac.uk/ --- -Original Message- From: CCP4 bulletin board on behalf of Nicholas Keep Sent: Wed 2/16/2011 12:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Liquid nitrogen resistant flooring Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] CNS and protein structure refinement
Yes X 2 Boaz - Original Message - From: REX PALMER rex.pal...@btinternet.com Date: Wednesday, February 16, 2011 15:32 Subject: [ccp4bb] CNS and protein structure refinement To: CCP4BB@JISCMAIL.AC.UK Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement? Rex Palmer Birkbeck College Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] CNS and protein structure refinement
Ditto. YES, still generally prefer CNS v1.3 to REFMAC, especially due to composite and simulated-annealing maps. Different set of flagged reflections, so it might very well be different. Also, the low-resolution solvent scaling is different between the two refinements. Bernie Santarsiero On Wed, February 16, 2011 7:53 am, Boaz Shaanan wrote: Yes X 2 Boaz - Original Message - From: REX PALMER rex.pal...@btinternet.com Date: Wednesday, February 16, 2011 15:32 Subject: [ccp4bb] CNS and protein structure refinement To: CCP4BB@JISCMAIL.AC.UK Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement?  Rex Palmer  Birkbeck College Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaananâ
Re: [ccp4bb] CNS and protein structure refinement
Hi Rex, There will be small differences in particular due to the different ways of treating the solvent. How large of a difference are you talking about? Normally the difference should not be very large... And if this related to solvent effects, it will affect the low resolution reflections with a decrease in the effect when you go to higher and higher resolutions (but never completely disappear). Fred. REX PALMER wrote: Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement? Rex Palmer Birkbeck College
Re: [ccp4bb] Liquid nitrogen resistant flooring
Dear Nick, in the sample preparation areas of our beamlines we had the same problem. We have a new floor since mid 2009 and are so far happy with it. It was supplied by the IRL Industrial Flooring Group/Flowcrete UK (www.irlgroup.co.uk and www.flowcrete.com) The floor is Cat 3 compatible. Hope this helps, Ralf -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nicholas Keep Sent: 16 February 2011 12:21 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Liquid nitrogen resistant flooring Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] CNS and protein structure refinement
Dear Rex, Bernie and Fred, The following paper bears on the question of generally slight, but not always, R factor differences between published and recalculated Rfactors. [The paper is open access.] Greetings, John J. Appl. Cryst. (2010). 43, 669-676[ doi:10.1107/S0021889810015608 ] phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams Abstract: phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed. Keywords: PHENIX; Protein Data Bank; data quality; model quality; structure validation; R factors. On Wed, Feb 16, 2011 at 1:43 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi Rex, There will be small differences in particular due to the different ways of treating the solvent. How large of a difference are you talking about? Normally the difference should not be very large... And if this related to solvent effects, it will affect the low resolution reflections with a decrease in the effect when you go to higher and higher resolutions (but never completely disappear). Fred. REX PALMER wrote: Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement? Rex Palmer Birkbeck College -- Professor John R Helliwell DSc
[ccp4bb] MR problem in determining the number of identical molecules in ASU
Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei
[ccp4bb] how can i cinfirm the ligand bindind
Dear CCP4 colleague I just wanted to ask a simple question that if the ligand has bind the molecules so how can i confirm it either my ligand has bind or not and which program should i used to visualize it??? Best Regards AFSHAN
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
Well P4 isnt a subgroup of P43212 - you would need P43 MR programs will often let you test several spacegroups. See Phaser MR or MOLREP - I would try that and choose the best Eleanor On 02/16/2011 02:48 PM, Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei For molecular replacement: it does not matter if you carry out the rotation search in P422 or P43212. To understand this, ask youself the following question: what is the symmetry of the Patterson compared to that of the crystal? The symmetry of the Patterson is obtained from the symmetry of the crystal by converting all translation operators to the corresponding non-translation operators and adding a centre of symmetry. Hence for the rotation function, the symmetry of the Patterson will be P4/mmm for space group P422 and P4/mmm for P43212. Hence no difference for the rotation function. Different for P4 though: the symmetry of the Patterson there is P4/m. Hence the rotation function can be computed once for all space groups that have Patterson symmetry P4/mmm. No need to repeat the rotation function calculations several times. The situation is different for the translation function however. This is the stage at which you distinguish between all these space groups (including the pair of enantiomorphs P41212 and p43212). Failure to assign the proper space group cannot give you a satisfactory model. HTH, Fred.
Re: [ccp4bb] Liquid nitrogen resistant flooring
At ALS, we have a red epoxy-on-concrete floor, which is lN2 resistant but still cracks if abused. However, we have not repainted it for many years now. We found that one very good way to extend the life of the floor is to keep users from dumping their cryogens onto it. In Berkeley, it is easiest to appeal to their green sense and offer lN2 recycling. Simply place a coffee filter into a funnel (foam funnels are best) and pour your old, icy lN2 through the filter and voila! ice-free recycled nitrogen! It actually works very well (no snowball crystals), and you can see the pile of white fluffy snow left behind in the filter. Coffee filters are good, but a few layers of Kimwipe(TM) will also do in a pinch. Recycling also has the advantage of reducing the other factor that limits the lifetime of cryo-room floors, which is the crushing force of heavy supply dewar wheels (which you will be replacing less often). I have spent some time reading about this problem in the past, so although I do not have contact info for a cryogen-proof floor supplier, I can speak to the general principles. lN2 is the world's best paint remover, and this is because very few paints have exactly the same thermal expansion coefficient as the surface you painted. When exposed to cryogen, both substances become stiff, but shrink at different rates, and so tend to shear along the surface (peel). There are three ways to combat this: 1) find a paint that matches the expansion coefficient of the surface. Epoxy and concrete are a fairly good match, (and by some lucky miracle of civil engineering, so are steel and concrete), but for changes in temperature of 200 degrees, even slight differences in expansion coefficient can be important. This is probably why epoxy flooring is lN2 resistant and not lN2 proof. You might be able to find a better epoxy, but will probably have to do experiments to be sure. I doubt your paint supplier will have CTE data on their paint, and there is no way for them to know what it is for your floor. 2) find a paint that does not become brittle at cryogenic temperatures. Most steels are good for this, and also have the advantage of remarkably low thermal conductivity (for a metal). Invar steel has no expansion coefficient at all, but has the disadvantage of being the only stainless steel that rusts. Another one is teflon, which is still flexible under lN2, but (like most plastics) suffers from a high thermal expansion coefficient, meaning that a teflon floor would be under tremendous stress when cooled. The bigger the piece, the more peeling force generated at its ends. This brings me to the third point. 3) A trick I call macroscopic bonding. Expansion coefficient mismatch is only important if the stress induced by the temperature change exceeds the strength of the bond holding the floor together. If this bond is simply the Van der Waals between two smooth surfaces (like paint) it is relatively easy to make this slip along the plane of the surface (peel the paint). For example, if you try to epoxy together two smooth plates of aluminum (which has a VERY different expansion coefficient from epoxy) and then dunk the result into lN2, you will see everything readily crack apart. However, if you first drill a lot of little holes at criss-crossing angles into the aluminum, allowing the epoxy to fill the holes, then you will find the resulting bond remarkably resistant to lN2. This is because the covalent bonds in the bulk of the epoxy (occupying the holes) must be broken before the two materials can separate. In fact, this is what I did to get my crystal mounting robot's aluminum tong paddles to stick to the wooden pencils that hold them. This bond has shown no signs of loosening after thousands of dunkings into lN2. I think this is probably what happened in David Roberts's painted foam floor room. Cushioning probably plays a role too, but since foam has lots of nooks and crannies, the paint must break the covalent bonds holding its bulk together before it can separate from the foam. The foam probably shrinks tremendously more than the paint, but because the painted surface is not smooth, the forces of expansion-coefficient mismatch do not build up, but instead are transferred between the surfaces by the rivets of paint at each nook and cranny. No doubt, the nooks and crannies on the underside of high quality tile form a macroscopic bond to the mortar/grout beneath. So, perhaps a good BSL2 floor would be to find some stainless steel that is smooth on one side and holey on the other, then epoxy the holey side onto a (roughened) concrete floor? That is, if you don't mind working in a room that looks like a prison shower. -James Holton MAD Scientist On 2/16/2011 4:59 AM, David Roberts wrote: We went through a building renovation and this has been a problem for us too. In the old days, our building was simply sealed
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
I think the question was not concerning right vs wrong space group, but right vs a lower symmetry superset space group - P4322 vs P43 for example. I would also be interested in the answer. At first glance it appears harder in the lower symmetry because with each monomer you would be searching for a smaller fraction of the contents of the AU. But if the rotation function doesn't consider space group symmetry (?) does that matter? eab Vellieux Frederic wrote: Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei For molecular replacement: it does not matter if you carry out the rotation search in P422 or P43212. To understand this, ask youself the following question: what is the symmetry of the Patterson compared to that of the crystal? The symmetry of the Patterson is obtained from the symmetry of the crystal by converting all translation operators to the corresponding non-translation operators and adding a centre of symmetry. Hence for the rotation function, the symmetry of the Patterson will be P4/mmm for space group P422 and P4/mmm for P43212. Hence no difference for the rotation function. Different for P4 though: the symmetry of the Patterson there is P4/m. Hence the rotation function can be computed once for all space groups that have Patterson symmetry P4/mmm. No need to repeat the rotation function calculations several times. The situation is different for the translation function however. This is the stage at which you distinguish between all these space groups (including the pair of enantiomorphs P41212 and p43212). Failure to assign the proper space group cannot give you a satisfactory model. HTH, Fred.
Re: [ccp4bb] CNS and protein structure refinement
A quick PDB search reveals that 551 crystal structures were deposited in 2010 that were refined with CNS. On Wed, 2011-02-16 at 13:32 +, REX PALMER wrote: Does anyone still use CNS ? Do we expect Rfree from CNS for example to be different from the value given by Refmac at the end of the refinement? Rex Palmer Birkbeck College
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
In my experience, the success of molecular replacement depends primarily on the quality of the model. Thus if your model is good, even P1 will work. Two extreme cases that I encountered were searching with a monomer for what turned out to be 4 tetramers (thus first search only accounted for 1/16 of the asu) and getting a solid solution from 40% complete dataset at 3A-ish resolution with the search model being 25% of the asu. On the other end of the spectrum, I've seen molecular replacement fail to find the second copy using the first copy from the final refined structure. Bottomline: the limit to which MR can be pushed is inversely proportional to the quality of your model. Your question is that kind which is easier to answer if you specify what is that you are trying to accomplish. -- Hurry up, before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
The space group in which you do the RF makes no difference (assuming the model in each case is identical of course) because you're superposing the same amount of scattering matter: it has nothing to do with the fraction of the contents of the AU. In the high symmetry space group with say 1 instance of a differently oriented model per AU you are still only superposing 1 AU at a time, and each AU gives a separate peak in the RF (some of which may be related by the symmetry of the RF and some not: e.g. the 3-fold related peaks in cubic space groups). In the low symmetry space group you still get 1 peak per differently oriented instance of the model. This assumes that the high symmetry space group is the correct one; if it turns out that the subgroup is correct then of course that will give the better solution. -- Ian On Wed, Feb 16, 2011 at 5:57 PM, Edward A. Berry ber...@upstate.edu wrote: I think the question was not concerning right vs wrong space group, but right vs a lower symmetry superset space group - P4322 vs P43 for example. I would also be interested in the answer. At first glance it appears harder in the lower symmetry because with each monomer you would be searching for a smaller fraction of the contents of the AU. But if the rotation function doesn't consider space group symmetry (?) does that matter? eab Vellieux Frederic wrote: Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei For molecular replacement: it does not matter if you carry out the rotation search in P422 or P43212. To understand this, ask youself the following question: what is the symmetry of the Patterson compared to that of the crystal? The symmetry of the Patterson is obtained from the symmetry of the crystal by converting all translation operators to the corresponding non-translation operators and adding a centre of symmetry. Hence for the rotation function, the symmetry of the Patterson will be P4/mmm for space group P422 and P4/mmm for P43212. Hence no difference for the rotation function. Different for P4 though: the symmetry of the Patterson there is P4/m. Hence the rotation function can be computed once for all space groups that have Patterson symmetry P4/mmm. No need to repeat the rotation function calculations several times. The situation is different for the translation function however. This is the stage at which you distinguish between all these space groups (including the pair of enantiomorphs P41212 and p43212). Failure to assign the proper space group cannot give you a satisfactory model. HTH, Fred.
[ccp4bb] Low number of waters for a given resolution
Hello all, Some crystal structures seem to contain a very low number of water molecules given their resolution (e.g 1 water for every 10 amino acid residues at 2.2Angstrom, whereas probably around 0.6 waters per residue is expected on average). I was wondering if anybody has any insights (or better: a good reference) into the precise reasons. Of course general data quality comes into mind, or using data-to-parameter ratio rather than resolution. But how about intrinsic properties the protein? So my exact questions are: - How frequent is a very low number of visible waters observed? - What are the usual reasons? Cheers Filip Van Petegem -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] Low number of waters for a given resolution
You might want to take a look at the following paper: Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):479-83. How many water molecules can be detected by protein crystallography? Carugo Ohttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Carugo%20O%22%5BAuthor%5D, Bordo Dhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Bordo%20D%22%5BAuthor%5D . Mario Sanches On Wed, Feb 16, 2011 at 3:48 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Hello all, Some crystal structures seem to contain a very low number of water molecules given their resolution (e.g 1 water for every 10 amino acid residues at 2.2Angstrom, whereas probably around 0.6 waters per residue is expected on average). I was wondering if anybody has any insights (or better: a good reference) into the precise reasons. Of course general data quality comes into mind, or using data-to-parameter ratio rather than resolution. But how about intrinsic properties the protein? So my exact questions are: - How frequent is a very low number of visible waters observed? - What are the usual reasons? Cheers Filip Van Petegem -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/ -- Mario Sanches Postdoctoral Fellow Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches
[ccp4bb] Can REFMAC5.2 use the library from REFMAC5.6?
Hi, For some reasons, I need to use REFMAC5.2. But this version doesn't include library for some ligand (eg NDG FUC MAN...). I don't have too much clue as to how to manually build the library, and I tried to copy the cif file from REFMAC5.6 into the current lib/data/monomers folder. However, it just didn't work. Can anybody give me some suggestions? Thanks! Hailiang
Re: [ccp4bb] MR problem in determining the number of identical molecules in ASU
Another cause of difficulty - nothing really to do with the spacegroup selection - is when one copy of the model has much higher B factors than others. Most MR searches assume that the copies contribute more or less equally to scattering. If you assign too high a symmetry this will make MR less likely to work. This usually happens when the data is twinned. Eleanor On 02/16/2011 05:57 PM, Edward A. Berry wrote: I think the question was not concerning right vs wrong space group, but right vs a lower symmetry superset space group - P4322 vs P43 for example. I would also be interested in the answer. At first glance it appears harder in the lower symmetry because with each monomer you would be searching for a smaller fraction of the contents of the AU. But if the rotation function doesn't consider space group symmetry (?) does that matter? eab Vellieux Frederic wrote: Ting-Wei Jiang wrote: Dear experts, Sorry for a simple question but confusing me so much! Does it make bad effects on determining the number of identical molecules in ASU by choosing low symmetry space group. For example,If I choose lowest symmetry(p4) instead of higher one(p43212). Does it cause any trouble in determining structure while we try to find the solution by molrep. If molrep compare the patterson of observe and model in P1 space group, it doesn't matter in choosing a lower s.g.? Any suggestion will be appreciated. Thanks in advance. Ting wei For molecular replacement: it does not matter if you carry out the rotation search in P422 or P43212. To understand this, ask youself the following question: what is the symmetry of the Patterson compared to that of the crystal? The symmetry of the Patterson is obtained from the symmetry of the crystal by converting all translation operators to the corresponding non-translation operators and adding a centre of symmetry. Hence for the rotation function, the symmetry of the Patterson will be P4/mmm for space group P422 and P4/mmm for P43212. Hence no difference for the rotation function. Different for P4 though: the symmetry of the Patterson there is P4/m. Hence the rotation function can be computed once for all space groups that have Patterson symmetry P4/mmm. No need to repeat the rotation function calculations several times. The situation is different for the translation function however. This is the stage at which you distinguish between all these space groups (including the pair of enantiomorphs P41212 and p43212). Failure to assign the proper space group cannot give you a satisfactory model. HTH, Fred.
