Re: [ccp4bb] summary: off topic: advice for crystallography workstation/server
Hi, First of all, thanks for all the suggestions and comments! I'll sum up a few of the replies here. It seems that most people would favor going for the route of having multiple, individual computers (iMacs, mac minis, etc) instead of having one workhorse. This mainly due to the fact that anything 3D would be needed to be run locally. This is indeed the way we have things setup currently, and it is working fine. However, as some of the computers are getting older (and our structures getting bigger), especially the number crunching takes a hit. My idea was then revolving around buying new laptops/deskops, or continue using the ones we have (which do work fine) and buy a singe workhorse (mac pro). My initial idea was indeed using the Mac Pro as Jürgen described, thus mainly as a number crunching workhorse, with all building in Coot etc done locally on the existing laptops. This can be done just by using ssh and running the normal os x on the machine, and not using vnc (or similar). I believe this might work quite well in our lab, but I'll need to give some thought. Again, thanks for your suggestions. Cheers, Ronnie On Dec 15, 2010, at 20:07, Bosch, Juergen wrote: We have a slightly different approach to this. Local machines are laptops if you want to do model building you can do it locally either 2d or connected to a Zalman in 3D. I have one Mac mini hooked up to a Zalman as permanent 3D station. The dual HexaCore MacPro (16 GB RAM) is connected also to a Zalman but is mostly used remotely via ssh in X11. Since you most likely want to use the MacPro for number crunching the ssh connection is fast enough, also for bringing up the ccp4I interface it still works fine even from home. I have a second 8core MacPro in my office used the same way, although right now I only have a 2D display connected to it, but the cores are accessible for number crunching. We are not using OSX Server, multiple users can have simultaneous ssh sessions. I link to a central .bashrc script so that every user has access to all software as soon as they log in. This requires me when setting up a new user to change the local .bashrc file to instead read the /etc/.bashrc that's all. So not sure if you really need OSX Server for your purposes. Maybe if you could specify what types of things you want to run on those machines it would be easier to make suggestions. I would not built in Coot over the network, that's just frustratingly slow and you don't get the benefit of graphics acceleration. Here's an incomplete list of stuff on those MacPros: USF stuff e.g Moleman etc. Coot, Pymol Docking software CCP4 package Phenix XDS Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Dec 15, 2010, at 12:51 PM, Francis E Reyes wrote: Dear all, We are currently considering buying a computer which can be used by multiple people, via our existing network, as a workstation for crystallography purposes. My thoughts are currently going towards a 8-core Apple Pro (or 12-core) with a lot of RAM, with OS X Server, which in theory should be able to handle multiple (up to 4) users simultaneously running crystallography software. The idea would be to have the users access this computer using their own laptops (starting their own virtual sessions?) connected to the same network. Does this sound like a viable strategy, or should it be setup in a different way? In that case how? Would it need advanced setup and maintenance, or would it be possible to jsut set up a number of user accounts in OS X Server, and let it run? I'm reasonably computer savvy, but haven't really done something like this before, so I would very much appreciate your advice or personal experiences regarding this matter. I know that I could probably get a cheaper computer if I went for a pc with linux, but I have more experience with OS X, and would therefore want to stay with it. Thank you in advance, Ronnie Berntsson -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate
80% saturated lithium sulfate should have about the correct ionic strength to match your crystallization conditions. The crystals need to be transfered with as little mother liquor as possible to avoid lithium phosphate crystallization. Robert Kirchdoerfer suggestion is also excellent, but careful about matching the pH. Enrico. -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dale The reward of the full calculation is that all the complications you describe disappear. An atom that sits 0.001 A from a special position is not unstable in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But there must still be some threshold of distance at which even that fails? Presumably within rounding error? Or are you saying (I assume you aren't!) that you can even refine all co-ordinates of an atom exactly on a special position? Say the x and z co-ordinates of an atom at (0,y,0) in monoclinic? Presumably the atom would have to be given a random push one way or the other (random number generators are generally not a feature of crystallographic refinement programs, with the obvious exception of simulated annealing!)? ? I always avoid programing tests of a == b for real numbers because the round-off errors will always bite you at some point. This means that a test of an atom exactly on a special position can't be done reliably in floating point math. Obviously common sense has to be applied here and tests for strict floating-point equality studiously avoided. But this is very easily remedied, my optimisation programs are full of tests like IF(ABS(X-Y).LT.1E-6) THEN ... and I'm certain so are yours (assuming of course you still program in Fortran!). This implies that in the case that an atom is off-axis and disordered you have to take care not to place it within say a few multiples of rounding error of the axis, since then it might be indeed be confused with one 'on' the special position. However if someone claims that an atom sits within say 10*rounding error of an axis as distinct from being on the axis, then a) there's no way that can be proved, and b) it would be indistinguishable from being on the s.p. and the difference in terms of structure factors and maps would be insignificant anyway, so it may as well be on-axis. I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. Your preferred assumption is that any atom near enough to a special position is really on the special position and should have an occupancy of one. My assumption is that no atom is every EXACTLY on the special position and if they are close enough to their symmetry image to forbid coexistence the occupancy should be 1/n. I think either assumption is reasonable but, of course, prefer mine for what I consider practical reasons. It helps that I have to code to make mine work. Whichever way it's done is only a matter of convention (clearly both ways work just as well), however I would reiterate that my main concern here is that convention and practice appear to have parted company in this particular instance! Cheers -- IAn
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Or you could write and ask the author, who is always willing to help (sorry, David!)... On 16 Dec 2010, at 11:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Cheers -- Ian Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. Cheers, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 6:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms That's my whole point, it's not an arbitrary threshold, it's determined completely by what the data are capable of telling you about the structure, depending on the resolution. Either you have sufficient resolution to be able to say that the atom is disordered off the s.p. or you don't and you have no choice but to constrain it to the s.p., whether it's actually disordered or not. In any case there is no discontinuous change in occupancy at all, I never suggested that there should be. Say at high resolution you see 2 disordered atoms off-axis each with 1/2 occupancy, so total occupancy = 1. At lower resolution you see 1 ordered atom on-axis with occupancy 1 - so no change in total occupancy. It makes absolutely no difference if instead if you store multiplicity*occupancy in the file, the total occupancy is still 1. However multiplicity*occupancy is not conserved so will change discontinuously (off-axis total = 1, on-axis total = 1/2); occupancy is conserved (it represents real atoms after all!). I have no issue with Shel-X if it's writing out the occupancy for deposition (or at least making best efforts to do so). What it does for intermediate files is the user's own data conversion problem if s/he decides to switch between different programs. Cheers -- Ian On Wed, Dec 15, 2010 at 5:20 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: I agree with Herman. It is simply not acceptable to have a sudden discontinuous change in effective occupancy at some arbitrary point as a disordered atom approaches a special position. Anyway, whatever the CIF people decide, I will not introduce an incompatibility between different versions of SHELX. When SHELXL produces a small molecule CIF for depostion, it of course attempts to generate the occupancy according to the CIF definition. Not too surprisingly, there are a few complicated cases of 'nearly special positions' where the program gets this wrong. This is probably the most serious known 'bug' in SHELXL, but is proving rather difficult to eliminate completely. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Dec 2010, Ian Tickle wrote: Hi Herman What makes an atom on a special position is that it is literally ON the s.p.: it can't be 'almost on' the s.p. because then if you tried to refine the co-ordinates perpendicular to the axis you would find that the matrix would be singular or at least so badly conditioned that the solution would be poorly defined. The only solution to that problem is to constrain (i.e. fix) these co-ordinates to be exactly on the axis and not attempt to refine them. The data are telling you that you have insufficient resolution so you are not justified in placing the atom very close to the axis; the best you can do is place the atom with unit occupancy exactly _on_ the axis. It's only once the atom is a 'significant' distance (i.e. relative to the resolution) away from the axis that these co-ordinates can be independently refined. Then the data are telling you that the atom is disordered. If you collected higher resolution data you might well be able to detect successfully refine disordered atoms closer to the axis than with low resolution data. So it has nothing to do with the programmer setting an arbitrary threshold. This would have to be some complicated function of atom type, occupancy, B factor, resolution, data quality etc to work properly anyway so I doubt that it
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. Switching between interpretations happens all the time as higher resolution data is obtained! Let's say at low resolution you see density apparently for one copy of a side-chain (i.e. the density is not of sufficient resolution to warrant interpreting it as disordered two half side-chains) and you fit that. To keep it simple I'm assuming it's on a general, not a special position. Then you collect high-resolution data and now you see that the same side-chain is disordered. Rephrasing your statement: somewhere in between you or the program has to decide whether you still see one (ordered, with occupancy=1) side-chain or if the data (resolution) warrants such a statement and you switch to the two side-chain (disordered, now with sum occupancy=1) model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. I'm sorry I don't see this discontinuity that you are referring to at all (I think you have forgotten to include the symmetry copy), and I'm certainly not claiming there is any quantum transition. Let's start with a disordered (1/2 occupancy) atom off a 2-fold axis and see what happens to the electron density as it approaches and finally sits on the 2-fold. Here are the electron densities (this would obviously look at lot better graphed - my apologies!): 1 6 10 6 1 * 1 6 10 6 1 Now move the atom closer in steps to the axis so it overlaps more and more with its symmetry copy: * 1 6 10 6 2 6 10 6 1 1 6 10 7 7 10 6 1 1 6 11 12 11 6 1 1 7 16 16 7 1 2 12 20 12 2 * On the final step the fully overlapped atom has twice the occupancy (i.e. 1 instead of 1/2) as the original as evidenced by a peak height of 20 units, compared with 10. In which step did the discontinuity occur? Clearly we could make the steps as small as we like, and you would see a smooth transition from 2 1/2 atoms to 1 whole one. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. I completely agree, both ways of doing it work equally well and it's all down to convention. As I pointed out to Dale, the way I'm describing does work in practice, as evidenced by the fact that CRYSTALS which does it the way I describe, has been doing it this way for the last 40 years. So I can't accept that it can't work in practice when plainly it does! This issue here is purely one of divergence of agreed convention (CIF, mmCIF PDB) and practice. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Jon, try this: http://www.xtl.ox.ac.uk/download.html -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wri...@esrf.fr wrote: On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear Ian, Of course there is no dicontinuity, but you create one the moment you decide that certain symmetry operators no longer apply to certain atoms. Confusion arises e.g. when you download a pdb file of fairly high resolution and find a water molecule with an occupancy of e.g. 0.45 at 0.02 Å from a symmetry axis. Is it a special water suffering from some rounding errors with a total occupancy of 0.45, or a rotationally disordered water (perhaps refined by an overzealous crystallographer) with a combined occupancy of 0.90? This in my eyes unneccessary distinction between special and non-special positions does create confusion and unnecessarily complicates the programming of programs working with coordinates files. If certain refinement program have difficulties with atoms close to symmetry axes, one could always add the approprioate constraints of restraints. Cheers, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 16, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not warrant such a statement and you switch to the one-atom model. Switching between interpretations happens all the time as higher resolution data is obtained! Let's say at low resolution you see density apparently for one copy of a side-chain (i.e. the density is not of sufficient resolution to warrant interpreting it as disordered two half side-chains) and you fit that. To keep it simple I'm assuming it's on a general, not a special position. Then you collect high-resolution data and now you see that the same side-chain is disordered. Rephrasing your statement: somewhere in between you or the program has to decide whether you still see one (ordered, with occupancy=1) side-chain or if the data (resolution) warrants such a statement and you switch to the two side-chain (disordered, now with sum occupancy=1) model. As George Sheldrick confirmed, there is a discontinuous transition between the two, which does not correspond to the physical reality. There is no quantum transition or something when the atom get closer than a certain limit to a crystallographic symmetry element. The atom does not care, its position is just determined by the local force fields and if those force fields have two local minima close together, the atom will be disordered. I'm sorry I don't see this discontinuity that you are referring to at all (I think you have forgotten to include the symmetry copy), and I'm certainly not claiming there is any quantum transition. Let's start with a disordered (1/2 occupancy) atom off a 2-fold axis and see what happens to the electron density as it approaches and finally sits on the 2-fold. Here are the electron densities (this would obviously look at lot better graphed - my apologies!): 1 6 10 6 1 * 1 6 10 6 1 Now move the atom closer in steps to the axis so it overlaps more and more with its symmetry copy: * 1 6 10 6 2 6 10 6 1 1 6 10 7 7 10 6 1 1 6 11 12 11 6 1 1 7 16 16 7 1 2 12 20 12 2 * On the final step the fully overlapped atom has twice the occupancy (i.e. 1 instead of 1/2) as the original as evidenced by a peak height of 20 units, compared with 10. In which step did the discontinuity occur? Clearly we could make the steps as small as we like, and you would see a smooth transition from 2 1/2 atoms to 1 whole one. The decision to switch from a model where the atom is added once with full occupancy to the fourier transform calculation, or whether the atom is added twice with half occupancy is an arbitrary decision, made by the programmer or the user of the program. I completely agree, both ways of doing it work equally well and it's all down to convention. As I pointed out to Dale, the way I'm describing does work in practice, as evidenced by the fact that CRYSTALS which does it the way I describe, has been doing it this way for the last 40 years. So I can't accept that it can't work in practice when plainly it does! This issue here is purely one of divergence of agreed convention (CIF, mmCIF PDB) and practice. Cheers -- Ian
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Ooops sorry that's only the executable, I guess to have to contact David for the source. -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wri...@esrf.fr wrote: On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
[ccp4bb] Postdoctoral position available in Bethesda, Maryland
A postdoctoral position is available immediately at the Department of Biochemistry, Uniformed Services University to perform structural and biochemical research on potential drug target proteins from Mycobacterium tuberculosis. The candidate will be involved in recombinant protein expression and purification, biochemical analysis, and crystal structure determination. Qualified applicants must have a recent Ph.D. degree in biochemistry or a related field, with experience in bacterial protein expression and purification. Prior experience in X-ray crystallography is preferred. Uniformed Services University is located across the street from the National Institute of Health (NIH) campus in Bethesda, Maryland. To apply for the position, please send CV with names and contact information of at least two referees by e-mail to: Shuishu Wang Assistant Professor Department of Biochemistry Uniformed Services University 4301 Jones Bridge Road Bethesda, Maryland 20814 e-mail: shuis...@gmail.com
Re: [ccp4bb] Map Sharpening
On Thu, 2010-12-16 at 03:53 +0100, Raspudin wrote: I hope, am not mixing up different things together. Perhaps you are. Map sharpening (iiuc) is done by applying B-factor-like correction to amplitudes and has only, according to coot manual, an educational value. Meaning that it's great if it helps you to rebuild side chains, but that's all. It has little to do with individual B-factor refinement (which is, btw, definitely informative at 2.85A). -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On Thu, Dec 16, 2010 at 1:18 PM, herman.schreu...@sanofi-aventis.com wrote: Of course there is no dicontinuity, but you create one the moment you decide that certain symmetry operators no longer apply to certain atoms. Change 'atoms' in that statement to 'reflections', or to 'map grid points', then read it again. Does the (-h,k,-l) operator apply to the (0,k,0) reflections or the (-x,y,-z) operator to the grid points (0,y,0)? Do you multiply the intensities of the (0,k,0) reflections or the electron densities of the (0,y,0) points by 0.5 because they are on the axis in order to make it easier to program, or do you decide that will confuse the user, and instead deal with the multiplicity factor internally in the program? Confusion arises e.g. when you download a pdb file of fairly high resolution and find a water molecule with an occupancy of e.g. 0.45 at 0.02 Å from a symmetry axis. Is it a special water suffering from some rounding errors with a total occupancy of 0.45, or a rotationally disordered water (perhaps refined by an overzealous crystallographer) with a combined occupancy of 0.90? For the sake of argument let's say that 0.02 Ang is too big to be rounding error. So if you see that big a shift then the intention of the refinement program (or rather the programmer) which allowed such a value to be appear in the output should be that it's real. If the intention of the user was that the atom is actually on axis then the program should not have allowed such a large shift, since it will be interpreted as 'much bigger than rounding error' and therefore 'significantly off-axis'. Of course even if the intention of the user was that splitting the atom across the 2-fold is meaningful, the user may still have got it wrong if the data doesn't justify splitting the atom like that. The important point is how the program's actions are interpreted by other programs and users - that's why we have conventions. Single precision floating point rounding error is ~ 1 in 10^7, so even if we allow 100 times that with a 100 Ang axis it's still only 0.001 Ang. Despite Dale being able to successful refine a 1/2 atom 0.001 Ang from an axis I don't think he can claim that moving an atom by 0.001 Ang makes any difference above rounding error to the structure factors. If the data can't detect the difference, then the user should not be claiming that there is one, and programs should not allow atoms to be set as close as 0.001 Ang, (or whatever the consensus is a suitable multiple of the rounding error) from an axis: it just makes no sense. You just have to decide what is the smallest realistic shift that the best data could possibly detect under optimal conditions, agree that programs can't set an off-axis shift below that, and set the rounding error test lower than that (say by an order of magnitude for safety). As I said CRYSTALS must do something like this and it has worked fine for the last 40 years on small molecules where clearly the resolution is going to allow you to detect much smaller off-axis shifts than for macromolecules, so the choice of rounding threshold will be even more critical. This in my eyes unneccessary distinction between special and non-special positions does create confusion and unnecessarily complicates the programming of programs working with coordinates files. I suspect the reason that the CIF committee decided that it was necessary to adopt this convention is that it makes transparent the connection between occupancy, the chemical formula and static disorder, i.e. if you see partial occupancy then you know its disordered; occupancy=1 simply and clearly signifies that a whole atom is present. This connection is obfuscated by multiplying by the point multiplicity, which is really just an algorithmic issue for the programmer to deal with internally (exactly as for reflections and map grid points), and shouldn't 'leak out' into the user's domain. It's a very minor complication compared with everything else that goes on in a refinement program. If you're dealing with reflections or maps you still have to program the point multiplicity, you can't avoid it. So it's not as though you have to write additional subroutines specifically for atoms. Cheers -- Ian
[ccp4bb] Fw: Virus alert
- Forwarded Message From: Dean Palmer dpal...@blpmail.org.uk To: Rex Palmer rex.pal...@btinternet.com Sent: Thursday, 16 December, 2010 12:08:20 Subject: FW: Virus alert From: amanda.po...@uk.henkel.com [amanda.po...@uk.henkel.com] Sent: 16 December 2010 10:20 To: dpal...@bucksgfl.org.uk Subject: Fw: Virus alert Dean Please forward this to your dad and anyone else who you feel should know. Amanda Pople HR Administrator, Schwarzkopf Henkel, Aylesbury Tel: 01296 314177 Fax: 01296 433587 Hours of work 0930 to 1430 Monday to Friday - Forwarded by Amanda Pople/UK/EMEA/HENKEL on 16/12/2010 10:18 - Stephen Beazley/UK/EMEA/HENKEL 16/12/2010 10:14 To Carveley Mark, ca...@jackiewilsher.com, pbeaz...@aylesburyvaledc.gov.uk, Aimee Sage/UK/EMEA/hen...@henkel, Alan Bliss/UK/EMEA/hen...@henkel, Alan Bowles/UK/EMEA/hen...@henkel, Alan Hughes/UK/EMEA/hen...@henkel, Alan Jenkins/UK/EMEA/hen...@henkel, Alan Rattenbury/UK/EMEA/hen...@henkel, Alex Salter/UK/EMEA/hen...@henkel, Alicia Preece/UK/EMEA/hen...@henkel, Amanda Obrien/UK/EMEA/hen...@henkel, Amanda Pople/UK/EMEA/hen...@henkel, Amanda Willis/UK/EMEA/hen...@henkel, Angela Holloway/UK/EMEA/hen...@henkel, Anne Andrews/UK/EMEA/hen...@henkel, Anthony Allanson/UK/EMEA/hen...@henkel, Anthony Paola/Ext/UK/EMEA/hen...@henkel, Armando Colucci/UK/EMEA/hen...@henkel, Avril Wright/UK/EMEA/hen...@henkel, Barrie Watson/UK/EMEA/hen...@henkel, Ben Haxworth/UK/EMEA/hen...@henkel, Brendon Thompson/UK/EMEA/hen...@henkel, Brian Cameron/UK/EMEA/hen...@henkel, Brian Haule/Ext/UK/EMEA/hen...@henkel, Brian Sinclair/UK/EMEA/hen...@henkel, Briene Moss/UK/EMEA/hen...@henkel, Camila Lobo-Guerrero/UK/EMEA/hen...@henkel, Carol Flint/UK/EMEA/hen...@henkel, Carole Barker/UK/EMEA/hen...@henkel, Catherine Adams/UK/EMEA/hen...@henkel, Celeste DSouza/UK/EMEA/hen...@henkel, Charles Dunn/UK/EMEA/hen...@henkel, Charlie Cottam/UK/EMEA/hen...@henkel, Charlotte Keohane/UK/EMEA/hen...@henkel, Chris Cameron/UK/EMEA/hen...@henkel, Christopher Hunnings/UK/EMEA/hen...@henkel, Claire Bradley/UK/EMEA/hen...@henkel, Claire Gibbs/UK/EMEA/hen...@henkel, Claire Hayes/UK/EMEA/hen...@henkel, Claire Sherwood-Gee/UK/EMEA/hen...@henkel, Clare Hutchinson/UK/EMEA/hen...@henkel, Colin Sillery/UK/EMEA/hen...@henkel, Collette Mahoney/UK/EMEA/hen...@henkel, Craig Hope/UK/EMEA/hen...@henkel, Daniel Patchett/UK/EMEA/hen...@henkel, Dave J Jackson/UK/EMEA/hen...@henkel, David Wright/Ext/UK/EMEA/hen...@henkel, Debbie Campbell/UK/EMEA/hen...@henkel, Denise Campbell-Kinch/UK/EMEA/hen...@henkel, Eamon Confrey/IE/EMEA/hen...@henkel, Elaine Hart/UK/EMEA/hen...@henkel, Emily Schofield/UK/EMEA/hen...@henkel, Emma Mitchell/UK/EMEA/hen...@henkel, Emma Siddon/Ext/UK/EMEA/hen...@henkel, Erika Feather/UK/EMEA/hen...@henkel, Fiona Ewers/UK/EMEA/hen...@henkel, Fiona Matheson/UK/EMEA/hen...@henkel, Florian Mayr/DE/EMEA/hen...@henkel, Gary Deans/UK/EMEA/hen...@henkel, George Grant/UK/EMEA/hen...@henkel, Gill Angles/UK/EMEA/hen...@henkel, Glenn Kitteridge/UK/EMEA/hen...@henkel, Graham Glover/UK/EMEA/hen...@henkel, Graham Jarvis/UK/EMEA/hen...@henkel, Graham Oakes/UK/EMEA/hen...@henkel, Graham Taylor/UK/EMEA/hen...@henkel, Hardip Jhitta/UK/EMEA/hen...@henkel, Harriet Churchard/UK/EMEA/hen...@henkel, Hayley Barker/UK/EMEA/hen...@henkel, Hayley Barrett/UK/EMEA/hen...@henkel, Heath Donnelly/UK/EMEA/hen...@henkel, Helen Ladd/UK/EMEA/hen...@henkel, Helen Ruiz/UK/EMEA/hen...@henkel, Ian Emett/UK/EMEA/hen...@henkel, Ian Harris/UK/EMEA/hen...@henkel, Jamie Farrar/UK/EMEA/hen...@henkel, Jannine Buck/UK/EMEA/hen...@henkel, Jenny Bettis/UK/EMEA/hen...@henkel, Jereme Driver/UK/EMEA/hen...@henkel, Jerome Wilson/UK/EMEA/hen...@henkel, Jill Jennings/UK/EMEA/hen...@henkel, Jo Thorne/UK/EMEA/hen...@henkel, Joanna Whitley/Ext/UK/EMEA/hen...@henkel, John Arlott/UK/EMEA/hen...@henkel, Jonathan Quail/UK/EMEA/hen...@henkel, Joseph Baron/UK/EMEA/hen...@henkel, Julian Crane/UK/EMEA/hen...@henkel, Julie OConnor/UK/EMEA/hen...@henkel, Karen Thomas/UK/EMEA/hen...@henkel, Katie Swift/UK/EMEA/hen...@henkel, Kay Brady/UK/EMEA/hen...@henkel, Keith Farron/UK/EMEA/hen...@henkel, Kerry Pratt/UK/EMEA/hen...@henkel, Lauren Brickley/UK/EMEA/hen...@henkel, Lee Bradshaw/IE/EMEA/hen...@henkel, Leigh Connolly/UK/EMEA/hen...@henkel, Lena Clinton/UK/EMEA/hen...@henkel, Leon Westerman/UK/EMEA/hen...@henkel, Les Philo/UK/EMEA/hen...@henkel, Lesley Robertson/UK/EMEA/hen...@henkel, Lew Vine/UK/EMEA/hen...@henkel, Linton Husbands/UK/EMEA/hen...@henkel, Lois Aspinall/UK/EMEA/hen...@henkel, Lorna Clelland/UK/EMEA/hen...@henkel, Lorna James/UK/EMEA/hen...@henkel, Louise Hall/UK/EMEA/hen...@henkel, Lucie Craddock/UK/EMEA/hen...@henkel, Lynne Boyce/UK/EMEA/hen...@henkel, Lynne Trueick/UK/EMEA/hen...@henkel, Maggie Davis/UK/EMEA/hen...@henkel, Mandy Keep/Ext/UK/EMEA/hen...@henkel, Mandy Tapping/UK/EMEA/hen...@henkel, Marcus Peacock/UK/EMEA/hen...@henkel, Maria
Re: [ccp4bb] Fw: Virus alert
Well, there are postcard viruses, which is why you should always open e-cards through the company's web site rather than by clicking on the link in the e-mail message. This particular message, however, is a hoax (http://www.snopes.com/computer/virus/postcard.asp). Eric - HUGE VIRUS COMING ! PLEASE READ Hi All, I checked with Norton Anti-Virus, and they are gearing up for this virus! I checked Snopes, and it is for real. Get this E-mail message sent around to your contacts ASAP. PLEASE FORWARD THIS WARNING AMONG FRIENDS, FAMILY AND CONTACTS! You should be alert during the next few days. Do not open any message with an attachment entitled 'POSTCARD FROM HALLMARK,'regardless of who sent it to you. It is a virus which opens A POSTCARD IMAGE, which 'burns' the whole hard disc C of your computer. This virus will be received from someone who has your e-mail address in his/her contact list. This is the reason why you need to send this e-mail to all your contacts. It is better to receive this message 25 times than to receive the virus and open it. If you receive a mail called' POSTCARD,' even though sent to you by a friend, do not open it! Shut down your computer immediately. This is the worst virus announced by CNN. It has been classified by Microsoft as the most destructive virus ever. This virus was discovered by McAfee yesterday, and there is no repair yet for this kind of virus. This virus simply destroys the Zero Sector of the Hard Disc, where the vital information is kept. COPY THIS E-MAIL, AND SEND IT TO YOUR FRIENDS. REMEMBER: IF YOU SEND IT TO THEM, YOU WILL BENEFIT ALL OF US Think before you print - Do you really need to print this e-mail? Worth School, Registered Charity Number 1093914, Company Number 4476558 A company limited by guarantee registered in England and Wales Registered Office: Worth School, Paddockhurst Road, Turners Hill, West Sussex, RH10 4SD Worth Abbey, Registered Charity Number 1093913, Company Number 4475556 A company limited by guarantee registered in England and Wales Registered office: Worth Abbey, Paddockhurst Road, Turners Hill, West Sussex, RH10 4SB -- The opinions expressed are those of the individual and not the school. Internet communications are not secure and therefore the school does not accept legal responsibility for the content of this message. If the reader of this message is not the intended recipient, or the user responsible for delivering this communication to the intended recipient, you are hereby notified that any disclosure, distribution or copying of this communication is strictly prohibited. -- This message contains information from Belfast Health And Social Care Trust which may be privileged and confidential. If you believe you are not the intended recipient any disclosure, distribution or use of the contents is prohibited. If you have received this message in error please notify the sender immediately. This email has been scanned for the presence of computer viruses. Henkel - A Brand Like a Friend www.henkel.com Henkel is a leader with brands and technologies that make people's lives easier, better and more beautiful. This message may contain confidential and/or privileged information. If you are not the intended recipient please do not use its contents for any purpose, advise the sender immediately by reply e-mail and delete this message and any attachments without retaining a copy. The following Henkel Group companies are registered in England Wales at Apollo Court, 2 Bishop Square Business Park, Hatfield, AL10 9EY; Henkel Limited company number 00215496 Henkel Orbseal Limited company number 03304266 For more information about Henkel, please visit www.Henkel.co.uk This email has been scanned for viruses and inappropriate content This email has been sent from the Bucks LEA. If you have cause for complaint regarding the content of this email please contact ab...@bucksgfl.org.uk
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 12/16/10 03:06, Ian Tickle wrote: Dale The reward of the full calculation is that all the complications you describe disappear. An atom that sits 0.001 A from a special position is not unstable in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But there must still be some threshold of distance at which even that fails? Presumably within rounding error? Or are you saying (I assume you aren't!) that you can even refine all co-ordinates of an atom exactly on a special position? Say the x and z co-ordinates of an atom at (0,y,0) in monoclinic? Presumably the atom would have to be given a random push one way or the other (random number generators are generally not a feature of crystallographic refinement programs, with the obvious exception of simulated annealing!)? To be frank, I wrote this code about 15 years ago, it works, and I've not given any thought to atoms on special positions since. I'll have to go back to my notes and code to dig up the exact method. Anyone with a copy of TNT can look up the code. I am, however, not in the least concerned about what happens when an atom falls exactly on a special position because I just don't think that any part of a protein model can be considered exact. If I have a model with two atoms, of occ=1/2 each, sitting 0.0001 A apart - it fits the density and I think everyone knows what that model means, or at least they should. If you decide to shove them each 0.5 A and call them a single atom with occ=1, your model will fit the density just as well and I have no problem with that either. By the way, the refinement issue has nothing to do with special positions. The instability you observe occurs any time you build two atoms into the same bit of density. If your model has two atoms, at a general position, with exactly the same coordinates the Normal matrix will have a singularity. The problem doesn't come up much because we normally choose not to build such models. It can be an issue in models with disorder where different conformations interpenetrate each other but the stereochemical restraints usually come to the rescue then. ? I always avoid programing tests of a == b for real numbers because the round-off errors will always bite you at some point. This means that a test of an atom exactly on a special position can't be done reliably in floating point math. Obviously common sense has to be applied here and tests for strict floating-point equality studiously avoided. But this is very easily remedied, my optimisation programs are full of tests like IF(ABS(X-Y).LT.1E-6) THEN ... and I'm certain so are yours (assuming of course you still program in Fortran!). This implies that in the case that an atom is off-axis and disordered you have to take care not to place it within say a few multiples of rounding error of the axis, since then it might be indeed be confused with one 'on' the special position. However if someone claims that an atom sits within say 10*rounding error of an axis as distinct from being on the axis, then a) there's no way that can be proved, and b) it would be indistinguishable from being on the s.p. and the difference in terms of structure factors and maps would be insignificant anyway, so it may as well be on-axis. If the difference is insignificant, it may as well be off-axis. I guess if the difference is insignificant it just comes down to personal preferences. Dale Tronrud I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. Your preferred assumption is that any atom near enough to a special position is really on the special position and should have an occupancy of one. My assumption is that no atom is every EXACTLY on the special position and if they are close enough to their symmetry image to forbid coexistence the occupancy should be 1/n. I think either assumption is reasonable but, of course, prefer mine for what I consider practical reasons. It helps that I have to code to make mine work. Whichever way it's done is only a matter of convention (clearly both ways work just as well), however I would reiterate that my main concern here is that convention and practice appear to have parted company in this particular instance! Cheers -- IAn
Re: [ccp4bb] Cys auxotroph
For those interested in our paper using non-auxotroph strains for SE-Cys labelling, it's now published: http://journals.iucr.org/d/issues/2011/01/00/dz5216/index.html http://journals.iucr.org/d/issues/2011/01/00/dz5216/index.htmlPlease cite this reference if you use our method in the future. Best regards Paula On 20 October 2010 12:00, Paula Salgado p.salg...@imperial.ac.uk wrote: We are still waiting for proofs, so it might be a few weeks before its published. If anyone is interested, please email me requesting a preview version. Paula PS: Francois, we did cite and used your work as starting point. On 20 October 2010 10:39, francois@cbs.cnrs.fr francois@cbs.cnrs.fr wrote: Hi Paula Also our publication: http://www.ncbi.nlm.nih.gov/pubmed/14604526 We can provide you the Cys-auxotroph strain of E. coli Francois === Francois Hoh, PhD CBS Phone : (33) 4 67 41 77 06 29 rue de Navacelles Fax : (33) 4 67 41 79 13 34090 MONTPELLIER francois@cbs.cnrs.fr France www.cbs.cnrs.fr I would also try non-auxotrophic strains. We have recently had successful double SeCys + SeMet using BL21. Paper has just been accepted in Acta D, should be published soon. Paula On 18 October 2010 16:05, Yogesh Gupta yogesh.gupt...@gmail.com wrote: Does anyone know a commercial source of Cys-auxotroph strain of E. coli to prepare a doubly (Se-Cys + Se-Met) labeled protein? I would appreciate if you can share your experience if you have labeled your protein in this way to improve Se signal for phasing. Thanks, -Yogesh -- -- Yogesh K. Gupta, Ph.D. Dept of Structural Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute 1 Gustave L. Levy Place, Box 1677 New York, NY, USA 10029 Tel:+1 212-659-8639 --
[ccp4bb] Please apply for RapiData 2011, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 12/16/10 06:47, Ian Tickle wrote: For the sake of argument let's say that 0.02 Ang is too big to be rounding error. So if you see that big a shift then the intention of the refinement program (or rather the programmer) which allowed such a value to be appear in the output should be that it's real. If the intention of the user was that the atom is actually on axis then the program should not have allowed such a large shift, since it will be interpreted as 'much bigger than rounding error' and therefore 'significantly off-axis'. I would certainly hope that no one believes that the precision of the parameters in a PDB file are significant to the level of round-off error! It's bad enough that a small number of people take the three decimal points of precision in the PDB file seriously. When a person places an atom in a model they aren't stating a believe that that is the EXACT location of the atom, only that they believe the center of the locus of all equivalent atoms in the crystal falls near that spot. If it's 0.02 A from a special position (and the SU of the position is larger than that) then it might be on the special position and it might not. If I come across one of your models and you have an atom exactly on a special position (assuming you're able to do that with three decimal points in a PDB file) I'd still assume that you only intend that there is an atom in the vicinity of that point and it might be exactly on the axis but it might be a little off. All structural models are fuzzy. Dale Tronrud
[ccp4bb] Coot 0.6.2 CRYST1 problems ?
Dear BB, I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot 0.6.2-pre-1 (revision 3290) [with guile 1.8.7 embedded] [with python 2.7.1 embedded] and found out that I can not display any symmetry related molecules anymore. Coot complains about a problem in the CRYST card. Is this a feature or a know bug ? Any help Paul ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/
