Re: [ccp4bb] Question about TEV cleavage
We've been using the S219V mutant for cleaving out tags. We usually do our cleavage reactions in an overnight dialysis after a Ni-column into 50mM Tris, 100-200 mM NaCl, 5 mM BME at 4C. I've never found problems with losing any protein in the reaction and recover usually 90% of the protein after passing through the column a second time to remove the tag and protease. Feel free to contact me if you have any questions. Best of luck, Peter
Re: [ccp4bb] Question about GST cleavage
Agitation can cause denaturation of proteins resulting in loss of activity, precipitation and even cross-beta amyloid fibre growth. Partial unfolding will probably make most proteins more protease sensitive. Alun. On 31/03/2011 20:41, gauri misra wrote: Just an offshoot of the same Question.. I would like to ask whether the same applies for GST-tag digestion using thrombin.. No agitation gives better results in the above case too... Any personal experiences On Thu, Mar 31, 2011 at 11:29 AM, Klaus Piontek klaus.pion...@ocbc.uni-freiburg.de mailto:klaus.pion...@ocbc.uni-freiburg.de wrote: And not at full moon! Klaus Am 31.03.2011 um 16:23 schrieb Xiaopeng Hu: Our experience is do not shake the tube during TEV cleavage,I dont know why, but it does help. xiaopeng Dr. Klaus Piontek Albert-Ludwigs-University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 tel:%2B%2B49-761-203-6036 Fax: ++49-761-203-8714 tel:%2B%2B49-761-203-8714 Email: klaus.pion...@ocbc.uni-freiburg.de mailto:klaus.pion...@ocbc.uni-freiburg.de Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/ -- Alun R. Coker Centre for Amyloidosis and Acute Phase Proteins Division of Medicine (Royal Free Campus) University College London Rowland Hill Street London NW32PF Tel: +44(0)20 7433 2764 Fax: +44(0)20 7433 2776
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Hi Ethan, Awsome progress! Really, I looked for other options like such. 2011 will be a good year for crystallography. I should implement this in PDB_REDO. Cheers, Robbie Date: Thu, 31 Mar 2011 23:06:47 -0700 From: merr...@u.washington.edu Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of our models, especially on the title pages of the electronic versions of journals. There could even be a special July-14th-mode (http://de.wikipedia.org/w/index.php?title=Datei:DESYNebelkammer.jpgfiletimestamp=20090223134909). Cheers, Tim On Fri, Apr 01, 2011 at 11:15:36AM +0200, Flip Hoedemaeker wrote: Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- -- 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
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
I'm pretty sure Coot has been displaying it all along. In the early days it displayed it much better, I must say, which is why it tended to crash. Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of our models, especially on the title pages of the electronic versions of journals. There could even be a special July-14th-mode (http://de.wikipedia.org/w/index.php?title=Datei:DESYNebelkammer.jpgfiletimestamp=20090223134909). Cheers, Tim On Fri, Apr 01, 2011 at 11:15:36AM +0200, Flip Hoedemaeker wrote: Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter
Re: [ccp4bb] xds question: inverse beam, lots of wedges
Hi I'd just process it in iMosflm, and run the Quickscale task after integration. With almost no effort you should get a rapid visual indicator (in the graphs produced by Scala) of the discontinuities between the wedges. If the discontinuities are too big, then you might encounter some items of interest during the integration stage... On 31 Mar 2011, at 23:08, Patrick Loll wrote: We've just collected a number of inverse beam data sets. It turns out the crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg for each crystal, broken up into 30 deg wedges. The collection order went like this: 0-30 deg, 180-210, 30-60, 210-240, etc. Now, assuming no slippage, I could simply integrate the first set of data (non-inverse?) in one run: 0-360 deg. However, since the 12 individual wedges making up this 360 deg sweep were not collected immediately one after the other, I don't expect the scale factors for individual images to vary smoothly (there should be discontinuities at the boundaries between wedges). If I do integrate the data in one fell swoop, am I in danger of introducing errors? For example, I seem to recall that denzo had built-in restraints to ensure that scale factors for adjacent images didn't vary by too much. Is there a similar restraint that in XDS that I might run afoul of? The alternative is to integrate each each wedge separately, but with 24 wedges per xtal, this is starting to look a little tedious. Cheers, Pat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Have you noticed the date ? It's April 1! At 10:31 01-04-2011, Frank von Delft wrote: I'm pretty sure Coot has been displaying it all along. In the early days it displayed it much better, I must say, which is why it tended to crash. Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of our models, especially on the title pages of the electronic versions of journals. There could even be a special July-14th-mode (http://de.wikipedia.org/w/index.php?title=Datei:DESYNebelkammer.jpgfiletimestamp=20090223134909). Cheers, Tim On Fri, Apr 01, 2011 at 11:15:36AM +0200, Flip Hoedemaeker wrote: Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Well played, Ethan! At 07:06 01-04-2011, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
Re: [ccp4bb] problem of conventions
On Fri, Apr 1, 2011 at 5:30 AM, Santarsiero, Bernard D. b...@uic.edu wrote: Ian, I think it's amazing that we can program computers to resolve a b c but it would be a major undertaking to store the matrix transformations for 22121 to 21212 and reindex a cell to a standard setting. I think you misunderstood the point I was making. Multiply your one by the several hundred datasets we sometimes collect for the various clones and crystallisation conditions needed to optimise the crystal form for soaking - that's what I mean by 'major undertaking'. As I explained all the datasets collected for a given crystal form have to be indexed the same way (even if only for archival purposes) before we can store them in the database (otherwise we would end up in an awful muddle!). I don't have a batch script to filter all the relevant datasets from the database, re-index each one (that's the easy part!), and re-register them all as a new crystal form. Why should I? - no-one has given me a cogent reason to re-index them in the first place which would justify the resulting downtime of the project (OK call me lazy!). I hope you see that doing each one manually is a non-starter: the project would have to be locked during the period of the operation so no new datasets could be down- or uploaded (which would further cause the upstream pipeline to backup). Operations that appear trivial when you only have to do them once suddenly become big problems when they have to be performed on an industrial scale! I was also told that I was lazy to not reindex to the standard setting when I was a grad student. Now it takes less than a minute to enter a transformation and re-index. They told you wrong! The conventional cell is the convention (by definition!), and the standard setting doesn't always correspond to the conventional cell (though in most cases it does). There's a reason for the distinction between meanings of 'standard' and 'conventional' - the meanings are very precise and non-interchangeable. The orthorhombic rule of a b c makes sense in 222 or 212121, but when there is a standard setting of the 2-fold along the c-axis, then why not adopt that? As I explained, sometimes we don't know the true space group (in terms of assigning the screw axes) until further along the pipeline (e.g. after MR or refinement), or at least it's always safer to be non-committal beyond P222 - why commit oneself to an irrevocable decision before it's absolutely necessary? You don't need to know the exact space group just to screen crystals for diffracting power! Adopting the standard setting would in the particular case of SGs 5, 17 18 require later re-indexing I hope you see why for us that's a non-starter. I'm not a believer in conventions for their own sake - a convention is merely a default set of rules which you apply when you have no sound basis on which to make a choice - the convention makes what is effectively a totally arbitrary choice for you. Conventions do have the advantage that if other people follow them then they will make the same decisions as you. The moment I have sufficient justification (e.g. as I said isomorphism overrides convention) to break with convention then I would have no hesitation in doing so. The fact that the standard setting has a 2-fold along c is merely an arbitrary choice and doesn't seem to me to be a good enough reason to break with the unit-cell convention. -- Ian On Thu, March 31, 2011 5:48 pm, Ian Tickle wrote: On Thu, Mar 31, 2011 at 10:43 PM, James Holton jmhol...@lbl.gov wrote: I have the 2002 edition, and indeed it only contains space group numbers up to 230. The page numbers quoted by Ian contain space group numbers 17 and 18. You need to distinguish the 'IT space group number' which indeed goes up to 230 (i.e. the number of unique settings), from the 'CCP4 space group number' which, peculiar to CCP4 (which is why I called it 'CCP4-ese'), adds a multiple of 1000 to get a unique number for the alternate settings as used in the API. The page I mentioned show the diagrams for IT SG #18 P22121 (CCP4 #3018), P21221 (CCP4 #2018) and P21212 (CCP4 #18), so they certainly are all there! Although I am all for program authors building in support for the screwy orthorhombics (as I call them), I should admit that my fuddy-duddy strategy for dealing with them remains simply to use space groups 17 and 18, and permute the cell edges around with REINDEX to put the unique (screw or non-screw) axis on the c position. Re-indexing is not an option for us (indeed if there were no alternative, it would be a major undertaking), because the integrity of our LIMS database requires that all protein-ligand structures from the same target crystal form are indexed with the same (or nearly the same) cell and space group (and it makes life so much easier!). With space-groups such as P22121 it can happen (indeed it has happened) that it was not possible to define the
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
The program appears a bit black-box to me, could you provide more details (today of course). Mark Sent from my HTC - Reply message - From: Robbie Joosten robbie_joos...@hotmail.com Date: Fri, Apr 1, 2011 11:04 Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi Ethan, Awsome progress! Really, I looked for other options like such. 2011 will be a good year for crystallography. I should implement this in PDB_REDO. Cheers, Robbie Date: Thu, 31 Mar 2011 23:06:47 -0700 From: merr...@u.washington.edu Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
[ccp4bb] problem of conventions
Excuse my naive (perhaps ignorant) question: when was the abc rule/convention/standard/whatever introduced? None of the textbooks I came across mentions it as far as I could see (not that this is reason for or against this rule of course). Thanks, Boaz 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] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
Hi Frank, I described in the previous e-mail the probabilistic interpretation of B-factors. In the case of very high uncertainty = poorly ordered side chains, I prefer to deposit the conformer representing maximum a posteriori, even if it does not represent all possible conformations. Maximum a posteriori will have significant contribution from the most probable conformation of side chain (prior knowledge) and should not conflict with likelihood (electron density map). Thus, in practice I model the most probable conformation as long as it it in even very weak electron density, does not overlap significantly with negative difference electron density and do not clash with other residues. If it's probability you're after, if there's no density to guide you (very common!) you'd have to place all likely rotamers that don't clash with anything, and set their occupancies to their probability (as encoded in the rotamer library). Which library? The one for all side chains of a specific type, or the one for a specific type with a given backbone conformation? These are quite different and change with the content of the PDB. 'Hacking' the occupancies is risky bussiness in general: errors are made quite easily. I frequently encounter side chains with partial occupancies but no alternatives, how can I relate this to the experimental date? Even worse, I also see cases where the occupancies of alternates sum up to values 1.00. What does that mean? Is that a local increase of DarmMatter accidentally encoded in the occupancy? This is now veering into data-free protein modeling territory... wasn't the idea to present to the downstream user an atomic representation of what the electron density shows us? Yes, but what we see can be deceiving. Worse, what we're also doing is encoding multiple different things in one place - what database people call poorly normalised, i.e. to understand a data field requires further parsing and if statements. In this case: to know whether there was no density, as end-user I'd have to have to second-guess what exactly those high-B-factor-variable-occupancy atoms mean. Until the PDB is expanded, the conventions need to be clear, and I thought they were: High B-factor == means atom is there but density is weak Atom missing == no density to support it. Unfortunately, it is not trivial to decide when there is 'no density'. We must have a good metric to do this, but I don't think it exists yet. Removing atoms is thus very subjective. This explaines why I frequently find positive difference density peaks near missing side chains. Leaving side chains in sometimes gives negative difference density but refining them with proper B-factor restrainsts reduces the problem a lot. There is still the problem of radiation damage, but that is relatively small. At least refining the B-factor is more reproducible and less subjective than making the binary choice to keep or remove an atom. Cheers, Robbie Oh well... phx.
Re: [ccp4bb] what to do with disordered side chains
Dear Gerard, I agree with you based on debates at some conferences. But, based on what I have seen here so far, it seems to me that everybody knows exactly what to do with disordered side chains. People that want to build structures to best fit the data tend to prefer omitting disordered side chains. On the other hand, people that want to build structures to best represent reality tend to prefer building them. I don't see any disagreement here nor do I see any problems with either approach. Different people collect the same data to study different things and I feel that they are entitle to view and interpret the data the way that they fine most meaningful. Equations are attempts to describe reality, I don't see why we should constrain reality to fit equations. Cheers, Quyen On Mar 31, 2011, at 12:21 PM, Gerard Bricogne wrote: Dear Quyen, On Thu, Mar 31, 2011 at 11:27:58AM -0400, Quyen Hoang wrote: Thank you for your post, Herman. Since there is no holy bible to provide guidance, perhaps we should hold off the idea of electing a powerful dictator to enforce this? - at least until we all can come to a consensus on how the dictator should dictate... ... but that might well be even harder than to decide what to do with disordered side chains ... . With best wishes, Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === On Mar 31, 2011, at 10:22 AM, herman.schreu...@sanofi-aventis.com wrote: Dear Quyen, I am afraid you won't get any better answers than you got so far. There is no holy bible telling you what to do with disordered side chains. I fully agree with James that you should try to get the best possible model, which best explains your data and that will be your decision. Here are my 2 cents: -If you see alternative positions, you have to build them. -If you do not see alternative positions, I would not replace one fantasy (some call it most likely) orientation with 2 or 3 fantasy orientations. -I personally belong to the let the B-factors take care of it camp, but that is my personal opinion. Leaving side chains out could lead to misinterpretations by slightly less savy users of our data, especially when charge distributions are being studied. Besides, we know (almost) for sure that the side chain is there, it is only disordered and as we just learned, even slightly less savy users know what flaming red side chains mean. Even if they may not be mathematically entirely correct, huge B-factors clearly indicate that there is disorder involved. -I would not let occupancies take up the slack since even very savy users have never heard of them and again, the side chain is fully occupied, only disordered. Of course if you build alternate positions, you have to divede the occupancies amongst them. Best, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Quyen Hoang Sent: Thursday, March 31, 2011 3:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what to do with disordered side chains We are getting off topic a little bit. Original topic: is it better to not build disordered sidechains or build them and let B-factors take care of it? Ed's poll got almost a 50:50 split. Question still unanswered. Second topic introduced by Pavel: Your B-factors are valid within a harmonic (small) approximation of atomic vibrations. Larger scale motions you are talking about go beyond the harmonic approximation, and using the B-factor to model them is abusing the corresponding mathematical model. And that these large scale motions (disorders) are better represented by alternative conformations and associated with them occupancies. My question is, how many people here do this? If you're currently doing what Pavel suggested here, how do you decide where to keep the upper limit of B-factors and what the occupancies are for each atom (data with resolution of 2.0A or worse)? I mean, do you cap the B-factor at a reasonable number to represent natural atomic vibrations (which is very small as Pavel pointed out) and then let the occupancies pick up the slack? More importantly, what is your reason for doing this? Cheers and thanks for your contribution, Quyen On Mar 30, 2011, at 5:20 PM, Pavel Afonine wrote: Mark, alternative conformations and associated with them occupancies
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
Hi Robbie If it's probability you're after, if there's no density to guide you (very common!) you'd have to place all likely rotamers that don't clash with anything, and set their occupancies to their probability (as encoded in the rotamer library). Which library? The one for all side chains of a specific type, or the one for a specific type with a given backbone conformation? These are quite different and change with the content of the PDB. 'Hacking' the occupancies is risky bussiness in general: errors are made quite easily. I frequently encounter side chains with partial occupancies but no alternatives, how can I relate this to the experimental date? Even worse, I also see cases where the occupancies of alternates sum up to values 1.00. What does that mean? Is that a local increase of DarmMatter accidentally encoded in the occupancy? Actually, I wasn't advocating it - I was taking ZO's suggestion to it's logical conclusion to point out the problem, namely deciding what is most likely. This you underline with your (very valid) question. Until the PDB is expanded, the conventions need to be clear, and I thought they were: High B-factor == means atom is there but density is weak Atom missing == no density to support it. Unfortunately, it is not trivial to decide when there is 'no density'. We must have a good metric to do this, but I don't think it exists yet. Removing atoms is thus very subjective. This explaines why I frequently find positive difference density peaks near missing side chains. Leaving side chains in sometimes gives negative difference density but refining them with proper B-factor restrainsts reduces the problem a lot. There is still the problem of radiation damage, but that is relatively small. At least refining the B-factor is more reproducible and less subjective than making the binary choice to keep or remove an atom. (Radiation damage is NOT a relatively small problem.) The fundamental problem remains: we're cramming too many meanings into one number. This the PDB could indeed solve, by giving us another column. (He said airily, blithely launching a totally new flame war.) phx.
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
I assume TLS is supported or do we have to wait for version 1.1 ? When will you have a 10.7 (lion) standalone version compiled ? 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 Apr 1, 2011, at 2:06, Ethan Merritt merr...@u.washington.edu wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
Re: [ccp4bb] xds question: inverse beam, lots of wedges
On 03/31/11 18:08, Patrick Loll wrote: We've just collected a number of inverse beam data sets. It turns out the crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg for each crystal, broken up into 30 deg wedges. The collection order went like this: 0-30 deg, 180-210, 30-60, 210-240, etc. Now, assuming no slippage, I could simply integrate the first set of data (non-inverse?) in one run: 0-360 deg. However, since the 12 individual wedges making up this 360 deg sweep were not collected immediately one after the other, I don't expect the scale factors for individual images to vary smoothly (there should be discontinuities at the boundaries between wedges). So? Isn't that the purpose of scale factors? -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Hi Ethan, many thanks for that - your Dark Matter really (en)lightened my day! I wonder, how many pdb records in the future will contain the corresponding remark lines that your incredible perl script produces :-) Best regards, Dirk. Am 01.04.11 08:06, schrieb Ethan Merritt: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- *** 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 ***
Re: [ccp4bb] problem of conventions
Dear Boaz, I think you are the one who is finally asking the essential question. The classification we all know about, which goes back to the 19th century, is not into 230 space groups, but 230 space-group *types*, i.e. classes where every form of equivalencing (esp. by choice of setting) has been applied to the enumeration of the classes and the choice of a unique representative for each of them. This process of maximum reduction leaves very little room for the introducing conventions like a certain ordering of the lengths of cell parameters. This seems to me to be a major mess-up in the field - a sort of second-hand mathematics by (IUCr) committee which has remained so ill-understood as to generate all these confusions. The work on the derivation of the classes of 4-dimensional space groups explained the steps of this classification beautifully (arithmetic classes - extension by non-primitive translations - equivalencing under the action of the normaliser), the last step being the choice of a privileged setting *in termns of the group itself* in choosing the representative of each class. The extra convention abc leads to choosing that representative in a way that depends on the metric properties of the sample instead of once and for all (how about that for a brilliant step backward!). Software providers then have to de-standardise the set of 230 space group *types* (where each representative is uniquely defined once you give the space group (*type*) number) to accommodate all alternative choices of settings that might be randomly thrown at them by the metric properties of e.g. everyone's orthorhombic crystals. Mathematically, what one then needs to return to is the step before taking out the action of the normaliser, but this picture gets drowned in clerical disputes about low-level software issues. My own take on this (when I was writing symmetry-reduction routines for my NCS-averaging programs, along with space-group specific FFT routines in the dark ages) was: once you have a complete mathematical classification that is engraved in stone (i.e. in the old International Tables and in crystallographic software as we knew it), then stick to it and re-index back and forth to/from the unique representative listed under the IT number, as needed - don't try and extend group-theoretic Tables to re-introduce incidental metrical properties that had been so neatly factored out from the final symmetry picture. Otherwise you get a dog's dinner. So much for my 0.02 Euro. With best wishes, Gerard. -- On Fri, Apr 01, 2011 at 11:30:12AM +, Boaz Shaanan wrote: Excuse my naive (perhaps ignorant) question: when was the abc rule/convention/standard/whatever introduced? None of the textbooks I came across mentions it as far as I could see (not that this is reason for or against this rule of course). Thanks, Boaz 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 -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Do you have a list of dark-matter-aware PDB refinement programs? Adding dark matter and refining in TNT or Xplor gives me exactly the same R as without. Furthermore the final refined files have lost the dark matter as far as I can see. This leads me to believe these programs are completely ignoring the dark matter. Ed Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Oh, that is where those pesky inhibitors I couldn't find were hiding... On Thu, 2011-03-31 at 23:06 -0700, Ethan Merritt wrote: Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] SFCHECK produces incomplete postscript
Dear all, I have been trying to compare a model that I'm refining against the native SFs using SFCHECK. SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps files), but produces a postscript file with only the first page of output (and it is mostly blank). There is the typical light-grey panels on a dark-grey background format that I'm used to for SFCHECK postscript files, but there are no figures or data. Also, my mouse icon indicates it is hung trying to load/read the file (i.e. it's a moving busy icon under Linux). I've tried other postscript viewers without luck. I can successfully run SFCHECK on a completely different model/MTZ pair without problem though. So does anyone know of circumstances that would lead to a hung postscript file from SFCHECK? Thanks for your help, -Andy
Re: [ccp4bb] problem of conventions
Dear Gerard,
The theory's fine as long as the space group can be unambiguously
determined from the diffraction pattern. However practice is
frequently just like the ugly fact that destroys the beautiful theory,
which means that a decision on the choice of unit cell may have to be
made on the basis of incomplete or imperfect information (i.e.
mis-identification of the systematic absences). The 'conservative'
choice (particularly if it's not necessary to make a choice at that
time!) is to choose the space group without screw axes (i.e. P222 for
orthorhombic). Then if it turns out later that you were wrong it's
easy to throw away the systematic absences and change the space group
symbol. If you make any other choice and it turns out you were wrong
you might find it hard sometime later to recover the reflections you
threw away! This of course implies that the unit-cell choice
automatically conforms to the IT convention; this convention is of
course completely arbitrary but you have to make a choice and that one
is as good as any.
So at that point lets say this is the 1970s and you know it might be
several years before your graduate student is able to collect the
high-res data and do the model-building and refinement, so you publish
the unit cell and tentative space group, and everyone starts making
use of your data. Some years later the structure solution and
refinement is completed and the space group can now be assigned
unambiguously. The question is do you then revise your previous
choice of unit cell risking the possibility of confusing everyone
including yourself, just in order that the space-group setting
complies with a completely arbitrary 'standard' (and the unit cell
non-conventional), and requiring a re-index of your data (and
permutation of the co-ordinate datasets). Or do you stick with the IT
unit cell convention and leave it as it is? For me the choice is easy
('if it ain't broke then don't fix it!').
Cheers
-- Ian
On Fri, Apr 1, 2011 at 1:40 PM, Gerard Bricogne g...@globalphasing.com wrote:
Dear Boaz,
I think you are the one who is finally asking the essential question.
The classification we all know about, which goes back to the 19th
century, is not into 230 space groups, but 230 space-group *types*, i.e.
classes where every form of equivalencing (esp. by choice of setting) has
been applied to the enumeration of the classes and the choice of a unique
representative for each of them. This process of maximum reduction leaves
very little room for the introducing conventions like a certain ordering
of the lengths of cell parameters. This seems to me to be a major mess-up in
the field - a sort of second-hand mathematics by (IUCr) committee which
has remained so ill-understood as to generate all these confusions. The work
on the derivation of the classes of 4-dimensional space groups explained the
steps of this classification beautifully (arithmetic classes - extension by
non-primitive translations - equivalencing under the action of the
normaliser), the last step being the choice of a privileged setting *in
termns of the group itself* in choosing the representative of each class.
The extra convention abc leads to choosing that representative in a way
that depends on the metric properties of the sample instead of once and for
all (how about that for a brilliant step backward!). Software providers then
have to de-standardise the set of 230 space group *types* (where each
representative is uniquely defined once you give the space group (*type*)
number) to accommodate all alternative choices of settings that might be
randomly thrown at them by the metric properties of e.g. everyone's
orthorhombic crystals. Mathematically, what one then needs to return to is
the step before taking out the action of the normaliser, but this picture
gets drowned in clerical disputes about low-level software issues.
My own take on this (when I was writing symmetry-reduction routines for
my NCS-averaging programs, along with space-group specific FFT routines in
the dark ages) was: once you have a complete mathematical classification
that is engraved in stone (i.e. in the old International Tables and in
crystallographic software as we knew it), then stick to it and re-index back
and forth to/from the unique representative listed under the IT number, as
needed - don't try and extend group-theoretic Tables to re-introduce
incidental metrical properties that had been so neatly factored out from the
final symmetry picture. Otherwise you get a dog's dinner.
So much for my 0.02 Euro.
With best wishes,
Gerard.
--
On Fri, Apr 01, 2011 at 11:30:12AM +, Boaz Shaanan wrote:
Excuse my naive (perhaps ignorant) question: when was the
abc rule/convention/standard/whatever introduced? None of the
textbooks I came across mentions it as far as I could see (not that this is
reason for or against this rule of course).
Thanks,
[ccp4bb] early (incomplete model) refinement if you had the location of a bound (highly occupied) anomalous scatterer
Hi all, could you use its position in real space as a target for (to make it easy, rigid body) refinement? Real space meaning the electron density around the scatterer in an anomalous LLG map. Some other restraints: Say it's a metal cofactor and you know that it needs to be in a specific position with respect to your protein. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER some CRYSTALS with my on-board TNT into XPOWDER? I am still trying to GRASP the idea of AUTODOCKing on precise HKL locations based on the SHARP but CONVX images produced by CRYSTAL STUDIO. Quyen On Apr 1, 2011, at 2:06 AM, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
Re: [ccp4bb] problem of conventions
Dear Ian,
Well, it *IS* broke. If you are running some type of process, as you
implied in referring to LIMS, then there is a step in which you move from
the crystal system and point group to the actual space group. So, at that
point you identify P22121. The next clear step, automatically by software,
is to convert to P21212, and move on. That doesn't take an enormous amount
of code writing, and you have a clear trail on how you got there.
To be even more intrusive, what if you had cell parameters of 51.100,
51.101, and 51.102, and it's orthorhombic, P21212. For other co-crystals,
soaks, mutants, etc., you might have both experimental errors and real
differences in the unit cell, so you're telling me that you would process
according to the a b c rule in P222 to average and scale, and then it
might turn out to be P22121, P21221, or P21212 later on? When you wish to
compare coordinates, then you have re-assign one coordinate data to match
the other by using superposition, rather than taking on an earlier step of
just using the conventional space group of P21212?
Again, while I see use of the a b c rule when there isn't an
overriding reason to assign it otherwise, as in P222 or P212121, there
*is* a reason to stick to the convention of one standard setting. That's
the rationale on using P21/n sometimes vs. P21/c, or I2 vs C2, to avoid a
large beta angle, and adopt a non-standard setting.
Finally, if you think it's fine to use P22121, then can I assume that you
also allow the use of space group A2 and B2?
Bernie
Bernie
On Fri, April 1, 2011 8:46 am, Ian Tickle wrote:
Dear Gerard,
The theory's fine as long as the space group can be unambiguously
determined from the diffraction pattern. However practice is
frequently just like the ugly fact that destroys the beautiful theory,
which means that a decision on the choice of unit cell may have to be
made on the basis of incomplete or imperfect information (i.e.
mis-identification of the systematic absences). The 'conservative'
choice (particularly if it's not necessary to make a choice at that
time!) is to choose the space group without screw axes (i.e. P222 for
orthorhombic). Then if it turns out later that you were wrong it's
easy to throw away the systematic absences and change the space group
symbol. If you make any other choice and it turns out you were wrong
you might find it hard sometime later to recover the reflections you
threw away! This of course implies that the unit-cell choice
automatically conforms to the IT convention; this convention is of
course completely arbitrary but you have to make a choice and that one
is as good as any.
So at that point lets say this is the 1970s and you know it might be
several years before your graduate student is able to collect the
high-res data and do the model-building and refinement, so you publish
the unit cell and tentative space group, and everyone starts making
use of your data. Some years later the structure solution and
refinement is completed and the space group can now be assigned
unambiguously. The question is do you then revise your previous
choice of unit cell risking the possibility of confusing everyone
including yourself, just in order that the space-group setting
complies with a completely arbitrary 'standard' (and the unit cell
non-conventional), and requiring a re-index of your data (and
permutation of the co-ordinate datasets). Or do you stick with the IT
unit cell convention and leave it as it is? For me the choice is easy
('if it ain't broke then don't fix it!').
Cheers
-- Ian
On Fri, Apr 1, 2011 at 1:40 PM, Gerard Bricogne g...@globalphasing.com
wrote:
Dear Boaz,
  I think you are the one who is finally asking the essential
question.
  The classification we all know about, which goes back to the 19th
century, is not into 230 space groups, but 230 space-group *types*, i.e.
classes where every form of equivalencing (esp. by choice of setting)
has
been applied to the enumeration of the classes and the choice of a
unique
representative for each of them. This process of maximum reduction
leaves
very little room for the introducing conventions like a certain
ordering
of the lengths of cell parameters. This seems to me to be a major
mess-up in
the field - a sort of second-hand mathematics by (IUCr) committee
which
has remained so ill-understood as to generate all these confusions. The
work
on the derivation of the classes of 4-dimensional space groups explained
the
steps of this classification beautifully (arithmetic classes -
extension by
non-primitive translations - equivalencing under the action of the
normaliser), the last step being the choice of a privileged setting *in
termns of the group itself* in choosing the representative of each
class.
The extra convention abc leads to choosing that representative in a
way
that depends on the metric properties of the sample instead of once and
for
all
[ccp4bb] Disordered sidechains - a statement by the revolutionary non-dictator
People of the disordered sidechains, ave! - perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along these lines? And oblige us all to follow them? (Mark J van Raaij) - this discussion has flared up many times in the past, and maybe it's time for a powerful dictator at the PDB to create the law... (Filip Van Petegem) - Also, who should decide on the magic number: the all-knowing gurus at the protein data bank? Maybe we should really start using cif files (Herman Schreuder) - In response to recent calls for me to act as a crystallographic dictator to decide how disordered sidechains should be treated, I would like to issue the following abridged statement: I salute you - The youth of victory, People of the disordered sidechains, People of challenge, Youth of challenge, They are a generation of disorder and challenge. I salute you. You present the world the true pictures of the crystallographic community. You present the truth that the agents and cowards are trying to distort, to cover, to give a wrong picture of you before the world. Some CCP4BB readers are betraying you and depicting you as a bad people: Look at crystallographers, look at crystallographers! Crystallographers don't want victory. They don't want revolution. They want sidechains with high B-values. Crystallographers want occupancies. But here in Parkers Piece they want. Crystallography is leading continents, Africa, Asia and South America. Victory to the people of crystallography. And this is being pointed at the crystallographers. They want no identification, identity when they say to people, crystallography in PDB. When they say crystallography, Revolution, crystallography, Gerard, all X-ray generators consider us, as the mecca, rulers of the world, even the superpowers, they want to converge on Cambridge, on Uppsala. They give their insults of you in crystallographic bulletin boards, they want to insult you. We want to retrieve in the square, everywhere, Gerard K has no rule. He's not the President, he's the leader of a revolution, he has nothing to Resign. Revolution means always sacrifice until the end of the crystal. This is my field, the field of my great-grandfathers, we planted, and we watered it with our grandfather's crystallisation soup. We deserve crystallography from those rats and crystallisation agents, who are being paid by security persons, damn them, damn their phases, if they have phases, they don't have phases, they don't have cooridnates. All sidechains are with us here, they (American crystallographerss) can see us all chanting the same slogans. Everyone challenging, we challenge America with its mighty synchrotron, we challenge even the superpower in the world and we became victory. Here they put their heads down, crystallography even kissed the grave of the Leader of all Martyrs. It's not victory for the cities of crystallography, but victory for the crystallographic community. This is the victory they want to give a bad image about. Italy, the Empire of the time, fell apart on crystallographic soil. I am bigger than any job, I am a revolutionary, I am from the Netherlands, from oasis that brought victory, and enjoy it from generation to generation, crystallography will remain at the top and will lead Cambridge and South Kensington. We cannot hinder the process of this revolution from these greasy rats and cats. I am paying the price for staying here, and my grandfather who fell a martyr in 1911, I will not delete sidechain atoms and I will die as a martyr at the end, The remains of my father is the proof, grandfather, and my uncle Sheikh Alwyn, in the hills of Wales, I will not leave these righteous remains. He, Bricogne says that freedom cannot enjoy the shadow of these trees, we planted these trees and we watered it with our precipitants. I am talking to you from the house which was bombarded by a hundred and seventy X-rays, by ESRF and Diamond. They left all houses and were aiming for Gerard's houses. Is it because he is president of crystallography? They could have treated him like other presidents, but Gerard K is history, resistance, freedom, victory, revolution, high B-values. This is an admission from the biggest power that Gerard K is not the president, is not a normal person, you can't poison him or lead demonstrations against him. When X-rays were falling on my crystal, and killing my carboxylates, where were you, you rats? Where were you those with big crystals? Where were you? You were in America. You were applauding your master, the synchrotrons. One hundred and seventy X-rays, left all palaces and leaders and kings and came to the great portakabin of Gerard K. This is a victory we should not be relinquished by anybody, any country or people, in myself Cambridge or any mission fighting back the tyranny of the America, we did not give in, we were resilient, here. Now I want to tell
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Well, actually you probably haven't subtracted the dark R value from your final R. This and other values are available in a dark folder on your hard drive, which is impossible to see/read, but which contains a lot of important information which will make your structure have a much higher impact factor. You can probably make a maximum-likelihood approximation of the appropriate values, and apply them to your structure so that your R values correspond the majority in the PDB. HTH, JPK On Fri, Apr 1, 2011 at 8:30 AM, Edward A. Berry ber...@upstate.edu wrote: Do you have a list of dark-matter-aware PDB refinement programs? Adding dark matter and refining in TNT or Xplor gives me exactly the same R as without. Furthermore the final refined files have lost the dark matter as far as I can see. This leads me to believe these programs are completely ignoring the dark matter. Ed Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] [phenixbb] what to do with disordered side chains
Strangely enough, Nature may be the only journal that fully enables reviewers of protein crystallography to do the proper job - reviewer access is provided to unreleased coordinates AND diffraction data upon request! (no this is not April1 joke). There are reasons to suspect that the request is not made very often but that is more a shame on the reviewers than the willingness of the journal at this point in time. Of course, it is a confusing situation when you only see density for a part of a ligand and it comes up all the time. Thanks John Badger
[ccp4bb] Quick-and-dirty searches of both PDB and EMDB at PDBe
Hi all, As part of its recent winter update, the Protein Data Bank in Europe (PDBe; http://pdbe.org/) has improved its facility that allows for tandem searches of PDB and EMDB. It was designed to allow users to carry out many of their day-to-day searches (without the need to fill out a complex form or learn a special query syntax). Simply type what you are looking for, click the SEARCH button, and we will do our best to dig up relevant information, be it in the PDB, in EMDB or on our website. QUICK ACCESS TO ENTRIES, SERVICES, SEQUENCES If you go to the PDBe home page (http://pdbe.org/), you will see a Google-like search box in the friendly green banner near the top of the page (just below our motto, Bringing Structure to Biology). You can use this search box in a number of ways: - type a PDB code (e.g., 1cbs), and you will be taken directly to the summary page for that entry. You can type any valid code, even if it's not in the current release, so you can use this facility to obtain information about the status of entries that have not been released yet (e.g., 2yd0) or entries that are no longer in the archive (e.g., theoretical models). - type a valid EMDB code (e.g., 1607) and you will be taken straight to the summary page for that entry. HINT: if, instead of being taken directly to a summary page for a certain PDB or EMDB code, you want to actually search PDB and/or EMDB for references to that particular code, simply enclose it in double quotes. For instance, searching for 1mi6 will take you to the summary page for PDB entry 1mi6, whereas searching for 1mi6 will give you a set of hits in both PDB and EMDB that all contain a reference to 1mi6. - type something resembling a PDBe service or resource name and chances are that the name will be recognised and you will be taken straight to that service or resource (e.g., autodep, emdep, pdbemotif, pdbepisa, pdbefold, pdbechem, quips, portfolio, etc.). - you can search the protein sequences in the PDB by entering seq: (or sequence:) followed by a (partial) amino-acid sequence in one-letter code (e.g., seq:GNKKGSEQESVKEFLAKAKEDFLKKWETPSQNTA). The sequence will be compared to all protein sequences in the PDB using FastA, and the results will be presented to you for further analysis in the PDBe sequence browser (see http://pdbe.org/sequence). TEXT-BASED SEARCHES --- Of course you can do general text-based searches of the PDB and EMDB as well - just type one or more search terms in the box and hit the SEARCH button. - If you type a single search term and it gives hits in the PDB, you will get a results page with a tree structure on the left which shows in which categories the term was found. For instance, if you look for Jones, that could be an author, but it could also be part of the name of a molecule (e.g., Bence Jones protein). By clicking on an appropriate branch in the tree, you select only those entries for which the search term occurs in that data category (e.g., author or PDB compound). - If you type more than one search term, only entries that contain all these terms will be selected as hits. For instance, if you search for kleywegt po4 - without the quotes - you will get only one hit, 1CBQ. Note that if you enclose your search terms in double quotes, you will only get hits that match exactly (i.e., the complete search expression must occur somewhere in the entry, not just all of the keywords individually). For instance, searching for HCV NS3 protease yields 31 hits in the PDB if you enclose the terms in double quotes, but 177 hits if you don't. Note that there are two tabs on the results page - one labelled PDB entries and the other EMDB entries. If you do a search for Baumeister, you will get 14 hits in the PDB. If you click on the EMDB entries tab, you will find that there are 10 hits in EMDB. HINT: if you want the EMDB results tab to become active straightaway, preface your search term(s) by emdb: (without the quotes), e.g. search for emdb:saibil and you will immediately get the list of 56 EMDB hits. SEARCH RESULTS -- The search results are sorted by release date by default, with the most recently released entries at the top. This ensures that if you read an exciting paper about new ClpC structures, a search for clpc will give you the latest entries first. You can change the sort order and criterion with a drop-down menu. Each entry that is found as a hit in a search is shown in a panel that contains useful summary information and allows you to launch various searches and services with a single mouse-click. If you do a search for hiv-1, for example, you will get many hits in the PDB and two dozen in EMDB: - For each PDB hit you will see: the PDB code, a small image of the structure, the resolution (for X-ray and EM structures), the title of the entry, a set of PDBprints that provide
[ccp4bb] program to calculate electron density at x,y,z
I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Thanks in advance, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] SFCHECK produces incomplete postscript
If you have break in the protein chain, this problem will occur. Put TER card in the PDB file where ever the chain break is there, then run SFCHECK. The .ps output now will be complete and should be able to see in the viewer. HTH -Karthik Dear all, I have been trying to compare a model that I'm refining against the native SFs using SFCHECK. SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps files), but produces a postscript file with only the first page of output (and it is mostly blank). There is the typical light-grey panels on a dark-grey background format that I'm used to for SFCHECK postscript files, but there are no figures or data. Also, my mouse icon indicates it is hung trying to load/read the file (i.e. it's a moving busy icon under Linux). I've tried other postscript viewers without luck. I can successfully run SFCHECK on a completely different model/MTZ pair without problem though. So does anyone know of circumstances that would lead to a hung postscript file from SFCHECK? Thanks for your help, -Andy
Re: [ccp4bb] SFCHECK produces incomplete postscript
April 1st, 2011 Dear Andy, We have observed the same problem before, and just today we could finally find an explanation. Apparently, a new (still undocumented) functionality was quietly introduced into few widely used oscillation data processing programs, enabling the recording of the scattering from antimatter atoms traditionally ignored in crystallography (see a related discussion on this BB earlier today!). While obviously a welcomed improvement, the inclusion of antimatter SFs in the calculations has resulted in aberrant behaviour of some other programs. This apparently includes SFCHECK which attempts to calculate the R-factor and further statistics, but since the data for matter and antimatter cancel out, all you get is a blank output. I wonder if Alexei already has a new version of SFCHECK that outputs the matter and antimatter SF statistics separately - ? HTH, Sergei Dear all, I have been trying to compare a model that I'm refining against the native SFs using SFCHECK. SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps files), but produces a postscript file with only the first page of output (and it is mostly blank). There is the typical light-grey panels on a dark-grey background format that I'm used to for SFCHECK postscript files, but there are no figures or data. Also, my mouse icon indicates it is hung trying to load/read the file (i.e. it's a moving busy icon under Linux). I've tried other postscript viewers without luck. I can successfully run SFCHECK on a completely different model/MTZ pair without problem though. So does anyone know of circumstances that would lead to a hung postscript file from SFCHECK? Thanks for your help, -Andy
Re: [ccp4bb] program to calculate electron density at x,y,z
Ed Pozharski wrote: I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? fft to calculate the map, then mapman with the peek value command. Give it a pdb file (fek.pdb) with the coordinates of the atoms, it returns a pdb file with electron density at those points in the B-factor column. Several options for interpolating map values to the chosen point, iirc. Something like: setenv MAPSIZE 500 /data/trp/berry/usf/rave/lx_mapman -b eof re m1 d.map CCP4 !norm m1 !pick level 5.2 !pick peaks m1 danopeaks.pdb pdb peek value m1 fek.pdb fepkhght.pdb int quit eof If I would have to bring a dependency into this, the best choice for me would be clipper libs. Thanks in advance, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] What happened to this innovative method by MV King?
Le 01/04/11 12:39, REX PALMER a écrit : Dear Protein Crystallographers I would like to share with you something I came across today. Unfortunately I was only able to copy the first 4 pages of the article by MV King as I need to post the email before 12am and the quality of the copy is somewhat lacking. I was wondering if anyone knows if anything came of the proposed method of heavy atom substitution as a Google Scholar search has failed to bring anything up. Best wishes Rex Palmer Birkbeck College, London They said: In Gold we thrust and so they did. No other crystal phases survived and hence all this messy problem. The locusts have no King, yet go they forth all of them by bands -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] program to calculate electron density at x,y,z
Hi Ed, if you are familiar with CCTBX then map_value = map_data.eight_point_interpolation(site_fractional) Also, there is a similar method that will just give you the density value at closes grid point. Let me know if interested, and I can send you a 10 lines Python script-example that will do it. Pavel. On Fri, Apr 1, 2011 at 8:16 AM, Ed Pozharski epozh...@umaryland.edu wrote: I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Thanks in advance, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
The meaning of B-factor is the (scaled) sum of all positional uncertainties, and not just its one contributor, the Atomic Displacement Parameter that describes the relative displacement of an atom in the crystal lattice by a Gaussian function. That meaning (the sum of all contributions) comes from the procedure that calculates the B-factor in all PDB X-ray deposits, and not from an arbitrary decision by a committee. All programs that refine B-factors calculate an estimate of positional uncertainty, where contributors can be both Gaussian and non-Gaussian. For a non-Gaussian contributor, e.g. multiple occupancy, the exact numerical contribution is rather a complex function, but conceptually it is still an uncertainty estimate. Given the resolution of the typical data, we do not have a procedure to decouple Gaussian and non-Gaussian contributors, so we have to live with the B-factor being defined by the refinement procedure. However, we should still improve the estimates of the B-factor, e.g. by changing the restraints. In my experience, the Refmac's default restraints on B-factors in side chains are too tight and I adjust them. Still, my preference would be to have harmonic restraints on U (square root of B) rather than on Bs themselves. It is not we who cram too many meanings on the B-factor, it is the quite fundamental limitation of crystallographic refinement. Zbyszek Otwinowski The fundamental problem remains: we're cramming too many meanings into one number [B factor]. This the PDB could indeed solve, by giving us another column. (He said airily, blithely launching a totally new flame war.) phx.
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
In my experience, the Refmac's default restraints on B-factors in side chains are too tight and I adjust them. Concur. See BMC p 640. BR
Re: [ccp4bb] What happened to this innovative method by MV King?
This was not so much an advance but a remarkable observation. We have since learned that these clathrates are entirely impractical. The problem is not so much their dextrorotatory properties, which are more or less a nuisance, but that they are too dense and have absolutely no affinity for other compounds. James On Apr 1, 2011, at 3:39 AM, REX PALMER wrote: Dear Protein Crystallographers I would like to share with you something I came across today. Unfortunately I was only able to copy the first 4 pages of the article by MV King as I need to post the email before 12am and the quality of the copy is somewhat lacking. I was wondering if anyone knows if anything came of the proposed method of heavy atom substitution as a Google Scholar search has failed to bring anything up. Best wishes Rex Palmer Birkbeck College, London King_1.jpgKing_2.jpgKing_3.jpgKIng_4.jpg
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
I'm not sure I entirely agree with ZO's assessment that a B factor is a measure of uncertainty. Pedantically, all it really is is an instruction to the refinement program to build some electron density with a certain width and height at a certain location. The result is then compared to the data, parameters are adjusted, etc. I don't think the B factor is somehow converted into an error bar on the calculated electron density, is it? For example, a B-factor of 500 on a carbon atom just means that the peak to build is ~0.02 electron/A^3 tall, and ~3 A wide (full width at half maximum). By comparison, a carbon with B=20 is 1.6 electrons/A^3 tall and ~0.7 A wide (FWHM). One of the bugs that Dale referred to is the fact that most refinement programs do not plot electron density more than 3 A away from each atomic center, so a substantial fraction of the 6 electrons represented by a carbon with B=500 will be sharply cut off, and missing from the FC calculation. Then again, all 6 electrons will be missing if the atoms are simply not modeled, or if the occupancy is zero. The point I am trying to make here is that there is no B factor that will make an atom go away, because the way B factors are implemented is to always conserve the total number of electrons in the atom, but just spread them out over more space. Now, a peak height of 0.02 electrons/A^3 may sound like it might as well be zero, especially when sitting next to a B=20 atom, but what if all the atoms have high B factors? For example, if the average (Wilson) B factor is 80 (like it typically is for a ~4A structure), then the average peak height of a carbon atom is 0.3 electrons/A^3, and then 0.02 electrons/A^3 starts to become more significant. If we consider a ~11 A structure, then the average atomic B factor will be around 500. This B vs resolution relationship is something I derived empirically from the PDB (Holton JSR 2009). Specifically, the average B factor for PDB files at a given resolution d is: B = 4*d^2+12. Admittedly, this is on average, but the trend does make physical sense: atoms with high B factors don't contribute very much to high-angle spots. More formally, the problem with using a high B-factor as a flag is that it is not resolution-general. Dale has already pointed this out. Personally, I prefer to think of B factors as a atom-by-atom resolution rather than an error bar, and this is how I tell students to interpret them (using the B = 4*d^2+12 formula). The problem I have with the error bar interpretation is that heterogeneity and uncertainty are not the same thing. That is, just because the atom is jumping around does not mean you don't know where the centroid of the distribution is. The u_x in B=8*pi^2*u_x^2 does reflect the standard error of atomic position in a GIVEN unit cell, but since we are averaging over trillions of cells, the error bar on the AVERAGE atomic position is actually a great deal smaller than u. I think this distinction is important because what we are building is a model of the AVERAGE electron density, not a single molecule. Just my 0.02 electrons -James Holton MAD Scientist On Fri, Apr 1, 2011 at 10:57 AM, Zbyszek Otwinowski zbys...@work.swmed.edu wrote: The meaning of B-factor is the (scaled) sum of all positional uncertainties, and not just its one contributor, the Atomic Displacement Parameter that describes the relative displacement of an atom in the crystal lattice by a Gaussian function. That meaning (the sum of all contributions) comes from the procedure that calculates the B-factor in all PDB X-ray deposits, and not from an arbitrary decision by a committee. All programs that refine B-factors calculate an estimate of positional uncertainty, where contributors can be both Gaussian and non-Gaussian. For a non-Gaussian contributor, e.g. multiple occupancy, the exact numerical contribution is rather a complex function, but conceptually it is still an uncertainty estimate. Given the resolution of the typical data, we do not have a procedure to decouple Gaussian and non-Gaussian contributors, so we have to live with the B-factor being defined by the refinement procedure. However, we should still improve the estimates of the B-factor, e.g. by changing the restraints. In my experience, the Refmac's default restraints on B-factors in side chains are too tight and I adjust them. Still, my preference would be to have harmonic restraints on U (square root of B) rather than on Bs themselves. It is not we who cram too many meanings on the B-factor, it is the quite fundamental limitation of crystallographic refinement. Zbyszek Otwinowski The fundamental problem remains: we're cramming too many meanings into one number [B factor]. This the PDB could indeed solve, by giving us another column. (He said airily, blithely launching a totally new flame war.) phx.
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Congratulations on your amazing discovery, which immediately suggests many new lines of inquiry: Does dark matter affect macromolecular stability? Can it explain the difficulty some students have in sample preparation? Is it found in higher concentrations in brains that are thought to be denser (we won't say by whom)? = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 31 Mar 2011 23:06:47 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Ethan Merritt merr...@u.washington.edu) Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
In this case, I'm more on ZO's side. Let's say that the refinement program can't get an atom to the right position (for instance, to pick a reasonably realistic example, because you've put a leucine side chain in backwards). In that case, the B-factor for the atom nearest to where there should be one in the structure will get larger to smear out its density and put some in the right place. To a good approximation, the optimal increase in the B-factor will be the one you'd expect for a Gaussian probability distribution, i.e. 8Pi^2/3 times the positional error squared. So a refined B-factor does include a measure of the uncertainty or error in the atom's position. Best wishes, Randy Read On Apr 1 2011, James Holton wrote: I'm not sure I entirely agree with ZO's assessment that a B factor is a measure of uncertainty. Pedantically, all it really is is an instruction to the refinement program to build some electron density with a certain width and height at a certain location. The result is then compared to the data, parameters are adjusted, etc. I don't think the B factor is somehow converted into an error bar on the calculated electron density, is it? For example, a B-factor of 500 on a carbon atom just means that the peak to build is ~0.02 electron/A^3 tall, and ~3 A wide (full width at half maximum). By comparison, a carbon with B=20 is 1.6 electrons/A^3 tall and ~0.7 A wide (FWHM). One of the bugs that Dale referred to is the fact that most refinement programs do not plot electron density more than 3 A away from each atomic center, so a substantial fraction of the 6 electrons represented by a carbon with B=500 will be sharply cut off, and missing from the FC calculation. Then again, all 6 electrons will be missing if the atoms are simply not modeled, or if the occupancy is zero. The point I am trying to make here is that there is no B factor that will make an atom go away, because the way B factors are implemented is to always conserve the total number of electrons in the atom, but just spread them out over more space. Now, a peak height of 0.02 electrons/A^3 may sound like it might as well be zero, especially when sitting next to a B=20 atom, but what if all the atoms have high B factors? For example, if the average (Wilson) B factor is 80 (like it typically is for a ~4A structure), then the average peak height of a carbon atom is 0.3 electrons/A^3, and then 0.02 electrons/A^3 starts to become more significant. If we consider a ~11 A structure, then the average atomic B factor will be around 500. This B vs resolution relationship is something I derived empirically from the PDB (Holton JSR 2009). Specifically, the average B factor for PDB files at a given resolution d is: B = 4*d^2+12. Admittedly, this is on average, but the trend does make physical sense: atoms with high B factors don't contribute very much to high-angle spots. More formally, the problem with using a high B-factor as a flag is that it is not resolution-general. Dale has already pointed this out. Personally, I prefer to think of B factors as a atom-by-atom resolution rather than an error bar, and this is how I tell students to interpret them (using the B = 4*d^2+12 formula). The problem I have with the error bar interpretation is that heterogeneity and uncertainty are not the same thing. That is, just because the atom is jumping around does not mean you don't know where the centroid of the distribution is. The u_x in B=8*pi^2*u_x^2 does reflect the standard error of atomic position in a GIVEN unit cell, but since we are averaging over trillions of cells, the error bar on the AVERAGE atomic position is actually a great deal smaller than u. I think this distinction is important because what we are building is a model of the AVERAGE electron density, not a single molecule. Just my 0.02 electrons -James Holton MAD Scientist On Fri, Apr 1, 2011 at 10:57 AM, Zbyszek Otwinowski zbys...@work.swmed.edu wrote: The meaning of B-factor is the (scaled) sum of all positional uncertainties, and not just its one contributor, the Atomic Displacement Parameter that describes the relative displacement of an atom in the crystal lattice by a Gaussian function. That meaning (the sum of all contributions) comes from the procedure that calculates the B-factor in all PDB X-ray deposits, and not from an arbitrary decision by a committee. All programs that refine B-factors calculate an estimate of positional uncertainty, where contributors can be both Gaussian and non-Gaussian. For a non-Gaussian contributor, e.g. multiple occupancy, the exact numerical contribution is rather a complex function, but conceptually it is still an uncertainty estimate. Given the resolution of the typical data, we do not have a procedure to decouple Gaussian and non-Gaussian contributors, so we have to live with the B-factor being defined by the refinement procedure. However, we should still improve the estimates of the B-factor,
[ccp4bb] OT: PCR instrument
Dear All, I was polled for a recommendation for a good PCR instrument, but I am not much of a molecular biology person - if someone could please help and kindly send some recommendations to Eric W. Reinheimer ewreinhei...@csupomona.edu Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
Re: [ccp4bb] SFCHECK produces incomplete postscript
Dear Karthik and Sergei, Thank you for the replies (helpful and humorous). Karthik, I confirmed that the chain breaks in my .PDB have TER cards, but I arrive at the same result. Perhaps dark matter is to blame for this singularity after all... In that case, maybe I just need to try again tomorrow. I'll post the solution if I find it before moving on. Regards, -Andy -Original Message- From: S. Karthikeyan [mailto:skart...@imtech.res.in] Sent: Friday, April 01, 2011 11:21 AM To: Andrew T. Torelli Cc: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] SFCHECK produces incomplete postscript If you have break in the protein chain, this problem will occur. Put TER card in the PDB file where ever the chain break is there, then run SFCHECK. The .ps output now will be complete and should be able to see in the viewer. HTH -Karthik Dear all, I have been trying to compare a model that I'm refining against the native SFs using SFCHECK. SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps files), but produces a postscript file with only the first page of output (and it is mostly blank). There is the typical light-grey panels on a dark-grey background format that I'm used to for SFCHECK postscript files, but there are no figures or data. Also, my mouse icon indicates it is hung trying to load/read the file (i.e. it's a moving busy icon under Linux). I've tried other postscript viewers without luck. I can successfully run SFCHECK on a completely different model/MTZ pair without problem though. So does anyone know of circumstances that would lead to a hung postscript file from SFCHECK? Thanks for your help, -Andy
[ccp4bb] phenix library issues
Dear all, sorry for being off-topic! I have been experimenting with the latest phenix build [1]. I am fairly impressed with phenix.canephor [2]. At first sight the projected density looked a little week until I realised that I had used phenix.project.mediterranean. As I switched to phenix.project.occidental, the result was expectedly a good average. The rmsd of about 5e12A was also fairly acceptable, it seemed to me. Subsequently I attempted to improve the result using phenix.calzone [3]. Unfortunately this program crashed because of a missing libcapsicum.so.4.01.11 which I could not finde anywhere on the web. Could anyone please let me know where to find this library? Best wishes, Tim P.S. How about the resolution limit of 2.56A - couldnin principle one should be able to improve this significantly by switching from CuKa to, e.g MoKa radiation? [1] PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). [2] Crystal cookery - using high-throughput technologies and the grocery store as a teaching tool. J. R. Luft, N. M. Furlani, R. E. NeMoyer, E. J. Penna, J. R. Wolfley, M. E. Snell, S. A. Potter and E. H. Snell J. Appl. Cryst. (2010). 43, 1189-1207 -- [3] Structure and stereochemistry of (24R)-27-nor-5[alpha]-cholestane-3[beta],4[beta],5,6[alpha],7[beta],8,14,15[alpha],24-nonaol: a highly hydroxylated marine steroid from the starfish Archaster typicus. C. A. Mattia, L. Mazzarella, R. Puliti, R. Riccio and L. Minale. Acta Cryst. (1988). C44, 2170-2173 -- 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
Re: [ccp4bb] phenix library issues
On Friday, April 01, 2011 01:51:31 pm Tim Gruene wrote: Subsequently I attempted to improve the result using phenix.calzone [3]. This program comes in both Chicago and New York localizations. Do you know which one you have? Unfortunately this program crashed because of a missing libcapsicum.so.4.01.11 which I could not finde anywhere on the web. Could anyone please let me know where to find this library? I think the upstream source is here: http://tinyurl.com/2wcbq7q A more general substitute might be: http://tinyurl.com/3c5z589 You might also be able to extract it from libsalsa: http://tinyurl.com/3orwygl cheers, Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
How *did* those physicists get such a convenient hypothesis, when the rest of us have only light matter to work with! ...Or do we also really have our dark matter too? JPK On Fri, Apr 1, 2011 at 2:12 PM, Phoebe Rice pr...@uchicago.edu wrote: Congratulations on your amazing discovery, which immediately suggests many new lines of inquiry: Does dark matter affect macromolecular stability? Can it explain the difficulty some students have in sample preparation? Is it found in higher concentrations in brains that are thought to be denser (we won't say by whom)? = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 31 Mar 2011 23:06:47 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Ethan Merritt merr...@u.washington.edu) Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
It may simply be the case that all those seleniums scattering anomalously are pumping the dark matter. Sent via BlackBerry by ATT -Original Message- From: Jacob Keller j-kell...@fsm.northwestern.edu Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Fri, 1 Apr 2011 17:25:02 To: CCP4BB@JISCMAIL.AC.UK Reply-To: Jacob Keller j-kell...@fsm.northwestern.edu Subject: Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 How *did* those physicists get such a convenient hypothesis, when the rest of us have only light matter to work with! ...Or do we also really have our dark matter too? JPK On Fri, Apr 1, 2011 at 2:12 PM, Phoebe Rice pr...@uchicago.edu wrote: Congratulations on your amazing discovery, which immediately suggests many new lines of inquiry: Does dark matter affect macromolecular stability? Can it explain the difficulty some students have in sample preparation? Is it found in higher concentrations in brains that are thought to be denser (we won't say by whom)? = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 31 Mar 2011 23:06:47 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Ethan Merritt merr...@u.washington.edu) Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
Personally I think it is a _good_ thing that those missing atoms are a pain, because it helps ensure you are aware of the problem. As somebody who is in the business of supplying non-structural people with models, and seeing how those models are sometimes (mis)interpreted, I think it's better to inflict that pain than it is to present a model that non-structural people are likely to over-interpret. The PDB provides various manipulated versions of crystal structures, such as biological assemblies. I don't think it would necessarily be a bad idea to build missing atoms back into those sorts of processed files but for the main deposited entry the best way to make sure the model is not abused is to leave out atoms that can't be modeled accurately. Just as an example since you mention surfaces, some of the people I work with calculate solvent accessible surface areas of individual residues for purposes such as engineering cysteines for chemical conjugation, and if residues are modeled into bogus positions just to say all the atoms are there, software that calculates per-residue SASA has to have a reliable way of knowing to ignore those atoms when calculating the area of neighboring residues. Ad hoc solutions like putting very large values in the B column are not clear cut for such a software program to interpret. Leaving the atom out completely is pretty unambiguous. -Eric On Mar 31, 2011, at 7:34 PM, Scott Pegan wrote: I agree with Zbyszek with the modeling of side chains and stress the following points: 1) It drives me nuts when I find that PDB is missing atoms from side chains. This requires me to rebuild them to get any use out of the PDB such as relevant surface renderings or electropotential plots. I am an experienced structural biologist so that I can immediately identify that they have been removed and can rebuild them. I feel sorry for my fellow scientists from other biological fields that can't perform this task readability, thus removing these atoms from a model limits their usefulness to a wider scientific audience. 2) Not sure if any one has documented the percentage of actual side chains missing from radiation damage versus heterogeneity in confirmation (i.e. dissolved a crystal after collection and sent it to Mass Spec). Although the former likely happens occasionally, my gut tells me that the latter is significantly more predominant. As a result, absence of atoms from a side chain in the PDB where the main chain is clearly visible in the electron density might make for the best statistics for an experimental model, but does not reflect a reality. Scott
Re: [ccp4bb] program to calculate electron density at x,y,z
Hi Ed, I wrote a short program name HYDENS that takes a PDB file and an H K L amplitude phase file for a full hemisphere of data. You can make the latter from an MTZ with sftools. The program is on my website at http://129.128.24.248/highlights.html. There is a linux executable as well as the source code that should compile with any standard fortran compiler. Bart On 11-04-01 09:16 AM, Ed Pozharski wrote: I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Thanks in advance, Ed. -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
