[ccp4bb] CCP4 School in Osaka
Dear All there will be a CCP4 school at Osaka University from 8 - 12 November 2010. The aim of this school will be to cover all aspects of the structure solution process in macromolecular crystallography, starting from data processing, through phasing and refinement, and ending with validation and deposition. The school will cover many popular programs used for data processing and structure solution with the software developers available to help throughout the week. Programs covered will include: Mosflm, Scala, Refmac, ArpWarp, Phaser, Coot, SHELXC/D/E, Balbes, Mrbump, Buccaneer and many more. Details are available at http://www.ccp4.ac.uk/schools/Japan-2010/ Speakers include Garib Murshudov, Phil Evans, Gerrit Langer, Nobutoshi Ito and Min Yao. First priority will be given to Japanese students Charles Ballard CCP4
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Dear Ian and contributors to this interesting thread, (please, scroll down a little bit) Am 15.09.10 23:34, schrieb Ian Tickle: I should just like to point out that the main source of the disagreement here seems to be that people have very different ideas about what a 'model' is or should be. Strictly a model is a purely mathematical construct, in this case it consists of the appropriate equation for the calculated structure factor and the best-fit values of the various parameters (scattering factors, atomic positions, occupancies, B factors, TLS parameters etc.) that appear in it. A mathematical model is inevitably going to be an imperfect representation of reality, but hopefully it's the best one we can come up with, in the sense of best explaining the data without significant overfitting. The problem arises because many users of the PDB, and I suspect many contributors to this BB, particularly non-crystallographers, don't see it like that, because they view a PDB file as a physical model, i.e. not as the best fit to the data (assuming that the non-crystallographers even know what the data are!), but the closest representation of reality. The difference between the N-H bond lengths that Ed referred to illustrates the distinction between the mathematical and the physical model. The mathematical model requires that the bond length is 0.86 Ang because that value gives the best fit of the assumed spherical scattering factor of H to the deformation density of the X-H covalent bond. The physical model requires that it be 1.00 Ang because that is the internuclear distance found by spectroscopic methods predicted by QM calculations. The same goes for B factors and TLS: to a large extent they are a mathematical construct whose purpose is to provide an optimal fit to the data. The connection of Bs TLS with reality is tenuous at best, nevertheless people obviously would like to have a physical interpretation such as rigid-body correlated motion. The fact that Bragg scattering provides no information about correlated motion (you need to measure the diffuse scattering for that) doesn't seem to deter them! I have no doubt in my mind that it is the mathematical model that should be published, because hopefully it's the best available interpretation of the data. Whether that involves publishing the riding H atoms explicitly, or alternatively the formulae and parameters that were used to calculate their positions I don't mind, as long as I can faithfully reproduce the Fcalcs to check the validity of the model. Then users of the PDB are free to *interpret* the mathematical models as physical models in a appropriate manner (e.g. by adjusting the bond lengths to H), and crystallographers have the untainted mathematical models needed to reproduce the Fcalcs. so, wouldn't be the deposition of the final model's Fcalc, Phic (and their weights) along with the final coordinates be the best solution? The final Fcalc are our best model and can be used to reproduce the final statistics (which would remove the sfcheck annoyance) and to reproduce the final electron density maps, and the coordinates can be used for what ever purpose they are needed, irrespective of adding riding hydrogens or not. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Most Disagreeable Reflections
Dear CCP4 users The Shelx lst file includes the entry: Most Disagreeable Reflections (* if suppressed or used for Rfree) and includes 50 hkl's with h k lFo^2 Fc^2 Delta(F^2)/esd Fc/Fc(max) Resolution(A) Is there a corresponding or similar facility in CCP4? Rex Palmer Birkbeck College, London
Re: [ccp4bb] Deposition of riding H
Hi Pavel, Note that in the ultra-high resolution structure of aldose reductase http://www.ncbi.nlm.nih.gov/pubmed/15146478 we didn't see all (or most) hydrogens. So, the converse question one could ask is why we didn't see all of them? Was it only because of higher B-factors or because some of them were stripped during data collection? Note that in my original message I said they are, in most cases, still assumed. Ultra-high resolution structures are exactly what I meant under few cases when some of the positions are not assumed, so thanks for pointing that out. It's not all or nothing - some hydrogens will be stripped and some won't. But since we don't know which ones are gone, depositing the coordinates of all of them may be misleading. It can be particularly dangerous for structure-based functional interpretations because several publications suggest that active sites are one of the first ones to suffer from radiation damage. And aren't the functional interpretations the ultimate goal of protein structures? Cheers, N. From: Pavel Afonine [mailto:pafon...@lbl.gov] Sent: Wed 9/15/2010 5:56 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Deposition of riding H Hi Nukri, thanks for the paper (I haven't read the paper yet), I definitely missed this one! Interesting though, if we assume that they get stripped off during data collection, how you could see so many hydrogen atoms in Fo-Fc residual maps for Aldose Reductase structure at 0.66A? B. Guillot, C. Jelsch, N. Muzet, C. Lecomte, E. Howard, B. Chevrier, A. Mitschler, A. Podjarny, A. Cousson, R. Sanishvili A. Joachimiak (2000). Multipolar refinement of aldose reductase at subatomic resolution. Acta Cryst. A56, s199. E. I. Howard, R. Cachau, A. Mitschler, P. Barth, B. Chevrier, V. Lamour, A. Joachimiak, R. Sanishvili, M. Van Zandt, D. Moras A. Podjarny (2000). Crystallization of Aldose Reductase leading to Single Wavelength (0.66 Å) and MAD (0.9 Å) subatomic resolution studies. Acta Cryst. A56, s57. A. D. Podjarny, A. Mitschler, I. Hazemann, T. Petrova, F. Ruiz, E. Howard, C. Darmanin, R. Chung, T. R. Schneider, R. Sanishvili, C. Schulze-Briesse, T. Tomizaki, M. Van Zandt, M. Oka, A. Joachimiak O. El-Kabbani (2005). Inhibitor binding to aldose reductase studied at subatomic resolution. Acta Cryst. A61, c122. Pavel. On 9/15/10 3:34 PM, Sanishvili, Ruslan wrote: Hi All, I have not read all messages in the trace so my apologies if somebody already pointed out what I have to say. There is lot of talk about how this or that software treats the riding hydrogens. What to do with the fact that however these hydrogens are treated in calculations, they are, in most cases, still assumed? Meents et al http://scripts.iucr.org/cgi-bin/paper?xh0004 showed that proteins are stripped of hydrogens during X-ray data collection. So, IMHO it is a good argument against depositing the H coordinates in PDB. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George M. Sheldrick Sent: Wednesday, September 15, 2010 5:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Deposition of riding H Pavel: In my original email I very carefully gave credit for IMPLEMENTING the TLS concept. Of course the ideas and some programs had been around long before, but it was the IMPLEMENTATION IN REFMAC that resulted in TLS becoming widely used. I had actually considered putting it into SHELXL but had not done so for two reasons (a) I was too lazy and (b) I missed an essential trick that REFMAC introduced, namely the combination of TLS with an additive isotropic B-value for each atom. Dale: You are quite correct that AFIX 137 breaks my argument about not depositing (SHELX) hydrogen atoms because they can be recalculated with no loss of experimental information. However to be fair, if you generate the first .ins file using SHELXPRO (the recommended procedure) you will get AFIX 33 that doesn't have this problem. For Pavel and others unfamiliar with SHELXL, AFIX 33 is a pure riding model with a staggered methyl group but AFIX 137 assumes local threefold symmetry, finds the initial torsion angle by a three-fold averaged fit to the difference density and then refines the torsion angle in the following cycles. Since this torsion angle is not given explicitly in the output files, if AFIX 137 hydrogens are not deposited, they cannot be regenerated except by a full refinement against the experimental data. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 15 Sep 2010,
Re: [ccp4bb] Deposition of riding H- Are they or are they not? Additional experiments are needed
Well , maybe they are there (hydrogens), maybe they are not (also depends on location). They, or something else also boils sometimes. I also understand from some other publications such as doi:10.1107/S090904509002192 (cyclosporine) that hydrogen abstraction is irreversible. Is it supported my Mass Spectroscopy post mortem in the case of cyclosporine and aldose reductase? Just what left from the irradiated crystals - molecules with or without hydrogens can be checked in mass-spectrometer. BTW, part of my early life I practiced small molecule X-ray crystallography, which is by definition ultra-high resolution. When we wished to know in critical cases were hydrogens are and if they are, we exchanged them with deuterium in large crystals and performed neutron diffraction. One major advantage of neutron diffraction over X-ray diffraction is that the latter is rather insensitive to the presence of hydrogen (H) in a structure, whereas the nuclei 1H and 2H (i.e. Deuterium, D) are strong scatterers for neutrons. This means that the position of deuterium in a crystal structure and its thermal motions can be determined far more precisely with neutrons Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 16, 2010, at 15:45 , Sanishvili, Ruslan wrote: Hi Pavel, Note that in the ultra-high resolution structure of aldose reductase http://www.ncbi.nlm.nih.gov/pubmed/15146478 we didn't see all (or most) hydrogens. So, the converse question one could ask is why we didn't see all of them? Was it only because of higher B-factors or because some of them were stripped during data collection? Note that in my original message I said they are, in most cases, still assumed. Ultra-high resolution structures are exactly what I meant under few cases when some of the positions are not assumed, so thanks for pointing that out. It's not all or nothing - some hydrogens will be stripped and some won't. But since we don't know which ones are gone, depositing the coordinates of all of them may be misleading. It can be particularly dangerous for structure-based functional interpretations because several publications suggest that active sites are one of the first ones to suffer from radiation damage. And aren't the functional interpretations the ultimate goal of protein structures? Cheers, N. From: Pavel Afonine [mailto:pafon...@lbl.gov] Sent: Wed 9/15/2010 5:56 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Deposition of riding H Hi Nukri, thanks for the paper (I haven't read the paper yet), I definitely missed this one! Interesting though, if we assume that they get stripped off during data collection, how you could see so many hydrogen atoms in Fo-Fc residual maps for Aldose Reductase structure at 0.66A? B. Guillot, C. Jelsch, N. Muzet, C. Lecomte, E. Howard, B. Chevrier, A. Mitschler, A. Podjarny, A. Cousson, R. Sanishvili A. Joachimiak (2000). Multipolar refinement of aldose reductase at subatomic resolution. Acta Cryst. A56, s199. E. I. Howard, R. Cachau, A. Mitschler, P. Barth, B. Chevrier, V. Lamour, A. Joachimiak, R. Sanishvili, M. Van Zandt, D. Moras A. Podjarny (2000). Crystallization of Aldose Reductase leading to Single Wavelength (0.66 Å) and MAD (0.9 Å) subatomic resolution studies. Acta Cryst. A56, s57. A. D. Podjarny, A. Mitschler, I. Hazemann, T. Petrova, F. Ruiz, E. Howard, C. Darmanin, R. Chung, T. R. Schneider, R. Sanishvili, C. Schulze-Briesse, T. Tomizaki, M. Van Zandt, M. Oka, A. Joachimiak O. El-Kabbani (2005). Inhibitor binding to aldose reductase studied at subatomic resolution. Acta Cryst. A61, c122. Pavel. On 9/15/10 3:34 PM, Sanishvili, Ruslan wrote: Hi All, I have not read all messages in the trace so my apologies if somebody already pointed out what I have to say. There is lot of talk about how this or that software treats the riding hydrogens. What to do with the fact that however these hydrogens are treated in calculations, they are, in most cases, still assumed? Meents et al http://scripts.iucr.org/cgi-bin/paper?xh0004 showed that proteins are stripped of hydrogens during X-ray data collection. So, IMHO it is a good argument against depositing the H coordinates in PDB. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George M. Sheldrick Sent: Wednesday, September 15, 2010 5:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb]
Re: [ccp4bb] Deposition of riding H
Hi Nukri, Note that in the ultra-high resolution structure of aldose reductase http://www.ncbi.nlm.nih.gov/pubmed/15146478 we didn't see all (or most) hydrogens. So, the converse question one could ask is why we didn't see all of them? Was it only because of higher B-factors or because some of them were stripped during data collection? yes, we saw ~54% of them - I used to work on this at some point too ( Blakeley MP, Ruiz F, Cachau R, Hazemann I, Meilleur F, Mitschler A, Ginell S, Afonine P, Ventura ON, Cousido-Siah A, et al. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Proc Natl Acad Sci U S A.2008;105(6):1844--1848.) My impression at that point was that we did not see the rest partially because the model was not good enough (in terms of seeing fine details). What I mean is that improving model from R-factor~10 to R~9% resulted in adding ~10% more visible H atoms. When I then refined the model down to ~7% using Interatomic Scatterers model (to account for deformation density) the amount of observable H atoms increased from published 54% up to ~68% or so (writing from memory). So, hypothetically, I guess, if we could refine it down to some lower R-factor we then would see even more H atoms (and the rest, if we finally don't see them - would probably be those that gone). The resolution and B-factors are necessary but not enough to see H atoms - the overall noise level is a key too. All the best! Pavel.
[ccp4bb] Postdoctoral positions available
SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA Postdoctoral positions in protein biochemistry and structural biology are available for suitably qualified PhD graduates to pursue research into improving our understanding of the relationship between protein structure and function - one of the foremost challenges in post-genomic biology. To this end, our research interests are consolidated into two main areas: (1) the stability, dynamics and folding mechanisms of multidomain and oligomeric proteins, and, (2) the structural and energetic foundations of molecular recognition between proteins and other molecules such as drugs, proteins and membranes. Proteins under investigation are of relevance to human health and include proteins involved in molecular toxicology, oxidative stress, cancer, apoptosis and HIV/AIDS. Excellent in-house facilities are available for protein expression, purification and crystallisation as well as for state-of-the-art biophysical techniques such as protein crystallography, UV/Vis, CD and fluorescence spectroscopy, isothermal titration calorimetry, and stopped-flow kinetics. Successful candidates should have a PhD degree in biochemistry, molecular biology, chemistry or crystallography. Good communication (written and verbal) and interpersonal skills, and computer literacy are absolute requirements. Interested applicants should send a letter of motivation, CV, PhD synopsis, certified copy of PhD degree, and a list of three references with their email addresses to: Prof Heini Dirr, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa. E-mail heinrich.d...@wits.ac.za. htmlpfont face = verdana size = 0.8 color = navyThis communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html image001.jpg
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote: so, wouldn't be the deposition of the final model's Fcalc, Phic (and their weights) along with the final coordinates be the best solution? The final Fcalc are our best model and can be used to reproduce the final statistics (which would remove the sfcheck annoyance) and to reproduce the final electron density maps, and the coordinates can be used for what ever purpose they are needed, irrespective of adding riding hydrogens or not. Now I'm confused. Isn't that already the recommended, if not required, practice? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Hi Dirk, so, wouldn't be the deposition of the final model's Fcalc, Phic (and their weights) along with the final coordinates be the best solution? The final Fcalc are our best model and can be used to reproduce the final statistics (which would remove the sfcheck annoyance) and to reproduce the final electron density maps, and the coordinates can be used for what ever purpose they are needed, irrespective of adding riding hydrogens or not. it is a great idea and if you look in PDB deposited structure factors there is a number of them (but certainly not the majority) that are accompanied by Fcalc. However, a few things to keep in mind: - Imagine a (not very uncommon, unfortunately) situation when someone obtains the final model and Fcalc, and then, right before the PDB deposition does a final check in Coot, and moves/removes a few atoms (a few waters, or instance) here and there. Or may be does a real-space fit of a residue. Or removes H, if present. Or renames a ligand by request of PDB staff and accidentally change an atom parameter(s). All this in turn will invalidate the R-factors and make previously calculated Fcalc inconsistent with such a manipulated model. So, the bottom-line is: having a model that you can use to reproduce the reported statistics is important (for validation and database sanity at least, if someones believe that such a minor things wouldn't impair the biological interpretation - ultimate goal of protein structures). - To reproduce typically the most used electron density maps, such as 2mFo-DFc and mFo-DFc, you would also need to deposit coefficients m and D, or, alternatively, have a program and free-R flags handy to compute m and D yourself. - Requiring Fcalc, you would have to make sure that this is actually the total structure factors Fmodel = scales*(Fcalc_atoms + F_bulk_solvent) with all other appropriate scales included. Although, this is easy to do by computing the R-factor and comparing it with the reported number. All the best! Pavel.
[ccp4bb] Parrot versus prime-and-switch-phasing
Hi all, To decrease model bias from molecular replacement we can either use Parrot or prime-and-switch-phasing. What's the difference between these two programs? Which one is better? Thank you very much! Yamei Yu
Re: [ccp4bb] Parrot versus prime-and-switch-phasing
Try both and look at the maps. Both are easy to run. (Which works best seems to vary a lot from case to case.) Yamei Yu wrote: Hi all, To decrease model bias from molecular replacement we can either use Parrot or prime-and-switch-phasing. What's the difference between these two programs? Which one is better? Thank you very much! Yamei Yu -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my mtz file had Fc Phic FOM + other data put
out by Phenix - pavel can elaborate. rcsb stripped almost all of this
and the processed file has only:
HKL, Flag, Fc, SigmaF and FOC :{
What's a structural biologist to do?
--
Mark
[ccp4bb] Map density level
Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Map density level
Hi, It can, just do fm-mode select rmsd I am curious though, I have heard that it is 'better' to build in units of absolute density, but I couldn't find any values. Does any one have a suggestion as to what absolute electron density setting is 'correct' for an Fo-Fc difference map? Or do you just eyeball it? Nat On Thu, Sep 16, 2010 at 1:03 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Hi Mark,
I assume you deposited the mtz? This is what Ethan was referring to - the pdb
does not do well with maintaining all the relevant columns when submitting the
mtz file. However, if you convert your mtz to cif yourself and make sure it
has all the columns you would like to include and then submit this cif file to
the pdb, all the information is retained.
Eric
__
Eric Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Thu, 16 Sep 2010, Dr. Mark Mayer wrote:
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the the
riding H discussion, my mtz file had Fc Phic FOM + other data put out by
Phenix - pavel can elaborate. rcsb stripped almost all of this and the
processed file has only:
HKL, Flag, Fc, SigmaF and FOC :{
What's a structural biologist to do?
--
Mark
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
On Thursday 16 September 2010 09:56:14 am Dr. Mark Mayer wrote:
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my mtz file had Fc Phic FOM + other data put
out by Phenix - pavel can elaborate. rcsb stripped almost all of this
and the processed file has only:
HKL, Flag, Fc, SigmaF and FOC :{
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a description of the data
columns. The columns present depend on what you fed it, of course.
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.status
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.intensity_meas
_refln.intensity_sigma
_refln.F_calc
_refln.fom
_refln.phase_meas
Caveat:
I have never tried to deposit a structure factor file from phenix;
maybe that triggers some other processing pathway. Does anyone here know?
I would say that the simple, and almost guaranteed to work, procedure
is to do the cif conversion yourself and deposit the cif file.
I noted in another message that the auto-conversion script on
the PDB deposition site has a tendency to lose columns.
That's why it is better to do the conversion yourself.
I can't say that they _never_ lose columns in an uploaded cif file.
I have had that happen, but only once and quite a while ago.
What's a structural biologist to do?
The empiricist's approach.
Experiment till you find a procedure that works, then stick to it :-)
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
Re: [ccp4bb] Map density level
According to the really good documentation of O, e.g. at http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html you have to use the command fm_mode to change this (and while doing so might read Alwyns FM_Overview in the same documentation which I just did and found very interesting!). Cheers, Tim On Thu, Sep 16, 2010 at 01:03:38PM -0400, Hailiang Zhang wrote: Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Intl Conf on Structural Genomics, Toronto, Canada, May 10-14, 2011
Dear Colleagues, We are pleased to let you know about the upcoming International Conference on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics and structural/chemical biology, and their impact on research in biology, medicine and disease. A limited number of student travel fellowships will be available for travel to this meeting. A substantial number of short talks will be selected from poster abstracts. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
On Thu, Sep 16, 2010 at 10:19:14AM -0700, Ethan Merritt wrote: [...] What's a structural biologist to do? The empiricist's approach. Experiment till you find a procedure that works, then stick to it :-) ... or the social approach: communicate with the person at the PDB responsible for your deposition. So far that's work great for me (plaudit for the people at the PDB(e)). Tim -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Map density level
The main advantage of contouring in absolute units is consistency. The density for a water molecule with a B factor of 20 A^2 will look about the same even if the noise level of one map is higher than another. (Within limits, of course) This means that the actual value you contour at isn't as important as the choice of the same value all the time. You want to train your eye for what good density looks like at the level you use. I've picked 0.36 e/A^3 (don't get me started on units!) for density maps and 0.18 e/A^3 for difference maps as my personal values. The former is usually about 1 sigma and the latter about 3 sigma but of course the sigmas float based on other factors. I will look at the map contoured at lower levels when looking for atoms at lower than full occupancy, but I always start at the same place. When first learning model building it is useful to leave out a water molecule. That way you can see what a good water molecule looks like in your current difference map and can compare other potential water molecules to it. Dale Tronrud On 09/16/10 10:13, Nathaniel Clark wrote: Hi, It can, just do fm-mode select rmsd I am curious though, I have heard that it is 'better' to build in units of absolute density, but I couldn't find any values. Does any one have a suggestion as to what absolute electron density setting is 'correct' for an Fo-Fc difference map? Or do you just eyeball it? Nat On Thu, Sep 16, 2010 at 1:03 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang
[ccp4bb] Deposition of riding H: R-factor is overrated
Huh? That's not a cif fragment. What file are you looking at? In my experience the PDB feeds back to you a cif format structure factor file with a name like rcsb054058-sf.cif Near the top of that file you should find a description of the data columns. The columns present depend on what you fed it, of course. Come on guys - give me a break ... all I posted was just a list of the columns in the sf file - here's a cut and paste of what rcsb actually generated rcsb061284-sf.cif data_r3om0sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record'Initial release' loop_ _refln.wavelength_id _refln.crystal_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au _refln.fom 1 1 1 008 o 203.06.3 0.99 1 1 1 00 10 o 281.58.7 0.86 Below is mtzdmp of what I actually deposited (as MTZ) Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 46 0 100.00 17.7 17.7 31.88 1.40 H H 2 NONE 0 72 0 100.00 27.4 27.4 31.88 1.40 H K 3 NONE 0 81 0 100.00 30.5 30.5 31.88 1.40 H L 4 NONE3.3 2160.3 0 100.00 162.89 162.89 31.88 1.40 F FOBS 5 NONE0.960.0 0 100.00 5.36 5.36 31.88 1.40 Q SIGFOBS 6 NONE0.0 1.0 0 100.00 0.05 0.05 31.88 1.40 I R_FREE_FLAGS 7 NONE0.1 2253.6 0 100.00 157.73 157.73 31.88 1.40 F FMODEL 8 NONE -180.0 180.0 0 100.00 2.6590.13 31.88 1.40 P PHIFMODEL 9 NONE0.0 5823.1 0 100.00 219.29 219.29 31.88 1.40 F FCALC 10 NONE -180.0 180.0 0 100.00 3.2490.09 31.88 1.40 P PHIFCALC 11 NONE0.0 15330.0 0 100.00 141.04 141.04 31.88 1.40 F FMASK 12 NONE -180.0 180.0 0 100.00 4.2990.74 31.88 1.40 P PHIFMASK 13 NONE0.0 6909.4 0 100.0015.4215.42 31.88 1.40 F FBULK 14 NONE -180.0 180.0 0 100.00 4.2990.74 31.88 1.40 P PHIFBULK 15 NONE 0.803 1.199 0 100.001.0041.004 31.88 1.40 W FB_CART 16 NONE 0.001 1.000 0 100.000.8770.877 31.88 1.40 W FOM 17 NONE 0.576 0.754 0 100.000.7050.705 31.88 1.40 W ALPHA 18 NONE277.388 0 100.00 5655.391 5655.391 31.88 1.40 W BETA -- Mark
Re: [ccp4bb] Map density level
Thanks! According to the really good documentation of O, e.g. at http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html you have to use the command fm_mode to change this (and while doing so might read Alwyns FM_Overview in the same documentation which I just did and found very interesting!). Cheers, Tim On Thu, Sep 16, 2010 at 01:03:38PM -0400, Hailiang Zhang wrote: Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
On Thursday 16 September 2010 10:34:14 am Dr. Mark Mayer wrote:
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a description of the data
columns. The columns present depend on what you fed it, of course.
Come on guys - give me a break ... all I posted was just a list of
the columns in the sf file
I sincerely apologize.
Believe it or not, I mistook your emoticon for part of a file syntax
that I was not familiar with.
HKL, Flag, Fc, SigmaF and FOC :{
I thought that colon + curly bracket was some funky data delimiter.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
Re: [ccp4bb] ICCBM13 - webcast
Dear All, Thanks to all that sent comments/suggestions during the webcast that allows us to keep sound and video in the best conditions. We would like to have a few answers if you watched talks online (privately to me, not to the list). This will allow us to report to HEANET ( http://www.heanet.ie/) that kindly provided all the equipment and training to some of us to make this webcast free. (just for those that watched at least one talk) 1) Why haven't you participated in the conference a) To far / lack of funding b) Not on my direct area of interest c) I was unavailable at the dates of the Conference d) Other: 2) How many total hours of the conference have you watched a) 1h or less b) between 2h and 5h c) more then 5h 3) Did you consider valuable the existence of webcast? a) Yes b) No 4) Any other comment a) ___ Thanks very much in advance, David (one of the webcasters) ICCBM13 pictures and others on Facebook, http://tinyurl.com/iccbm13 --- David Aragão, Ph. D Membrane Structural Functional Biology Group Trinity College Dublin Ireland -- Forwarded message -- From: Valerie Pye val...@googlemail.com To: Date: Fri, 10 Sep 2010 09:31:34 +0100 Subject: Re: ICCBM13 - webcast Dear All, Lectures from the workshop and most presentations from the conference will be broadcast live. Please see http://www.iccbm13.ie/ for links. Best wishes, Val
Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules
From the idea you described, HET codes in the last pages of this article may be useful. http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1000context=chemistrypowers Best wishes, Duangrudee
