Re: [ccp4bb] choice of wavelength
Dear Colleagues, I think the following paper will be of particular interest for some aspects of this thread:- J. Appl. Cryst. (1984). 17, 118-119[ doi:10.1107/S0021889884011092 ] Optimum X-ray wavelength for protein crystallography U. W. Arndt Abstract: If the diffraction pattern from crystalline proteins is recorded with shorter wavelengths than is customary the radiation damage may be reduced and absorption corrections become less important. Best wishes, John Professor John R Helliwell DSc On Wed, Feb 15, 2012 at 11:55 PM, Bart Hazes bha...@ualberta.ca wrote: Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy, so doubling the wavelength gives 8 times diffraction intensity, but only 4 times the signal on integrating detectors (assuming the full photon energy is captured). So it would be interesting to see how the equation works out on the new counting detectors where the signal does not depend on photon energy. Another point to take into account is that beamlines can have different optimal wavelength ranges. Typically, your beamline guy/gal should be the one to ask. Maybe James Holton will chime in on this. Bart On 12-02-15 04:21 PM, Jacob Keller wrote: Well, but there is more scattering with lower energy as well. The salient parameter should probably be scattering per damage. I remember reading some systematic studies a while back in which wavelength choice ended up being insignificant, but perhaps there is more info now, or perhaps I am remembering wrong? Jacob On Wed, Feb 15, 2012 at 5:14 PM, Bosch, Juergenjubo...@jhsph.edu wrote: No impact ? Longer wavelength more absorption more damage. But between the choices given no problem. Spread of spots might be better with 1.0 versus 0.9 but that depends on your cell and also how big your detector is. Given your current resolution none of the mentioned issues are deal breakers. 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 Feb 15, 2012, at 18:08, Jacob Kellerj-kell...@fsm.northwestern.edu wrote: I would say the better practice would be to collect higher multiplicity/completeness, which should have a great impact on maps. Just watch out for radiation damage though. I think the wavelength will have no impact whatsoever. JPK On Wed, Feb 15, 2012 at 4:23 PM, Seungil Hanshan06...@gmail.com wrote: All, I am curious to hear what our CCP4 community thoughts are I have a marginally diffracting protein crystal (3-3.5 Angstrom resolution) and would like to squeeze in a few tenth of angstrom. Given that I am working on crystal quality improvement, would different wavelengths make any difference in resolution, for example 0.9 vs. 1.0 Angstrom at synchrotron? Thanks. Seungil Seungil Han, Ph.D. Pfizer Inc. Eastern Point Road, MS8118W-228 Groton, CT 06340 Tel: 860-686-1788, Fax: 860-686-2095 Email: seungil@pfizer.com -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** --
Re: [ccp4bb] DNA in coot
Le 15/02/12 11:36, Tim Gruene a écrit : Hello Lisa, which version of coot do you use? Maybe it is outdated and that function not yet properly implemented. I can confirm Bill's comment, and we work with coot 0.6.2. Cheers, Tim On 02/15/2012 09:01 AM, LISA wrote: Hi all, I am refining a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa Sorry for cross-posting, I thought some people might be interested and only in the coot list. Just to make clear my previous message: we have had exactly the same problem than Lisa reports using the latest version (0.7-pre-3971) available from Bill's repository of standalone Coot for Mac OSX 10.6. By default, this version uses Coot libraries (/Library/Coot/...) I managed to make it behave (in terms of DNA-related work) by forcing it to use CCP4 6.2.0 libraries and then adding (set-convert-to-v2-atom-names 0) to my ~/.coot file. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] All-D World
I believe Eric is paraphrasing Genesis 3. It's all the serpent's fault. http://www.ic.unicamp.br/~stolfi/PUB/misc-misc/GenesysParody.html http://www.ic.unicamp.br/%7Estolfi/PUB/misc-misc/GenesysParody.html On 16/02/2012 02:39, Eric Bennett wrote: Jacob, I wish it were that cheery. Do not forget the darker side of history. The prefix L- stands for levorotary. The levo comes from the Latin wording for left side. Left handedness is also known as sinistrality, from the Latin sinistra which also meant the left side, but over time took on the connotations that we currently associate with the word sinister. The latter word, of course, is generally associated with dark and evil. It is therefore erroneous to attribute the L amino acid to the Almighty. The L amino acid is in fact a diabolical corruption of cellular processes that begin with the D-nucleotide (D- meaning rotating to the right, but derived from dexter, meaning dextrous and skillful). The instrument which causes this perversion of God's perfect righteousness into a sign of evil deserves our strongest moral condemnation... I am referring, of course, to that devilish piece of cellular machinery known as the ribosome. The discovery of the ribosome was a significant blow to the success of what Charles Baudelaire famously called the devil's greatest trick. For years now, his acolytes have attempted to hide the truth about the ribosome by referring to its work with the neutral, innocent-sounding phrase translation. Don't be fooled, but instead pray for the development of the next generation of ribosome inhibitors, or at least dissolve the current generation in holy water before ingesting. -Eric On Feb 15, 2012, at 7:24 PM, Jacob Keller wrote: G-d is right-handed, so to speak: Ex 15:6 Thy right hand, O LORD, is become glorious in power: thy right hand, O LORD, hath dashed in pieces the enemy. Since we are made in His image, and our (chiral) molecules are the cause of making most of us right-handed, which enantiomer to use was not a real choice but rather flowed logically from His (right-handed) Essence. Our chirality is dictated by His, whatever that means! JPK On Wed, Feb 15, 2012 at 4:48 PM, William G. Scottwgsc...@ucsc.edu wrote: Hi Jacob: After giving this a great deal of reflection ….. I realized that you would face the same paradox that God had to resolve six thousand years ago at the Dawn of Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid proteins, and vice versa. Likewise, you would probably be faced with a situation where you need L-deoxyribose DNA to code for D-amino acid proteins, so once again, you need a ribozyme self-replicase to escape the Irreducible Complexity(™). (The Central Dogma at least is achiral.) At least it can be done six thousand years, which isn't unreasonable for a Ph.D. thesis project (especially when combined with an M.D.), and you, unlike Him, have access to a Sigma catalogue. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 15, 2012, at 10:28 AM, Jacob Keller wrote: So who out there wants to start an all-D microbial culture by total synthesis, a la the bacterium with the synthetic genome a while back? Could it work, I wonder? I guess that would be a certain benchmark for Man's conquest of nature. JPK ps maybe if there is a broadly-acting amino-acid isomerase or set of isomerases of appropriate properties, this could be helpful for getting the culture started--or even for preying on the L world? On Wed, Feb 15, 2012 at 12:17 PM, David Schullerdj...@cornell.edu wrote: On 02/15/12 12:41, Jacob Keller wrote: Are there any all-D proteins out there, of known structure or otherwise? If so, do enantiomer-specific catalyses become inverted? JPK What do you mean by Out There? If you mean in the PDB, then yes. As of two weeks ago, there are ~ 14 racemic structures deposited; most in space group P -1, with one outlier in space group I -4 C 2. This includes RNA, DNA, and PNA, but 6 entries are actually protein. The longest is over 80 residues. Theoretically, enantiomer-specific catalysis ought to be inverted, but most of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze protein, monellin, villin, and a designed peptide. On the other hand, if by out there you meant in nature outside of biochemistry and organic chemistry labs; then no, I am not aware of any all-D proteins. There are a few protein/peptides which include a small number of D-residues, which is marked up to nonribosomal synthesis. The first paper I managed to Google: http://jb.asm.org/content/185/24/7036.full Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic Peptides doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185 no.
Re: [ccp4bb] choice of wavelength
On 15 Feb 2012, at 23:55, Bart Hazes wrote: Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy, so doubling the wavelength gives 8 times diffraction intensity, but only 4 times the signal on integrating detectors (assuming the full photon energy is captured). So it would be interesting to see how the equation works out on the new counting detectors where the signal does not depend on photon energy. You make a good point about the variation in efficiency of the detectors, but I don't think your comment about the new counting detectors (assuming this refers to hybrid pixel detectors) is correct. The efficiency of the Pilatus detector, for example, falls off significantly at higher energies simply because the photons are not absorbed by the silicon (320 microns thick). The DQE for the Pilatus is quoted as 80% at 12KeV but only 50% at 16KeV and I think this variation is entirely (or at least mainly) due to the efficiency of absorption by the silicon. Andrew Another point to take into account is that beamlines can have different optimal wavelength ranges. Typically, your beamline guy/ gal should be the one to ask. Maybe James Holton will chime in on this. Bart On 12-02-15 04:21 PM, Jacob Keller wrote: Well, but there is more scattering with lower energy as well. The salient parameter should probably be scattering per damage. I remember reading some systematic studies a while back in which wavelength choice ended up being insignificant, but perhaps there is more info now, or perhaps I am remembering wrong? Jacob On Wed, Feb 15, 2012 at 5:14 PM, Bosch, Juergenjubo...@jhsph.edu wrote: No impact ? Longer wavelength more absorption more damage. But between the choices given no problem. Spread of spots might be better with 1.0 versus 0.9 but that depends on your cell and also how big your detector is. Given your current resolution none of the mentioned issues are deal breakers. 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 Feb 15, 2012, at 18:08, Jacob Kellerj-kell...@fsm.northwestern.edu wrote: I would say the better practice would be to collect higher multiplicity/completeness, which should have a great impact on maps. Just watch out for radiation damage though. I think the wavelength will have no impact whatsoever. JPK On Wed, Feb 15, 2012 at 4:23 PM, Seungil Hanshan06...@gmail.com wrote: All, I am curious to hear what our CCP4 community thoughts are I have a marginally diffracting protein crystal (3-3.5 Angstrom resolution) and would like to squeeze in a few tenth of angstrom. Given that I am working on crystal quality improvement, would different wavelengths make any difference in resolution, for example 0.9 vs. 1.0 Angstrom at synchrotron? Thanks. Seungil Seungil Han, Ph.D. Pfizer Inc. Eastern Point Road, MS8118W-228 Groton, CT 06340 Tel: 860-686-1788, Fax: 860-686-2095 Email: seungil@pfizer.com -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fwd: HR3699, Research Works Act
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM, Raji Edayathumangalam wrote: If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darst da...@mail.rockefeller.edu Date: Tue, Feb 14, 2012 at 12:40 PM Subject: HR3699, Research Works Act To: Rep. Caroline Maloney has not backed off in her attempt to put forward the interests of Elsevier and other academic publishers. If you oppose this measure, please sign this petition on the official 'we the people' White House web site. It needs 23,000 signatures before February 22nd and only 1100 so far. Please forward far and wide. Oppose HR3699, the Research Works Act HR 3699, the Research Works Act will be detrimental to the free flow of scientific information that was created using Federal funds. It is an attempt to put federally funded scientific information behind pay-walls, and confer the ownership of the information to a private entity. This is an affront to open government and open access to information created using public funds. This link gets you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPM3kUxlJ7aRr7hoRAsKYAKDIs/jZHPBIV4AB2qrpBdXrSOn+VwCePabR Nm6+LK17jLJnPTqkjsQ4fV8= =a27t -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
I initially thought that it had to do with a new Hampton Research thing. But can non-American citizens sign the petition too? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Thursday, February 16, 2012 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM, Raji Edayathumangalam wrote: If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darst da...@mail.rockefeller.edu Date: Tue, Feb 14, 2012 at 12:40 PM Subject: HR3699, Research Works Act To: Rep. Caroline Maloney has not backed off in her attempt to put forward the interests of Elsevier and other academic publishers. If you oppose this measure, please sign this petition on the official 'we the people' White House web site. It needs 23,000 signatures before February 22nd and only 1100 so far. Please forward far and wide. Oppose HR3699, the Research Works Act HR 3699, the Research Works Act will be detrimental to the free flow of scientific information that was created using Federal funds. It is an attempt to put federally funded scientific information behind pay-walls, and confer the ownership of the information to a private entity. This is an affront to open government and open access to information created using public funds. This link gets you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPM3kUxlJ7aRr7hoRAsKYAKDIs/jZHPBIV4AB2qrpBdXrSOn+VwCePabR Nm6+LK17jLJnPTqkjsQ4fV8= =a27t -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
I signed, and I think so. Further information can be found here: http://www.guardian.co.uk/science/2012/feb/02/academics-boycott-publisher-elsevier On 16 Feb 2012, at 11:41, Boaz Shaanan wrote: I initially thought that it had to do with a new Hampton Research thing. But can non-American citizens sign the petition too? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Thursday, February 16, 2012 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM, Raji Edayathumangalam wrote: If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darst da...@mail.rockefeller.edu Date: Tue, Feb 14, 2012 at 12:40 PM Subject: HR3699, Research Works Act To: Rep. Caroline Maloney has not backed off in her attempt to put forward the interests of Elsevier and other academic publishers. If you oppose this measure, please sign this petition on the official 'we the people' White House web site. It needs 23,000 signatures before February 22nd and only 1100 so far. Please forward far and wide. Oppose HR3699, the Research Works Act HR 3699, the Research Works Act will be detrimental to the free flow of scientific information that was created using Federal funds. It is an attempt to put federally funded scientific information behind pay-walls, and confer the ownership of the information to a private entity. This is an affront to open government and open access to information created using public funds. This link gets you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPM3kUxlJ7aRr7hoRAsKYAKDIs/jZHPBIV4AB2qrpBdXrSOn+VwCePabR Nm6+LK17jLJnPTqkjsQ4fV8= =a27t -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Reading the H.R.3699 bill as put forward (http://thomas.loc.gov/cgi-bin/bdquery/z?d112:HR03699:@@@Lsumm2=m;) it seems to be about prohibiting US federal agencies from having policies which permit, authorise or require authors' assent to break the law of copyright in respect of published journal articles describing work funded at least in part by a US federal agency. I'm assuming that network dissemination without the publisher's consent is the same thing as breaking the law of copyright. It seems to imply that it would still be legal for US federal agencies to encourage others to break the law of copyright in respect of journal articles describing work funded by say UK funding agences! - or is there already a US law in place which prohibits that? I'm only surprised that encouraging others to break the law isn't already illegal (even for Govt agencies): isn't that the law of incitement (http://en.wikipedia.org/wiki/Incitement)? This forum in fact already has such a policy in place for all journal articles (i..e not just those funded by US federal agencies but by all funding agencies), i.e. we actively discourage postings which incite others to break the law by asking for copies of copyrighted published articles. Perhaps the next petition should seek to overturn this policy? This petition seems to be targeting the wrong law: if what you want is free flow of information then it's the copyright law that you need to petition to overturn, or you get around it by publishing in someplace that doesn't require transfer of copyright. Cheers -- Ian On 16 February 2012 09:35, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM, Raji Edayathumangalam wrote: If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darst da...@mail.rockefeller.edu Date: Tue, Feb 14, 2012 at 12:40 PM Subject: HR3699, Research Works Act To: Rep. Caroline Maloney has not backed off in her attempt to put forward the interests of Elsevier and other academic publishers. If you oppose this measure, please sign this petition on the official 'we the people' White House web site. It needs 23,000 signatures before February 22nd and only 1100 so far. Please forward far and wide. Oppose HR3699, the Research Works Act HR 3699, the Research Works Act will be detrimental to the free flow of scientific information that was created using Federal funds. It is an attempt to put federally funded scientific information behind pay-walls, and confer the ownership of the information to a private entity. This is an affront to open government and open access to information created using public funds. This link gets you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPM3kUxlJ7aRr7hoRAsKYAKDIs/jZHPBIV4AB2qrpBdXrSOn+VwCePabR Nm6+LK17jLJnPTqkjsQ4fV8= =a27t -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers with the rights of authors and the interests of the scientific community. Most publishers fare quite well under a policy that gives them a year of exclusive control over papers, followed by open access. It is, unfortunately, a standard ploy in current American politics to make a law which does something likely to be very unpopular and very unreasonable sound like it is a law doing something quite different. Please reread it carefully. I think you will join in opposing this law. Science benefits from the NIH open access policy and the rights of all concerned are respected. It would be a mistake to allow the NIH open access policy to be killed. I hope you will sign the petition. Regards, Herbert On 2/16/12 6:29 AM, Ian Tickle wrote: Reading the H.R.3699 bill as put forward (http://thomas.loc.gov/cgi-bin/bdquery/z?d112:HR03699:@@@Lsumm2=m;) it seems to be about prohibiting US federal agencies from having policies which permit, authorise or require authors' assent to break the law of copyright in respect of published journal articles describing work funded at least in part by a US federal agency. I'm assuming that network dissemination without the publisher's consent is the same thing as breaking the law of copyright. It seems to imply that it would still be legal for US federal agencies to encourage others to break the law of copyright in respect of journal articles describing work funded by say UK funding agences! - or is there already a US law in place which prohibits that? I'm only surprised that encouraging others to break the law isn't already illegal (even for Govt agencies): isn't that the law of incitement (http://en.wikipedia.org/wiki/Incitement)? This forum in fact already has such a policy in place for all journal articles (i..e not just those funded by US federal agencies but by all funding agencies), i.e. we actively discourage postings which incite others to break the law by asking for copies of copyrighted published articles. Perhaps the next petition should seek to overturn this policy? This petition seems to be targeting the wrong law: if what you want is free flow of information then it's the copyright law that you need to petition to overturn, or you get around it by publishing in someplace that doesn't require transfer of copyright. Cheers -- Ian On 16 February 2012 09:35, Tim Gruenet...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM, Raji Edayathumangalam wrote: If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darstda...@mail.rockefeller.edu Date: Tue, Feb 14, 2012 at 12:40 PM Subject: HR3699, Research Works Act To: Rep. Caroline Maloney has not backed off in her attempt to put forward the interests of Elsevier and other academic publishers. If you oppose this measure, please sign this petition on the official 'we the people' White House web site. It needs 23,000 signatures before February 22nd and only 1100 so far. Please forward far and wide. Oppose HR3699, the Research Works Act HR 3699, the Research Works Act will be detrimental to the free flow of scientific information that was created using Federal funds. It is an attempt to put federally funded scientific information behind pay-walls, and confer the ownership of the information to a private entity. This is an affront to open government and open access to information created using public funds. This link gets you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPM3kUxlJ7aRr7hoRAsKYAKDIs/jZHPBIV4AB2qrpBdXrSOn+VwCePabR Nm6+LK17jLJnPTqkjsQ4fV8= =a27t -END PGP SIGNATURE-
[ccp4bb] REFMAC 5.7
Dear board, How do I define base-pairing restraints in DNA in REFMAC 5.7? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University
[ccp4bb] offtopic : Signed binaries in the next OS X
It seems that Apple is building a higher walled garden for OS X in the form of signed binaries. They're not mandating every app come from the appstore but instead have a level that allows developers to 'sign' their binaries with their own developer ID (which of course costs $99USD/year). Or the user can go rogue and 'Ctrl-Click' install any application. http://www.apple.com/macosx/mountain-lion/security.html Personally I'll probably choose Mac App Store and identified developers. (I imagine this will be the default). - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] REFMAC 5.7
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Morten, the 'external' keyword as e.g. exploited by Rob Nicholls' prosmart http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ Software-ProSmart could probably do that. The syntax reads like exte dist first chain I resi 9 ins . atom N second chain I resi 9 ins . atom O value 3.35374 sigma 0.1 (all in one line) Read the prosmart documentation for how to use this in refmac. Tim On 02/16/2012 03:39 PM, Morten Groftehauge wrote: Dear board, How do I define base-pairing restraints in DNA in REFMAC 5.7? Cheers, Morten - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPRpaUxlJ7aRr7hoRAmOtAJ9myX62PYfbJ+c8hdi/BnL2PiZ8bgCdF0nK FhE25jTOTgzGrCx2+PeUrdo= =9Abc -END PGP SIGNATURE-
Re: [ccp4bb] offtopic : Signed binaries in the next OS X
Hi Tim The problem is not developers ensuring their identities by signing their apps. It's that there's now a (small) barrier for the end user in installing unsigned apps. The implementation has yet to be seen, but will getting around this barrier simply be a pop up (press OK if you really trust this software, the implementation most people are familiar with but largely ineffective IMHO), or will the INSTALL file include OS X specific directives to circumvent the walled garden? (OS X users must CTRL-Click to install this application). You could sign your own software (for free) and then distribute your public key to the community, in case you want to do something similar. [FUD] OS X won't trust those keys, only the ones that come from apple [/FUD] F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] offtopic : Signed binaries in the next OS X
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Francis, not sure what you are trying to say. Many people have been securing their software e.g. with md5sums or PGP-signatures. Debian do that, and they do it for free as far as I know. You could sign your own software (for free) and then distribute your public key to the community, in case you want to do something similar. Cheers, Tim P.S. If anyone happens to know Annie Schott (asch...@cipf.es) could they help her to set up her vacation notifier to send her spanish news only once per email address? I keep on getting her notification anytime I send an email to this board. On 02/16/2012 04:01 PM, Francis E Reyes wrote: It seems that Apple is building a higher walled garden for OS X in the form of signed binaries. They're not mandating every app come from the appstore but instead have a level that allows developers to 'sign' their binaries with their own developer ID (which of course costs $99USD/year). Or the user can go rogue and 'Ctrl-Click' install any application. http://www.apple.com/macosx/mountain-lion/security.html Personally I'll probably choose Mac App Store and identified developers. (I imagine this will be the default). - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPRwLUxlJ7aRr7hoRAqKCAJ9ls/8obgOQWV4fxNbPPW+3VNV3nQCfQVTs LANAnhO3bft5FYVXQUQq1CA= =BlB9 -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers with the rights of authors and the interests of the scientific community. Most publishers fare quite well under a policy that gives them a year of exclusive control over papers, followed by open access. It is, unfortunately, a standard ploy in current American politics to make a law which does something likely to be very unpopular and very unreasonable sound like it is a law doing something quite different. Please reread it carefully. I think you will join in opposing this law. Science benefits from the NIH open access policy and the rights of all concerned are respected. It would be a mistake to allow the NIH open access policy to be killed. I hope you will sign the petition. Regards, Herbert On 2/16/12 6:29 AM, Ian Tickle wrote: Reading the H.R.3699 bill as put forward (http://thomas.loc.gov/cgi-bin/bdquery/z?d112:HR03699:@@@Lsumm2=m;) it seems to be about prohibiting US federal agencies from having policies which permit, authorise or
Re: [ccp4bb] offtopic : Signed binaries in the next OS X
Hi Tim, we all get the aschott notification - I don't know her, but I do know about the CIPF, the Centro de Investigacion Principe Felipe in Valencia, Spain. This centre recently laid off an important number of researchers and I would guess she was one of them - so I doubt she will want anything to do with them. You can look up the CIPF administrators and send them a mail, but if they really are as incompetent as the news coverage suggest, I also doubt they will take any notice. See: http://www.nature.com/news/2011/01/full/news.2011.623.html I think the only solution is to ask the CCP4bb administrators to unsubscribe the email address for her... Mark Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 16 Feb 2012, at 16:08, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Francis, not sure what you are trying to say. Many people have been securing their software e.g. with md5sums or PGP-signatures. Debian do that, and they do it for free as far as I know. You could sign your own software (for free) and then distribute your public key to the community, in case you want to do something similar. Cheers, Tim P.S. If anyone happens to know Annie Schott (asch...@cipf.es) could they help her to set up her vacation notifier to send her spanish news only once per email address? I keep on getting her notification anytime I send an email to this board. On 02/16/2012 04:01 PM, Francis E Reyes wrote: It seems that Apple is building a higher walled garden for OS X in the form of signed binaries. They're not mandating every app come from the appstore but instead have a level that allows developers to 'sign' their binaries with their own developer ID (which of course costs $99USD/year). Or the user can go rogue and 'Ctrl-Click' install any application. http://www.apple.com/macosx/mountain-lion/security.html Personally I'll probably choose Mac App Store and identified developers. (I imagine this will be the default). - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPRwLUxlJ7aRr7hoRAqKCAJ9ls/8obgOQWV4fxNbPPW+3VNV3nQCfQVTs LANAnhO3bft5FYVXQUQq1CA= =BlB9 -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers with the rights of authors and the interests of the scientific community. Most publishers fare quite well under a policy that gives them a year of exclusive control over papers, followed by open access. It is, unfortunately, a standard ploy in current American politics to make a law which does something likely to be very unpopular and very unreasonable sound like it is a law doing something quite different. Please reread it carefully. I think you will join in opposing this law. Science benefits from the NIH open access policy and the rights of all concerned
Re: [ccp4bb] Fwd: HR3699, Research Works Act
May I also suggest reading these: https://intechweb.wordpress.com/2012/01/25/selected-reading-on-research-works-act-why-you-should-care/ https://intechweb.wordpress.com/2012/02/16/open-access-on-a-string-cut-it-and-it-will-grow-back/ Can non-US based scientists sign the petition, btw? There are also several blogposts and discussions around regarding RWA and subsequent calls for boycotts of publishers that support it. A few examples (mostly from the UK): http://cameronneylon.net/blog/the-research-works-act-and-the-breakdown-of-mutual-incomprehension/ http://gowers.wordpress.com/2012/01/21/elsevier-my-part-in-its-downfall/ http//www.elsevier.com/wps/find/intro.cws_home/elsevieropenletter http//occamstypewriter.org/scurry/2012/02/12/an-open-letter-to-elsevier/ And my (very) personal views on the matter: http://www.paulasalgado.org/archives/423 Best wishes Paula On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers
Re: [ccp4bb] Fwd: HR3699, Research Works Act
There was an op-ed piece in the NY Times last month about this issue written by Michael Eisen, a found of PLos: http://www.nytimes.com/2012/01/11/opinion/research-bought-then-paid-for.html?ref=carolynbmaloney On Feb 16, 2012, at 9:47 AM, Paula Salgado wrote: May I also suggest reading these: https://intechweb.wordpress.com/2012/01/25/selected-reading-on-research-works-act-why-you-should-care/ https://intechweb.wordpress.com/2012/02/16/open-access-on-a-string-cut-it-and-it-will-grow-back/ Can non-US based scientists sign the petition, btw? There are also several blogposts and discussions around regarding RWA and subsequent calls for boycotts of publishers that support it. A few examples (mostly from the UK): http://cameronneylon.net/blog/the-research-works-act-and-the-breakdown-of-mutual-incomprehension/ http://gowers.wordpress.com/2012/01/21/elsevier-my-part-in-its-downfall/ http//www.elsevier.com/wps/find/intro.cws_home/elsevieropenletter http//occamstypewriter.org/scurry/2012/02/12/an-open-letter-to-elsevier/ And my (very) personal views on the matter: http://www.paulasalgado.org/archives/423 Best wishes Paula On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Can non-US based scientists sign the petition, btw? Well there's nothing to stop you! It asks for your zip code, but I just left it blank and it accepted it. Cheers -- Ian
Re: [ccp4bb] Fwd: HR3699, Research Works Act
For what it's worth, my own experience with the issue of scholarly publication and open access is nuanced enough that perhaps my two-bits worth can add to this discussion. In short, I agree both with Ian's previous message and with Herbert, and feel that the incompatibility between them goes to the root of a problem for which the answer is certainly not quite there. I have been much influenced by the work done on this issue by Fred Dylla, Executive Director of the American Institute of Physics. Here is a link to recent information concerning his four-year effort to reach consensus on this issue: http://www.aip.org/aip/aipmatters/archive/2011/1_24_11.html I personally think that the NIH Open Access requirement is a vast overreach. PubMed Central is very difficult to use and ultimately has never satisfied me: I always go to the UNC library holdings. There are several reasons why. The most immediate is that PubMed Central almost never gives a satisfactory copy of a paper I want to read, and the most serious reason is that I am convinced that the overhead exacted on authors and PIs by the NIH means that few, if any authors give much more than a glance in the direction of updating deposited manuscripts from journals that do not automatically deposit the version of record. For this reason, many PubMed Central entries are likely to have more than minor errors corrected in proof only in the version of record. I don't personally see any way around the problem that there is only one version of record and that version is the one for which copyright is retained by the publisher. On the other hand, I am deeply sympathetic to the argument that publicly-funded research must be freely accessible. After talking intensely with the library administrators at UNC, I also believe deeply that university library subscriptions satisfy the need for open access. Casting aside for the moment the issue of Open Access journals, whose only real difference lies in who pays the costs of publication, I have long believed that careful validation through peer review constitutes serious added value and that journals are entitled to being paid for that added value. What makes this issue more difficult for me is that I share with many the deep suspicions of corporate (as opposed to Member Society) publishing organizations. Several years ago I withdrew my expertise from the Nature group in protest over what I felt (after, again, long discussions with our UNC librarians) was a power play designed only to weaken the library systems. I have similar views about Elsevier. Finally, I am inclined to sign this petition for other reasons, including the fact that HR 3699 appears to be as deeply flawed in the other direction as the original enabling legislation that vested such power in the NIH and, in the same act, all but eliminated any opposition by diluting responsibility for compliance to the fullest possible extent, by penalizing PIs for non-compliance. When I first read of this petition, I was deeply incensed that the wing nuts in Congress would craft a bill so obviously designed to reward the 1%, so to speak. In closing, I earnestly recommend that as many of you as possible look into Fred Dylla's work on this issue. The AIP is a publisher whose only revenue other than philanthropy comes from the intellectual property and added value of its journals, some of which represent the finest in physical chemistry relevant to our community. Dylla deserves kudos for his effort to find consensus, something that seems to have gone way out of fashion in recent years. Charlie On Feb 16, 2012, at 10:37 AM, Ian Tickle wrote: Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Can non-US residents sign this petition? You need a Whitehouse.gov account and in order to register you have to provide a U.S. (I presume) zipcode. At 15:37 16-02-2012, Ian Tickle wrote: Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers with the rights of authors and the interests of the scientific community. Most publishers fare quite well under a policy that gives them a year of exclusive control over papers, followed by open access. It is, unfortunately, a standard ploy in current American politics to make a law which does something likely to be very unpopular and very unreasonable sound like
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Pedro, Well it worked for me (and I see many others) without a zip code. I see that someone else typed Bayreuth in the zip code field - so I suspect you can type anything there! Cheers -- Ian On 16 February 2012 16:31, Pedro M. Matias mat...@itqb.unl.pt wrote: Can non-US residents sign this petition? You need a Whitehouse.gov account and in order to register you have to provide a U.S. (I presume) zipcode. At 15:37 16-02-2012, Ian Tickle wrote: Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the U.S. government, describing or interpreting research funded in whole or in part by a federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing, but does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research. == It is the second provision that really cuts the legs out from the NIH open access policy. What the NIH policy does is to make open access publication a condition imposed on the grant holders in publishing work that the NIH funded. This has provided the necessary lever for NIH-funded authors to be able to publish in well-respected journals and still to be able to require that, after a year, their work be available without charge to the scientific community. Without that lever we go back to the unlamented old system (at least unlamented by almost everybody other than Elsevier) in which pubishers could impose an absolute copyright transfer that barred the authors from ever posting copies of their work on the web. People affiliated with libraries with the appropriate subscriptions to the appropriate archiving services may not have noticed the difference, but for the significant portions of both researchers and students who did not have such access, the NIH open access policy was by itself a major game changer, making much more literature rapidly accessible, and even more importantly changed the culture, making open access much more respectable. The NIH policy does nothing more than put grant-sponsored research on almost the same footing as research done directly by the government which has never been subject to copyright at all, on the theory that, if the tax-payers already paid for the research, they should have open access to the fruits of that research. This law would kill that policy. This would be a major step backwards. Please read: http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/ http://www.taxpayeraccess.org/action/action_access/12-0106.shtml http://www.care2.com/causes/open-access-under-threat-hr-3699.html Please support the petition. This is a very bad bill. It is not about protecting copyright, it is an effort to restrict the free flow of scientific information in our community. Regards, Herbert On 2/16/12 9:02 AM, Fischmann, Thierry wrote: Herbert I don't see how the act could affect the NIH open access policy. Could you please shed some light on that? What I read seems reasonable and I intend to ask my representatives to support this text. But obviously I am missing something and like to learn from you first. Regards Thierry -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances
[ccp4bb] Bond Length Outliers (correction)
Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 - Original Message - From: Bernard D. Santarsiero b...@uic.edu To: Greg Costakes gcost...@purdue.edu Sent: Thursday, February 16, 2012 11:42:55 AM Subject: Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907
Re: [ccp4bb] Fwd: HR3699, Research Works Act
I am strongly in favour of Open Acess, but Open Access is not always helped by lack of money for editing etc. For example: Acta Crystallographica is not Open Acess. In one manner or another publishing must be financed. Libraries pay fees for the journals. The fees help the International Union of Crystallography. The money is used for sponsoring meetings, and some scientists that come from less rich institutions benefit from it. Open Acess to NIH sponsored scientific work will be for all world tax payers and tax doggers as well. OR May be you would suggest that NIH sponsored work should be accessed only by US tax payers with a valid social security number? The journal server will verify that Tax for the current year has been filed with the IRS server. A dangerous invasion of privacy! The more legislation we add the worse off we are. If the authors of a paper wants their work to be available to the general public there is Wikipedia. I strongly support an effort by all members of ccp4bb to contribute a general public summary of their work on Wikipedia. There are Open Source journals as well. I would urge everybody NOT to sign the petition. Elsevier will not last for ever, and the less accessible the work that they publish, the worse for them in terms of impact factor. In the old days, if your institution did not have the journal, most likely you would not reference the work and the journal was worth nothing. We are the ones that will decide the future of Elsevier. Elsevier will need to strike a balance between excellent publishing with resonable fees or not getting referenced. A law that enforces a copyright will not help them. They are wasting their money on lobbing. The argument that NIH scientist need to publish in High Impact Factor Journals by Elsevier does not hold up: 1) We should consider the use of impact factor as a NEGATIVE contribution to science. 2) Each article can now have its own impact factor on Google Scholar, independent on the journal it is published in. 3) Even for journals not indexed on PubMed, Google Scholar finds them. I hold the same opinion for the OsX debate. Don't buy Apple! Use linux instead. When enough people protest where it really hurts the company, they will no longer have the money to lobby the American Congressmen. If they make an excellent product, then they deserve the money and quite rightly they can try to build a monopoly around their technology. I fight that, I use LINUX. By signing petitions we acknowledge the power of the legislators. This is another form of lobbing. If we disapprove of lobbing we should not engage in the practice even if we give no money. We have more powerful means of protest. The 24 Hour shutdown of Wikipedia meets my approval. There is also patenting. How do we feel about it? Some of the work I have done has also been patented. I do not feel right about it. There is MONEY everywhere. This ruins our ability to acqure knowledge that should be free for everybody. But since it costs to acquire it, it cannot be free. LAWS should be for the benefit of the nation. But legislators have the problem of money to be re-elected. Can we trust them? Can we trust their laws? Companies also play very useful roles. Some companies less so. But at least they work for a profit and thus they must provide a worth while service. This is not true for politicians. Enrico. -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71 On Thu, 16 Feb 2012 16:47:26 +0100, Paula Salgado p.salg...@imperial.ac.uk wrote: May I also suggest reading these: https://intechweb.wordpress.com/2012/01/25/selected-reading-on-research-works-act-why-you-should-care/ https://intechweb.wordpress.com/2012/02/16/open-access-on-a-string-cut-it-and-it-will-grow-back/ Can non-US based scientists sign the petition, btw? There are also several blogposts and discussions around regarding RWA and subsequent calls for boycotts of publishers that support it. A few examples (mostly from the UK): http://cameronneylon.net/blog/the-research-works-act-and-the-breakdown-of-mutual-incomprehension/ http://gowers.wordpress.com/2012/01/21/elsevier-my-part-in-its-downfall/ http//www.elsevier.com/wps/find/intro.cws_home/elsevieropenletter http//occamstypewriter.org/scurry/2012/02/12/an-open-letter-to-elsevier/ And my (very) personal views on the matter: http://www.paulasalgado.org/archives/423 Best wishes Paula On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy,
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Charlie, A much more balanced view than others have posted. NIH Open Access requirement is a vast overreach. I agree. HR 3699 appears to be as deeply flawed. It could be made better with amendments? Enrico. On Thu, 16 Feb 2012 17:06:24 +0100, Charles W. Carter, Jr car...@med.unc.edu wrote: For what it's worth, my own experience with the issue of scholarly publication and open access is nuanced enough that perhaps my two-bits worth can add to this discussion. In short, I agree both with Ian's previous message and with Herbert, and feel that the incompatibility between them goes to the root of a problem for which the answer is certainly not quite there. I have been much influenced by the work done on this issue by Fred Dylla, Executive Director of the American Institute of Physics. Here is a link to recent information concerning his four-year effort to reach consensus on this issue: http://www.aip.org/aip/aipmatters/archive/2011/1_24_11.html I personally think that the NIH Open Access requirement is a vast overreach. PubMed Central is very difficult to use and ultimately has never satisfied me: I always go to the UNC library holdings. There are several reasons why. The most immediate is that PubMed Central almost never gives a satisfactory copy of a paper I want to read, and the most serious reason is that I am convinced that the overhead exacted on authors and PIs by the NIH means that few, if any authors give much more than a glance in the direction of updating deposited manuscripts from journals that do not automatically deposit the version of record. For this reason, many PubMed Central entries are likely to have more than minor errors corrected in proof only in the version of record. I don't personally see any way around the problem that there is only one version of record and that version is the one for which copyright is retained by the publisher. On the other hand, I am deeply sympathetic to the argument that publicly-funded research must be freely accessible. After talking intensely with the library administrators at UNC, I also believe deeply that university library subscriptions satisfy the need for open access. Casting aside for the moment the issue of Open Access journals, whose only real difference lies in who pays the costs of publication, I have long believed that careful validation through peer review constitutes serious added value and that journals are entitled to being paid for that added value. What makes this issue more difficult for me is that I share with many the deep suspicions of corporate (as opposed to Member Society) publishing organizations. Several years ago I withdrew my expertise from the Nature group in protest over what I felt (after, again, long discussions with our UNC librarians) was a power play designed only to weaken the library systems. I have similar views about Elsevier. Finally, I am inclined to sign this petition for other reasons, including the fact that HR 3699 appears to be as deeply flawed in the other direction as the original enabling legislation that vested such power in the NIH and, in the same act, all but eliminated any opposition by diluting responsibility for compliance to the fullest possible extent, by penalizing PIs for non-compliance. When I first read of this petition, I was deeply incensed that the wing nuts in Congress would craft a bill so obviously designed to reward the 1%, so to speak. In closing, I earnestly recommend that as many of you as possible look into Fred Dylla's work on this issue. The AIP is a publisher whose only revenue other than philanthropy comes from the intellectual property and added value of its journals, some of which represent the finest in physical chemistry relevant to our community. Dylla deserves kudos for his effort to find consensus, something that seems to have gone way out of fashion in recent years. Charlie On Feb 16, 2012, at 10:37 AM, Ian Tickle wrote: Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On 16 February 2012 15:24, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher; or *(2) requires that any actual or prospective author, or the author's employer, assent to such network dissemination. * Defines private-sector research work as an article intended to be published in a scholarly or scientific
Re: [ccp4bb] Bond Length Outliers (correction)
Hi, If I remember correctly this angle is for the planarity of the peptide bond. Maybe you have a real deviation which might occur not so seldom than expected. You have a quite high resolution. If the density is really convincing then you may accept this outlier. Not every outlier is a mistake. However with 2.55° the r.m.s.d. for your angles is quite high I think. Christian Am Donnerstag 16 Februar 2012 18:00:10 schrieb Greg Costakes: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 --- - - Original Message - From: Bernard D. Santarsiero b...@uic.edu To: Greg Costakes gcost...@purdue.edu Sent: Thursday, February 16, 2012 11:42:55 AM Subject: Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! - -- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 - ---
Re: [ccp4bb] Fwd: HR3699, Research Works Act
Dear Colleagues, If you want an excellent, painless transfer from journal to PUBMED, just stick to the IUCr journals. They do an excellent job of cooperating in the NIH open access policy with an automatic transfer of the clean refereeded and edited paper to PUBMED. Yes, the IUCr journal copy does look prettier -- more power to them -- but nothing is missing from the PUBMED version, so everybody benefits: the IUCr has its subscription money from libraries and individuals who need results as quickly as possible or in the best form, and students and researchers without an institutional subscription can still get a completely valid and complete copy on line. If you pay IUCr for open access and are NIH funded, they deposit in PUBMED immediately. If you don't pay IUCr for open access and are NIH funded, they deposit in PUBMED a year after publication. Either way it works and works well, you get excellent editing, you are publishing in very respectable journals, and your work ends up available to everybody. So, if you want a balanced, nuanced approach, please sign the petition, but also publish in the IUCr journals if you work fits, but don't publish in any journals that don't do automatic deposition or that support the NIH Open Access policy poorly. Regards, Herbert On 2/16/12 12:27 PM, Enrico Stura wrote: Charlie, A much more balanced view than others have posted. NIH Open Access requirement is a vast overreach. I agree. HR 3699 appears to be as deeply flawed. It could be made better with amendments? Enrico. On Thu, 16 Feb 2012 17:06:24 +0100, Charles W. Carter, Jr car...@med.unc.edu wrote: For what it's worth, my own experience with the issue of scholarly publication and open access is nuanced enough that perhaps my two-bits worth can add to this discussion. In short, I agree both with Ian's previous message and with Herbert, and feel that the incompatibility between them goes to the root of a problem for which the answer is certainly not quite there. I have been much influenced by the work done on this issue by Fred Dylla, Executive Director of the American Institute of Physics. Here is a link to recent information concerning his four-year effort to reach consensus on this issue: http://www.aip.org/aip/aipmatters/archive/2011/1_24_11.html I personally think that the NIH Open Access requirement is a vast overreach. PubMed Central is very difficult to use and ultimately has never satisfied me: I always go to the UNC library holdings. There are several reasons why. The most immediate is that PubMed Central almost never gives a satisfactory copy of a paper I want to read, and the most serious reason is that I am convinced that the overhead exacted on authors and PIs by the NIH means that few, if any authors give much more than a glance in the direction of updating deposited manuscripts from journals that do not automatically deposit the version of record. For this reason, many PubMed Central entries are likely to have more than minor errors corrected in proof only in the version of record. I don't personally see any way around the problem that there is only one version of record and that version is the one for which copyright is retained by the publisher. On the other hand, I am deeply sympathetic to the argument that publicly-funded research must be freely accessible. After talking intensely with the library administrators at UNC, I also believe deeply that university library subscriptions satisfy the need for open access. Casting aside for the moment the issue of Open Access journals, whose only real difference lies in who pays the costs of publication, I have long believed that careful validation through peer review constitutes serious added value and that journals are entitled to being paid for that added value. What makes this issue more difficult for me is that I share with many the deep suspicions of corporate (as opposed to Member Society) publishing organizations. Several years ago I withdrew my expertise from the Nature group in protest over what I felt (after, again, long discussions with our UNC librarians) was a power play designed only to weaken the library systems. I have similar views about Elsevier. Finally, I am inclined to sign this petition for other reasons, including the fact that HR 3699 appears to be as deeply flawed in the other direction as the original enabling legislation that vested such power in the NIH and, in the same act, all but eliminated any opposition by diluting responsibility for compliance to the fullest possible extent, by penalizing PIs for non-compliance. When I first read of this petition, I was deeply incensed that the wing nuts in Congress would craft a bill so obviously designed to reward the 1%, so to speak. In closing, I earnestly recommend that as many of you as possible look into Fred Dylla's work on this issue. The AIP is a publisher whose only revenue other than
Re: [ccp4bb] Bond Length Outliers (correction)
Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't distort anything, it should make it, cough, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 *From: *Bernard D. Santarsiero b...@uic.edu *To: *Greg Costakes gcost...@purdue.edu *Sent: *Thursday, February 16, 2012 11:42:55 AM *Subject: *Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907
Re: [ccp4bb] Bond Length Outliers (correction)
Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Bond Length Outliers (correction) Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't distort anything, it should make it, cough, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this? -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- -- -- -- *From: *Bernard D. Santarsiero b...@uic.edu *To: *Greg Costakes gcost...@purdue.edu *Sent: *Thursday, February 16, 2012 11:42:55 AM *Subject: *Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond length = 1.15A Ala: N--Ca , bond length = 1.43A Real space refinement in Coot does not help and if I Regularize the zone it completely distorts the backbone. So my question is, how do I fix these bond length outliers? Do I need to be concerned with them? Any advice will be much appreciated. Thank you! -- - Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- --
Re: [ccp4bb] surface residue mutation
Steve Kent has published a few more (at least 1 other) since HIV... 3ODV http://www.rcsb.org/pdb/explore/explore.do?structureId=3ODV Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Pentelute, B.L., Mandal, K., Gates, Z.P., Sawaya, M.R., Yeates, T.O., Kent, S.B., Journal: (2010) Chem.Commun.(Camb.) 46: 8174-8176 _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Thursday, 16 February 2012 7:36 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] surface residue mutation Right on the money! JPK On Wed, Feb 15, 2012 at 12:28 PM, David Schuller dj...@cornell.edu wrote: On 02/15/12 12:41, Jacob Keller wrote: Are there any all-D proteins out there, of known structure or otherwise? If so, do enantiomer-specific catalyses become inverted? JPK I looked a little harder, and at least one D-enantiomeric protein was an enzyme: Total chemical synthesis of a D-enzyme: the enatiomers of HIV-1 protease show demonstration of reciprocal chiral substrate specificty R.C. deL. Milton, S.C.F. Milton, S.B.H. Kent (1992) Science 256(5062) 1445-1448. I guess that answers your question. -- == = All Things Serve the Beam == = David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fwd: [ccp4bb] protein degradation
I agree with Mark, except that I wouldn't even try sonication, Triton or freeze/thaw cycles in that case. I'd look for emulsification (with a Homogenizer) in a cold room, but if you go quickly and gently with the French Press (either in a cold room or by using a cold piston) it might help. Don't use too much pressure, it heats up the sample. I also agree that if it migrates as a single peak in gel filtration and in heparin sepharose, there is no reason for not setting some drops with it. And if you decide to do it, then simplify the purification and avoid submitting the protein to treatments that are not helping to get it purer. (I just found it weird that your fraction 6 has a huge load of protein , I guess those are actually the beads from the purification or something like that? In any case it seems to me that the fraction volume could be increased) Carlos Em 15/02/2012, às 16:39, Mark J van Raaij escreveu: try experimenting with different, especially protease-deficient, E coli strains to express the protein and try different methods to lyse the bacteria (sonication, french-press, emulsification, bead-beater, mortar pestle under liquid nitrogen). on the other hand, if you are lucky, you are just proteolysing some surface loops and can still purify and crystallise the protein. This was done on purpose for the cap-binding complex, see: Crystal structure of the human nuclear cap binding complex. Mazza C, Ohno M, Segref A, Mattaj IW, Cusack S. Mol Cell. 2001 Aug;8(2):383-96. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 15 Feb 2012, at 14:09, Sivasankar Putta wrote: Dear All, Can anybody suggest the tricks and trades of stabilizing a 133 kDa (multi domain) DNA binding protein, that we are expressing at 18 degree Centigrade in E. Coli. The protein appears to degrade during purification; we have protease inhibitor cocktail (in the lysis buffer) as well as 2 mM PMSF, 1 mM EDTA and 1mM DTT throughout during purification ( right from lysis stage). We handle the protein at 4 degree Centigrade. Can you please suggest what precautions we can try to avoid such degradation ? Please find the attached gel picture regarding protein Sivasankar Putta proteingel.pdf
[ccp4bb] Bicelle Crystallization in a Gryphon Robot
Hello all; I am wondering if anyone has any experience getting a ARI Gryphon robot to pick up protein in a bicelle solution? The nano needle on our robot does not seem to want to suck the sample up in a variety of liquid class settings. Any suggestions out there on if this can be made to work? Cheers, Cory Cory Brooks,Ph.D. University of Alberta Postdoctoral Fellow
Re: [ccp4bb] Problem with COOT and MSE (SeMET ) residues
Do you use CCP4-6.2? I met the similar problem before. Try use the latest version of coot 0.7. On Wed, Feb 15, 2012 at 8:42 AM, Christopher Browning christopher.brown...@epfl.ch wrote: Hi Laurie, Not much, I did not get any useful feedback so I emailed Paul Emsley directly. Chris On Tue, 2012-02-14 at 22:43 -0500, Laurie Betts wrote: Problem with COOT and MSE (SeMET ) residues -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot
Hello Cory, Unfortunately your Crystal Gryphon was not designed to work with all bicelle solutions. However, your Crystal Gryphon is easily upgradeable with our new LCP attachment. This will allow you to do LCP, Bicelle and Sponge Phase experiments. If you have any further questions about the Gryphon please contact David Terrell or Dave Wright at our office (888 658 5300). Regards, Art Robbins On Thu, Feb 16, 2012 at 2:53 PM, Cory Brooks cbro...@uvic.ca wrote: Hello all; I am wondering if anyone has any experience getting a ARI Gryphon robot to pick up protein in a bicelle solution? The nano needle on our robot does not seem to want to suck the sample up in a variety of liquid class settings. Any suggestions out there on if this can be made to work? Cheers, Cory Cory Brooks,Ph.D. University of Alberta Postdoctoral Fellow
Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot
there is one nice JOVE video and article from Jeff Abramson lab which was neat showing using mosquito to set up bicelle. No offense to Art people J Vis Exp. 2012 Jan 9;(59). pii: 3383. doi: 10.3791/3383. High-throughput Crystallization of Membrane Proteins Using the Lipidic Bicelle Method. Ujwal R, Abramson J. link video http://www.jove.com/video/3383/high-throughput-crystallization-of-membrane-proteins-using-the-lipidic-bicelle-method padayatti On Thu, Feb 16, 2012 at 5:53 PM, Cory Brooks cbro...@uvic.ca wrote: Hello all; I am wondering if anyone has any experience getting a ARI Gryphon robot to pick up protein in a bicelle solution? The nano needle on our robot does not seem to want to suck the sample up in a variety of liquid class settings. Any suggestions out there on if this can be made to work? Cheers, Cory Cory Brooks,Ph.D. University of Alberta Postdoctoral Fellow -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot
Sorry for self promotion but you might also consider the HILIDE method which is very similar to bicelle and sponge, only having fully solubilized protein:lipid:detergent complexes as input sample and therefore being fully compatible with regular liquid handling robotics. See Gourdon P et al 2011, Crystal Growth Design 11, 2098-2106 for the method, and Sonntag Y et al 2011, Nature Comm 2, 304 for a direct look at the bilayers formed in the crystal Poul On 16/02/2012, at 23.53, Cory Brooks cbro...@uvic.ca wrote: Hello all; I am wondering if anyone has any experience getting a ARI Gryphon robot to pick up protein in a bicelle solution? The nano needle on our robot does not seem to want to suck the sample up in a variety of liquid class settings. Any suggestions out there on if this can be made to work? Cheers, Cory Cory Brooks,Ph.D. University of Alberta Postdoctoral Fellow
