Re: [ccp4bb] Problem with making a continuous nucleic acid chain
Why dont you try CCP4MG ? Eleanor On 22 April 2014 22:37, Xiaoming Ren xiaomingre...@gmail.com wrote: Dear all: I am facing a display issue in pymol. In my structure, there is a nucleic acid chain with some monomers which are modified nucleotides built in scketcher of ccp4 suite. However, When I showed the structure in pymol as cartoon, the nucleic acid chain was discontinuous where the monomers are placed. I could not get a intact nucleic acid chain except setting the cartoon_nucleic_acid_mode value to 1, with the backbone passing through ribose C3' atoms. I tried to add SEQRES lines into the pdb file according to the pdb instruction, but it doesn't work if I want the backbone to pass through phosphorus atoms. May I get some suggestions from you? Although it's not a big problem, it's really painful. Thanks a lot and best, Xiaoming
Re: [ccp4bb] metal ion coordination
Hi evey This discussion is very informative to fresher like me. Moreover, with most of the reading suggested in this discussion I read about the positively charged metal ions like Na, Ca, Mg and many more. I am curious about Cl in specific which could occur as a result of salt used in different crystallization condition. Any information for the Cl ion co-ordiantes? Thanking you in advance. World
[ccp4bb] PyMol and Schrodinger
Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] PyMol and Schrodinger
To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.cawrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio http://www.embios.com Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
Hi Since this is the CCP4 BB, I'd give ccp4mg a try... On 23 Apr 2014, at Wed23 Apr 16:43, Cygler, Miroslaw wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] PyMol and Schrodinger
No one is keeping you from downloading the source code and compiling. It's straightforward and free. Andreas On 23/04/2014 4:43, Cygler, Miroslaw wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] PyMol and Schrodinger
On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.cawrote: I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. This is no different than the licenses that for-profit companies are required to purchase for most crystallography software. In fact, it's actually considerably more liberal than most software*, because as Jim notes you can still obtain (and redistribute) most of the source code for free. From what I can tell Schrodinger has continued to make improvements to the open-source core; some of the newer features (and the native Mac GUI) are proprietary, but that was true ten years ago. -Nat (* although I believe ccp4mg is truly open-source like Coot, and unlike CCP4 etc. which still require a license for commercial use. Or am I misinformed?)
Re: [ccp4bb] PyMol and Schrodinger
I'd like to add the under-underdog then, Tim Fenn's povscript+ https://sites.google.com/site/timfenn/povscript. Makes really clear and nice figures and is rather simple to compile. For the most part you do not even need a mouse to use it ... Michael On 23.04.2014 18:21, mark.x.brooks wrote: And to stick up for the underdog, try Chimera from UCSF, which also has been coming along nicely (understatement!): http://www.cgl.ucsf.edu/chimera/ Mark On 23 Apr 2014, at 17:48, Jim Fairman fairman@gmail.com mailto:fairman@gmail.com wrote: To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca mailto:miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio http://www.embios.com Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com mailto:fairman@gmail.com jfair...@embios.com mailto:jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
And to stick up for the underdog, try Chimera from UCSF, which also has been coming along nicely (understatement!): http://www.cgl.ucsf.edu/chimera/ Mark On 23 Apr 2014, at 17:48, Jim Fairman fairman@gmail.com wrote: To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via yum ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) yum install pymol will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] metal ion coordination
On Wed, Apr 23, 2014 at 6:15 AM, World light bsub...@btk.fi wrote: This discussion is very informative to fresher like me. Moreover, with most of the reading suggested in this discussion I read about the positively charged metal ions like Na, Ca, Mg and many more. I am curious about Cl in specific which could occur as a result of salt used in different crystallization condition. Any information for the Cl ion co-ordiantes? From Dauter Dauter (2001) (http://www.ncbi.nlm.nih.gov/pubmed/11250204): The coordination geometry of halide ions is not specific. . . Halide ions usually accept hydrogen bonds from various donor groups from the protein and neighboring water molecules. In addition, they make van der Waals contacts with non-polar protein atoms. . . The halide anions are monoatomic and polarizable, and consequently able to engage in both polar and hydrophobic interactions. . . Of the sites that are best for phasing, most contain halide ions that are hydrogen-bonded to amide nitrogen atoms, either from the protein mainchain or asparagine and glutamine sidechains. In addition, good sites often make ionic pairs with arginine or lysine residues. Sometimes, hydrogen bonds to the hydroxyl groups of threonine or serine residues can also be observed. All halide ions are in contact with water molecules, which can be ordered or in the bulk solvent region. I believe chloride is a little more predictable in this respect than the other halides (especially iodine). Also worth quoting: All halide ions share their sites with water molecules. Their coordination, appearance in electron-density maps and behavior during structure refinement is almost identical to that of fully occupied water molecules and only rarely is it possible to differentiate bromide or chloride ions from waters, especially if the sites are partially occupied. These ions can, however, be easily identified by their anomalous scattering signal. -Nat
Re: [ccp4bb] PyMol and Schrodinger
In addition to what has been mentioned by others, Open-Source PyMOL installation instructions for various platforms are available on the PyMOL Wiki: http://pymolwiki.org/index.php/Linux_Install http://pymolwiki.org/index.php/MAC_Install http://pymolwiki.org/index.php/Windows_Install Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 23, 2014, at 1:02 PM, Guenter Fritz guenter.fr...@uni-konstanz.demailto:guenter.fr...@uni-konstanz.de wrote: Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via yum ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) yum install pymol will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] metal ion coordination
To find Cl its worth looking at anomalous maps, especially for home source data, since even with partial occupancy Cl is easily located. Also, for well ordered Cl ions, B-factor will often refine to lower value than coordinating atoms when its incorrectly refined as water. Finally, in a subset of cases chemical environment is what you'd expect for an anion, with main chain NH groups, Arg/Lys side chains, and or Ser/Thr OH groups coordinating the ion.
Re: [ccp4bb] PyMol and Schrodinger
On Apr 23, 2014, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder --
Re: [ccp4bb] PyMol and Schrodinger
Hi Mirek, If you happen to be using OS X, Fink makes it very easy to install recent open-source pymol. Best regards, Dmitry On 2014-04-23, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] PyMol and Schrodinger
On 4/23/14, 1:53 PM, Francis Reyes wrote: Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. And that's why I am sticking with my last copy of Adobe Creative Suite 6, as long as it will run on a computer. When CS6 no longer works, I might be interested in moving to gimp and inkscape, which I had never considered before. I fully support Schrodinger to charge for an update, and they have vastly improved PyMOL. But being told to re-buy PyMOL annoys me, even though I would renew anyway just to support PyMOL development, and I can compile it just fine. (The expiring XDS binaries are also annoying, but there the software is free and the only purpose of the expiration is to force people to update, which I fully support.) I am hoping that Schrodinger will have a different model for academics. SBGrid is a also good option if you can afford it. It comes with PyMOL licenses. Engin
[ccp4bb] books to go
Hi, I have a collection of books that I would gladly give away to someone who may cherish them. The list is enclosed. :) Ewa SJ Ewa Skrzypczak-Jankun, PhD DH r.2250 Prof. emerita ph 419-383-5414 or 419-383-6471 University of Toledo - HSC fax 419-383-3785 College of Medicine, Urology Mail Stop#1091 email: ewa.skrzypczak-jan...@utoledo.edu 3000 Arlington Ave. Toledo OH 43614, USA Books to go.docx Description: Books to go.docx
Re: [ccp4bb] PyMol and Schrodinger
Well as s/w improvements don't necessarily happen on a yearly basis, but people like being paid each year, I think the model is not unreasonable, as long as the cost is reasonable - which, for instance, the Adobe s/w isn't. As one can tell from the profit margins of s/w companies. So I do pay my Schrodinger PyMol licenses each year. just my 2c Adrian On 23 Apr 2014, at 20:24, Engin Özkan eoz...@uchicago.edu wrote: On 4/23/14, 1:53 PM, Francis Reyes wrote: Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. And that's why I am sticking with my last copy of Adobe Creative Suite 6, as long as it will run on a computer. When CS6 no longer works, I might be interested in moving to gimp and inkscape, which I had never considered before. I fully support Schrodinger to charge for an update, and they have vastly improved PyMOL. But being told to re-buy PyMOL annoys me, even though I would renew anyway just to support PyMOL development, and I can compile it just fine. (The expiring XDS binaries are also annoying, but there the software is free and the only purpose of the expiration is to force people to update, which I fully support.) I am hoping that Schrodinger will have a different model for academics. SBGrid is a also good option if you can afford it. It comes with PyMOL licenses. Engin
Re: [ccp4bb] books to go
Hey, Are you giving them away or selling them? ;) Cheers Joana Pereira -- PhD student Lamzin Group EMBL Hamburg ℅ DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Tel:+49 40 89902-276 On 23 Apr 2014, at 21:33, Skrzypczak-Jankun, Ewa ewa.skrzypczak-jan...@utoledo.edu wrote: Hi, I have a collection of books that I would gladly give away to someone who may cherish them. The list is enclosed. J Ewa SJ Ewa Skrzypczak-Jankun, PhD DH r.2250 Prof. emerita ph 419-383-5414 or 419-383-6471 University of Toledo – HSC fax 419-383-3785 College of Medicine, Urology Mail Stop#1091 email: ewa.skrzypczak-jan...@utoledo.edu 3000 Arlington Ave. Toledo OH 43614, USA Books to go.docx
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=ae7f982d2df966a2f95f73a794d46efffb16c227a75389fdd058f5cc62d1654d The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=eaa2ef06948e08de06b7fbd47cbfe0ec2c5dac82a4c70b2ffd055bbdf10311ec you will see the percentile sliders displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=106d86fcfd3fb5e631ca04b4d6f0be2adb8a60edf33ca698248517e47de9e5c7) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=455ace0917c519ea7f631e3906413c60cf63deb9c4512491003cebf397e148d0). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=88f1dd8be8660e1657bae27e311478f5ed3dfbd2922c198277688efbe98e7ba1 - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=26d1c36fa29104dc85265fe4997ceaafec2e797dded7fb1ea2e39ae02988262a If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=3f324c797061411513168635757d7fc61545406ac5203d849b72a712bbe5e644 The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=3f50278f4e3251a6c6efc1d0f293bed530f5fb4bcd94ef2a6426d1fbcffdfc7c Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=494f114fbff8c5913722a563f0fac87daa91b4a0943e65f0c0d0258697324e71 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=ceb8a826f9fd1bcb945c2d5d2108bfcd5af42fb57dd42c876d8e434f7e44302f you will see the percentile sliders displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=c36bb823c5eab11a764ba159a174b979be73b6a5afb1bdcd821b991dd813850d) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=09ba089e02bd4ac32ff47acb46f1659bfc50fd8dbf4b0064917cc1622f5bc36f). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=30a7f6e1086c7cf681d793b223a5f56a794439dc12a51b952b7ee69db0dfd24f - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=8384ec2de5f88f578d48e541831c47161606776d3787393f20fc9c6a59d4 If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=0af71922028784db5dee672128cc8d1a9131aba3b56f4777dc2bcbaa15c96a2c The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=4fe494878b502d19dedc40a0cfdeded207b166ca483a0d06643466303b4146b5 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=a4ec416976c036dba11dd2eba52f58ea7623cf9c77878158a2d68f57c854ea56 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=e31ebbe11650822dcddc95c8d732073824315aaa1ef0a85f6947ca3e78d08cfe you will see the percentile sliders displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=bb14504b68d5ac31e4d37c4a21b543c89a6fe18fac33b6c8b54db86869a541dd) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=9cfce1c69787f7b3b8c7aed8266cbc1a2f80474cd3a0e092aa23b32b22482dcf). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=899dc883a72c9aefd1cfa143a8a33e2ecc7bc1a7b0e3b42563c71730ddb8d141 - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=696eccc3065b76804f94f1b2ec49a7deede7cfe02e2251290f6a6d246cbaedff If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=3777dd064f5a5c7afd82c5e78bf77dc52fd85428c524d2083cd96316c6ff3527 The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=f8067c0121d03f420ec913cd927ad5a65c0bc1831b03ed4e43197317a3228336 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Studentship in Crystallography and Parasitology
Applications are invited for a three-year University of Leeds 110-year Anniversary Ph. D. studentship to work in the Goldman and Muench groups. The project will involve structural and functional studies of integral membrane pyrophosphatases, focussing on ones from pathogenic parasites such as Leishmania and Toxoplasma. The goal will be to solve the structure of one of these proteins, and use the resulting structure for drug design with collaborators in Chemistry. Candidates with a strong background in parasitology and crystallography as an undergraduate are encouraged to apply. The deadline for applications is April 21st at 4pm, because the funding scheme closes on April 28th. Interested applicants should fill in the web form at: https://urldefense.proofpoint.com/v1/url?u=http://www.leeds.ac.uk/rsa/postgraduate_scholarships/UoLARS-AppForm14k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=izuVxNVhpuUU8PMds6TAuIpyPZcXEYrAcbr1g1liYsQ%3D%0As=019501d4b704758630d7614492f89e9f9f65f3cd5bc83fe70ef7eda3ca9dda63 and send an email to a.gold...@leeds.ac.uk and s.p.mue...@leeds.ac.uk. Informal enquiries can be addressed to both Goldman and Muench at the addresses above. Adrian Goldman and Stephen Muench
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=4105ff6448d5bdbd51e474e89f5a06ee532f480bdcd7c0205ce5c6d91b48300e The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=032b800b3e9b3f00999a10131c588183b134c5a44c0c6d5dafd999b619326c1e you will see the percentile sliders displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=66fbe101d6708d887924bdc5bf25021570f9885c97daf3d064f9f7258c3303ad) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=1e6916c73273cdcf0e20a5b7d4ff23d7961c1d97a12988b072d32fcec45e7570). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=fd35f5139833bb5700372d7bf5f2398f28706b2154d8bc1d907eef9e82ac517f - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=11887d82818aef793f525049cf3b75a603cecba6cb0d7351fb3122b50d963f5a If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=83fb53eb3391a94d7ad7de7d2fcd02804657e56c7c0b5fb8aa3d655715d9a966 The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=57e3ff9f13e2ce786081e6f02d66213a2911f3d14ba6003a495ea2d5dd9c1650 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
If N goes to infinity, i.e. at high or very high data multiplicity Rmerge approaches Rmeas (Rrim). Sure. And there is nothing incorrect, because the formulas are identical. 0.8*sd(i)/I = 0.8/(I/sd(i)) But if you sum also over a shell of hs, that notation is incomplete losing the (or Mn). That is the confusion at least on my side. BR -Original Message- From: Manfred S. Weiss [mailto:manfred.we...@helmholtz-berlin.de] Sent: Thursday, April 17, 2014 8:46 AM To: b...@hofkristallamt.org Cc: Bernhard Rupp; CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd) That's not quite correct. If N goes to infinity, i.e. at high or very high data multiplicity Rmerge approaches Rmeas (Rrim). At this point it does not matter whether you write Rmerge or Rmeas equals 0.8 * sd(I) / I For low multiplicity Rrim (or Rmeas) = 0.8*sd(i)/I is the correct expression. Cheers, Manfred On 16.04.2014 22:16, Bernhard Rupp wrote: The 2006 Weiss expression - I guess from the context- is for a single reflection h measured N times (and then is identical to my 8-23) while (8-24) is valid for the Rmerge (defined in 8-15) of averaging over a shell with h reflections each measured N times , which also explains why the two related expressions in aimless necessarily have to be different. Somehow crystallographers historically invented their own linear merging statistics instead of 'standard' descriptive statistics like the standard error of the mean...still an unresolved mess see the papers/threads on cc1/2, cc* etc... Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: Wednesday, April 16, 2014 5:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd) Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge 0.8/I/s(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I so, First question: is it Rmerge or Rmeas (Rrim) that we are dealing with? Second question: at the denominator (of the Rupp way to write), it is the aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the aimless I/sigma (very different from Mn(I/sd) with high redundancy)? Thank you very much for the clarification. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/bessy-mxk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=BluB0Olw5XjapWHq%2FjaIGq1GNJvmY6kKVwfwCmjF4Io%3D%0As=9e7562553ee8f84971edcacb559c8ba8213457655195a6c8a2560601b7dac12f Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch ftsf hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=BluB0Olw5XjapWHq%2FjaIGq1GNJvmY6kKVwfwCmjF4Io%3D%0As=5df4cf19aaa9d014eb3f182aae2b75dd85fbb178301dd6bdff41b68585cc06f5
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
That's not quite correct. If N goes to infinity, i.e. at high or very high data multiplicity Rmerge approaches Rmeas (Rrim). At this point it does not matter whether you write Rmerge or Rmeas equals 0.8 * sd(I) / I For low multiplicity Rrim (or Rmeas) = 0.8*sd(i)/I is the correct expression. Cheers, Manfred On 16.04.2014 22:16, Bernhard Rupp wrote: The 2006 Weiss expression - I guess from the context- is for a single reflection h measured N times (and then is identical to my 8-23) while (8-24) is valid for the Rmerge (defined in 8-15) of averaging over a shell with h reflections each measured N times , which also explains why the two related expressions in aimless necessarily have to be different. Somehow crystallographers historically invented their own linear merging statistics instead of 'standard' descriptive statistics like the standard error of the mean...still an unresolved mess see the papers/threads on cc1/2, cc* etc... Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: Wednesday, April 16, 2014 5:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd) Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge 0.8/I/s(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I so, First question: is it Rmerge or Rmeas (Rrim) that we are dealing with? Second question: at the denominator (of the Rupp way to write), it is the aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the aimless I/sigma (very different from Mn(I/sd) with high redundancy)? Thank you very much for the clarification. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/bessy-mxk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=Bmb9nN0eEAg0yI3N0xkQkdpD%2BJyOWQhem2L9N7BX%2FS0%3D%0Am=ioF%2FNBln5i1F4HBuWvTEg%2FjRX8MQaGIyGtlimw4%2BUFg%3D%0As=b513370ad6484d4580d21215cd51c8bb1ac2ad1e55740901cdf35e0d4931d54a Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=Bmb9nN0eEAg0yI3N0xkQkdpD%2BJyOWQhem2L9N7BX%2FS0%3D%0Am=ioF%2FNBln5i1F4HBuWvTEg%2FjRX8MQaGIyGtlimw4%2BUFg%3D%0As=f425d33eab53ef7b63ca749f304cfbf564c480fc2f375df073d9130c31781bd7
[ccp4bb] Studentship in Crystallography and Parasitology
Applications are invited for a three-year University of Leeds 110-year Anniversary Ph. D. studentship to work in the Goldman and Muench groups. The project will involve structural and functional studies of integral membrane pyrophosphatases, focussing on ones from pathogenic parasites such as Leishmania and Toxoplasma. The goal will be to solve the structure of one of these proteins, and use the resulting structure for drug design with collaborators in Chemistry. Candidates with a strong background in parasitology and crystallography as an undergraduate are encouraged to apply. The deadline for applications is April 21st at 4pm, because the funding scheme closes on April 28th. Interested applicants should fill in the web form at: https://urldefense.proofpoint.com/v1/url?u=http://www.leeds.ac.uk/rsa/postgraduate_scholarships/UoLARS-AppForm14k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=AqDwo4LvguMtrub4NIDhryGOdOv4sA3cFYEqDsNmrM4%3D%0As=a5d63db0df301bc9666364d031f65baa3026855a33d1b0e1762a0a055f040efc and send an email to a.gold...@leeds.ac.uk and s.p.mue...@leeds.ac.uk. Informal enquiries can be addressed to both Goldman and Muench at the addresses above. Adrian Goldman and Stephen Muench
