Re: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)
What does ProCheck say? Xiaopeng Hu wrote: Dear all, I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes? Best wishes, xiaopeng
Re: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)
Oh god no don't ask Procheck , its Rama plot is a complete disaster zone - for one thing, it's * ancient*. Doesn't discriminate between amino avoid types. Grrr. To be avoided at all costs. Sent from tiny silly touch screen - Reply message - From: Edward A. Berry ber...@upstate.edu Date: Fri, Sep 30, 2011 07:12 Subject: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix) To: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK What does ProCheck say? Xiaopeng Hu wrote: Dear all, I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes? Best wishes, xiaopeng
[ccp4bb] Ramachandran Restraints in refmac
Hello everyone, I am refining a structure to 2.4A with 2-fold NCS and twinned. Maps look ok and Rfree is 0.27however as I start checking my validations I notice that after refinemnt my geomtry gets significantly worse. especially the rama plot. Initially I have 2 outliers and I end up with 32 (5%)!!! I played with the Xray weight term but alll it helped me with was rmsd bond/angles, rama is still messing up... Can I impose some ramachadran restraints or maybe have a reference model? best,
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Hi William, It is essentially BSD unix. So it should be fine, unless they continue to lobotomize everything and make it into an iPod on a stick. :-)) +1 Thankfully, it is possible to gcc-cross-compile for MacOSX (both i686 + ppc) from a GNU/Linux machine (the procedure for getting it to work was so convoluted that I keep three separate backups of all required directory trees, knowing that I won't be able to repeat it ;-). Having said that, the resulting executables work fine on a Snow Leopard machine (even Ygl-based graphics !), but I bet my luck won't last long ... All the best, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] Ramachandran Restraints in refmac
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Yuri, the ramachandran restraints can be imposed on with coot. I am not aware if refmac5 does that directly, but using a reference model should fix it. As far as I understand you cannot directly put in the reference model but have to use a tool like prosmart by Rob Nicholls (http://www.ysbl.york.ac.uk/mxstat/Rob/ - when I asked for a copy of the program I received a reply within the day :-) ) which creates a text file with external restraints. The user documentation of prosmart explains how to use it with refmac5, and it works really well. Cheers, Tim On 09/30/2011 09:01 AM, Yuri Pompeu wrote: Hello everyone, I am refining a structure to 2.4A with 2-fold NCS and twinned. Maps look ok and Rfree is 0.27however as I start checking my validations I notice that after refinemnt my geomtry gets significantly worse. especially the rama plot. Initially I have 2 outliers and I end up with 32 (5%)!!! I played with the Xray weight term but alll it helped me with was rmsd bond/angles, rama is still messing up... Can I impose some ramachadran restraints or maybe have a reference model? best, - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOhYCCUxlJ7aRr7hoRAnleAKC7tStLymhynei9qOmei0TGOFZOdgCghNRb 54kD2McQXFTefQyMqgm0E/Q= =nSo9 -END PGP SIGNATURE-
Re: [ccp4bb] Ligand Protein Connection
Hi Sam Except for torsion angles, here is a good tutorial for you (the second one) http://www.ysbl.york.ac.uk/mxstat/JLigand/ Andrey On 29 Sep 2011, at 22:12, Sam Arnosti wrote: Hi every one I have a problem with docking my ligand into the electron density map and make the connections ( bonds ) with the protein. It is a Lysine residue that makes a Schiff Base with a long chain aldehyde. I do not know how to make the bonds and control the torsion angles of the ligand. I am using the CCP4 and Coot program for refining. Thanks Sam
[ccp4bb] How to labe the stereo-view figs?
Dear members, I use stereo-view to show my structure, and label the residue name on the figs. But after labeling, the label and the residues are not in the same place from the stereo angle. Anyone know how to fix this? Regards, Yuan
Re: [ccp4bb] Ligand Protein Connection
On 09/29/2011 10:12 PM, Sam Arnosti wrote: Hi every one I have a problem with docking my ligand into the electron density map and make the connections ( bonds ) with the protein. It is a Lysine residue that makes a Schiff Base with a long chain aldehyde. I do not know how to make the bonds and control the torsion angles of the ligand. I am using the CCP4 and Coot program for refining. Thanks Sam If you build the ligand close to the LYS and run the review restraints option in REFMAC it will suggest a LINK cif file. Check it carefully and see if you agree with the supposed chemistry, then you can use it as part of your dictionary. You will need the LINKR record the program will have added to your pdb file Eleanor
Re: [ccp4bb] Ramachandran Restraints in refmac
On 09/30/2011 08:01 AM, Yuri Pompeu wrote: Hello everyone, I am refining a structure to 2.4A with 2-fold NCS and twinned. Maps look ok and Rfree is 0.27however as I start checking my validations I notice that after refinemnt my geomtry gets significantly worse. especially the rama plot. Initially I have 2 outliers and I end up with 32 (5%)!!! I played with the Xray weight term but alll it helped me with was rmsd bond/angles, rama is still messing up... Can I impose some ramachadran restraints or maybe have a reference model? best, Dont foreget the usual reason for Rama outliers is model error! Check c=O are correct - cis peptides correctly defined in PDB ( coot and REFMAC USED to get these knotted.. ) etc etc.. Eleanor
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Dear All, There is a free alternative to MS Office, OpenOffice from Oracle. It can read and write MS Word files and save as PDF. There are some issues with names of spreadsheet functions when moving from OO to MS Office. If you use latex and beamer then there is no need to either ;-). I use both Ubuntu and Mac with OO. Adam
Re: [ccp4bb] How to labe the stereo-view figs?
Dear Yuan, it depends which software you are using, usually it is not so convenient to add labels with good font sizes, colors etc. So the way I do it is to put the 2 pictures next to each other in powerpoint (at good resolution, e.g. A3 format), add labels on the one on the left in text mode, copy all labels and put them on the picture on the right on the same horizontal height. Then move labels one by one horizontally while looking in stereo at the pictures so that each label is at the correct depth. Hope it helps, Bruno De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de ?? Envoyé : Friday, September 30, 2011 11:05 AM À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] How to labe the stereo-view figs? Dear members, I use stereo-view to show my structure, and label the residue name on the figs. But after labeling, the label and the residues are not in the same place from the stereo angle. Anyone know how to fix this? Regards, Yuan ### Dr. Bruno P. Klaholz Department of Integrated Structural Biology Institute of Genetics and of Molecular and Cellular Biology IGBMC - UMR 7104 - U 964 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE Tel. from abroad: 0033.388.65.57.55 Tel. inside France: 03.88.65.57.55 Fax from abroad: 0033.388.65.32.76 Fax inside France: 03.88.65.32.76 e-mail: klah...@igbmc.frmailto:klah...@igbmc.fr websites: http://www.igbmc.fr/ http://igbmc.fr/Klaholz
Re: [ccp4bb] Linux vs MacOS for crystallographic software
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The actual free alternative is called libreoffice, the successor of openoffice after it was taken over by Oracle - a company, in my personal opinion, is by orders of magnitudes less 'free' than microsoft. On 09/30/2011 11:42 AM, Adam Ralph wrote: Dear All, There is a free alternative to MS Office, OpenOffice from Oracle. It can read and write MS Word files and save as PDF. There are some issues with names of spreadsheet functions when moving from OO to MS Office. If you use latex and beamer then there is no need to either ;-). I use both Ubuntu and Mac with OO. Adam - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOhZSzUxlJ7aRr7hoRAkkDAJwJAJ1EhBIy1sNCD+6gJhfD2l1hiQCeInJr REkBUvVBiNjynObYfNPxz/8= =SGr3 -END PGP SIGNATURE-
[ccp4bb] 3D Stereo on mac with 3D TV
Hello all, We have been looking for path to future for our aging CRT-Stereo solution and I found out that some people have successfully used Samsung 3D TV's for editing 3D Stereo movies on Macs. So my question is does anyone have experiences with such setup? One problem I can see is that the solution doesn't support 3D Stereo in window which would make it incompatible with current software. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kest...@helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Rather than crossover office we now use VirutalBox and have a Windows XP installation with Office for those of us who can't live without it. You can backup the virtual machine (which is simply a big file) for the virtual OS before you do an upgrade of your host OS (Ubuntu in my case) and copy that back, so you do not need to do a full Windows XP install every time you upgrade the host. Your linux disks (including NFS mounts) can be seen from the virtual windows machine, so you can have your files accessible in both operating systems. Also, with two monitors you can have one with your linux desktop and one with your virtual windows desktop, and you can even cut and paste between the two. Very useful when writing papers etc. With NX you can then use that setup elsewhere (at home) as well, without having to duplicate the whole lot. The virtual desktop works ok via NX, things like coot are a bit more tricky. Johan Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266 On 29 September 2011 13:07, Lucas lucasbleic...@gmail.com wrote: 2011/9/29 Simon Kolstoe s.kols...@ucl.ac.uk: Generally I think that the extra money spent on a Mac pays for less time spent messing around installing software, sorting out dependencies, swearing at the less than effective office software etc. that plagues Linux which is more of a computer experts platform. For some years I had dual-boot systems, but since the only thing in Windows that I can't live without is their Office suite, what I've been doing for a year or two is having an easy to maintain linux distribution in my desktop (I use Kubuntu since Dapper Drake, and by that time it seemed to be the only distro which was anything near easy to use, but there are probably other good options today) while running Microsoft Office via Crossover Office, a very cheap little program for running windows software on linux (they also have a version for Mac). It works just perfectly, and it means I only need an Office license (no need to install Windows, as some do in virtual machines). Also, back in 2003 setting up the video card was a nightmare even in more user-friendly linux distributions. It seems not to be the case nowadays, it's been a long time since I had that feeling for destroying the computer with a sledgehammer after trying the nth version of xorg.conf and still being unable to run coot. Lucas
Re: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)
Hi Xiaopeng, If you are feeding both programs exactly the same file then you are not doing anything wrong. Notice that, if you calculate the Ramachandran plot on Molprobity and then you go on coot, do a round of manual refinement, and only then calculate the Ramachandran, then that can be the source of the difference. But I would bet that it is because different programs have their own definition of what is allowed and what is an outlier. I personally use the Ramachandran plot on coot just to guide my refinement, but use another program (Molprobity is pretty good) to do a thorough validation. Good luck, Mario Sanches 2011/9/30 Xiaopeng Hu huxp...@mail.sysu.edu.cn Dear all, I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes? Best wishes, xiaopeng -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches
Re: [ccp4bb] Ramachandran Restraints in refmac
Dear Yuri, Since the number of reflections depends inversely on the cube of the resolution, it is easy to show that a perfectly twinned 2.4A structure will have the same data to parameter ratio as an untwinned 3.0A structure. This determines how much you can refine and which restraints are appropriate. In my experience, the 2.4A twinned difference maps will be even less informative than 3.0A difference maps. Fortunately, as is often the case with twinned structures, you also have 2-fold NCS, so you can recover part of the damage by applying tight NCS restraints. Best wishes, George On Fri, Sep 30, 2011 at 08:01:42AM +0100, Yuri Pompeu wrote: Hello everyone, I am refining a structure to 2.4A with 2-fold NCS and twinned. Maps look ok and Rfree is 0.27however as I start checking my validations I notice that after refinemnt my geomtry gets significantly worse. especially the rama plot. Initially I have 2 outliers and I end up with 32 (5%)!!! I played with the Xray weight term but alll it helped me with was rmsd bond/angles, rama is still messing up... Can I impose some ramachadran restraints or maybe have a reference model? best, -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Linux vs MacOS for crystallographic software
On 09/29/2011 03:55 PM, Dima Klenchin wrote: I have a feeling that the lack of Windows software continues to be mostly due to the irrational animosity toward it rather than the platform-specific issues. After all, there seemed to be many developers who were happy to code for MacOS 7-9 but refused to release anything that runs in Windows. Meanwhile, that is the only platform we never hear about installation and dependencies issues. Given the large number of Windows versions of CCP4 downloaded, I assume this is not because nobody actually installs Windows software. I can't speak for anyone else, but in my case this is not true. It's just down to convenience. I develop on Linux because I install the OS and have a complete software development environment with everything I need pre-installed, or at most accessible after less than 5 minutes of playing with the unified software manager. For OSX, we have machines about the lab I can ssh into where other people have set up the build environment so I can use it in almost exactly the same way. I don't know how much work that was for them. For Windows, I have to arrange a license, install, deal with a much more painful registration and security update process, and then install a load more 3rd party tools before I can even start working. That or try and figure out the convoluted steps required to get cross compilation to work. That's all there really is too it. Kevin
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Yes, Open Office has forked, and LibreOffice is now the choice in Fedora Linux. I have used OpenOffice and LibreOffice, and they have some trouble with recent .docx files generated in MS Word, specifically with embedded image files. On 09/30/11 06:06, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The actual free alternative is called libreoffice, the successor of openoffice after it was taken over by Oracle - a company, in my personal opinion, is by orders of magnitudes less 'free' than microsoft. On 09/30/2011 11:42 AM, Adam Ralph wrote: Dear All, There is a free alternative to MS Office, OpenOffice from Oracle. It can read and write MS Word files and save as PDF. There are some issues with names of spreadsheet functions when moving from OO to MS Office. If you use latex and beamer then there is no need to either ;-). I use both Ubuntu and Mac with OO. Adam -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Linux vs MacOS for crystallographic software
On 09/28/11 20:26, Jacqueline Vitali wrote: ... --I am happy with any Linux. However, the system needs updates for security purposes (the University requires it). Do I have to remake the NVidia driver every time there is a kernel update or is there a way around it for this NVidia card? For Fedora Linux, nVidia drivers are availabe through RPMfusion; and if you install with the akmod-nvidia package, the kernel module is automatically rebuilt for you when the kernel is updated. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Postdoc Position in Structural Biology of Microtubule Assembly
Postdoc Position in Structural Biology of Microtubule Assembly The Knossow group at the Laboratoire d’Enzymologie et Biochimie Structurales in Gif-sur-Yvette (near Paris), France seeks to recruit a postdoctoral scientist in structural biology. The research focus is directed towards structures of complexes of tubulin with proteins that regulate its assembly in microtubules. For this purpose, we are also very active in the development of well defined tubulin assemblies amenable to crystallization. The results of some of these studies have been published (Ravelli et al. Nature 2004 ; Dorléans et al. PNAS 2009 ; Nawrotek et al. J. Mol. Biol. 2011) and other complexes are at the final stage of their development. Information about our group can also be obtained from http://www.lebs.cnrs-gif.fr/ knossow/knossowang.html. The position requires a Ph. D. in biochemistry or a related field with a strong background in molecular biology and protein biochemistry. Experience in purifying protein complexes and/or X-ray crystallography are an advantage. The successful candidate is a highly motivated individual who enjoys working as part of a collaborative, multidisciplinary and interactive team. The laboratory, which is part of C.N.R.S., is excellently situated in the Molecular Biology environment of the Centre de Recherches de Gif in Gif-sur-Yvette. Access to synchrotron X-ray radiation (ESRF in Grenoble and SOLEIL, located nearby) and biophysical instrumentation (analytical ultracentrifugation, SEC - MALLS, Dynamic Light Scattering, microcalorimetry) is provided. The work will involve stays for limited periods of time in the Laboratory of Prof. A. Plückthun (U. Zürich) where the successful applicant will elicit DARPins specific of our proteins of interest (Zahnd et al. Nature Methods 2007). The position is available immediately and funded initially for one year. The salary, determined according to the CNRS postdoc salary scale, is close to 2050 € per month for a candidate who has obtained his/her Ph.D. less than two years before starting this position. To apply please send your CV, a statement of research interests and names (including Email addresses) of at least two referees to Dr. Marcel Knossow (knos...@lebs.cnrs-gif.fr). Applications will be accepted until the position is filled.
[ccp4bb] Could you please place my open positions on your website?
Hi there, I am a full professor at Harbin Institute of Technology, China. Could you please place my open positions on your website? Below is the details. Thanks in advance. Zhiwei *Location:* Harbin, China *Department: *Harbin Institute of Technology BIO-X Center *Start Date:* Negotiable *Duration:* 2-3 Years, extendable *Description:* Several postdoctoral positions are available in Dr. Zhiwei Huang’s newly established laboratory at Harbin Institute of Technology (HIT), China. Our research interests focus on the understanding of structure-function relationships of macromolecules (soluble/membrane proteins, nucleic acids), and the mechanisms of cellular signaling transduction in immunology and neurobiology fields. We use multi-disciplinary approaches including X-ray crystallography, biochemistry, molecular biology, cell biology, and mouse genetics in our studies. We are equipped with a state-of-the-art facility to conduct soluble/membrane protein crystallography and functional studies including a recently established home X-ray source, an automated crystallization screening device, and other setups such as ITC. A background in macromolecular X-ray crystallography, protein expression purification or biochemistry is preferred, but enthusiastic individuals with a Ph.D degree in microbiology, molecular biology, cell biology, biophysics, physics or related fields and interested in utilizing both in vivo and in vitro techniques to study structure-function relationships of important soluble/membrane proteins and important signaling pathways in immunology and neurobiology fields are also encouraged to apply. We offer competitive salary and benefits, which will be commensurate with experiences. For more information, please check the university website ( http://bio.hit.edu.cn/news/sub_szdw.asp?id=883) or contact me via email. Please send CV, a summary of research experience, and the contact information of three references to Zhiwei Huang at huangzhiwei2...@gmail.com *Please submit:* CV, Brief description of research experience, contact information of three references *Person to contact:* Zhiwei Huang *Email address:* huangzhiwei2...@gmail.com
Re: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)
2011/9/29 Xiaopeng Hu huxp...@mail.sysu.edu.cn I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes? It's not you - I believe that Coot and Molprobity/Phenix both use the Richardson lab's data, but this isn't the first complaint I've heard about discrepancies in the statistics, so I suspect that the cutoffs are slightly stricter in Coot. Will check this later today. -Nat
Re: [ccp4bb] Linux vs MacOS for crystallographic software
...resisted the temptation to express redundant/easily objectionable/useless opinion on the virtues of different OS environments for two days... can't hold any longer... the power of one ring is too strong... the only useful suggestion on automatic update of proprietary nvidia drivers has already been made... to minimize damage, must recycle the comment made on the same subject two years ago... On the emerged subject of which OS is best, I honestly think that modern computers have reached the point where $500 desktop satisfies all the needs of a protein crystallographer. Since that is the case, any OS can be used, and the discussion has, imho, nothing to do with efficiency and everything to do with personal preferences. As somebody who refuses to accept the marketing ploy of associating coolness with certain fruit logo, I have never used apple products (unless it's granny smith). Accordingly, I believe I have no right to comment on them. I am old enough to remember the blue screen of death, so I can't be Windows supporter. For an open source freedom fighter wannabee, Linux is a logical choice. In the end, our choice of OS today simply reflects who we are. Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] is codon optimization worth it?
Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] is codon optimization worth it?
On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote: Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Wait, isn't Rosetta optimized for mammalian genes, not yeast (but maybe codon bias in yeast matches that)? A sideways suggestion would be to express in yeast. Extra bonus - it smells like beer :) -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] is codon optimization worth it?
Rosetta strains carry a plasmid that supplies several tRNAs that match codons that are rare in E. coli. This is quite different than being explicitly optimized to express mammalian proteins. We (the Center for Eukaryotic Structural Genomics, a PSI-1 and PSI-2 center) used strains with the same tRNA plasmid (either pRARE or pRARE2) to express proteins from yeast, Arabidopsis, some thermophilic eukaryotes, mouse, frog, human and zebrafish proteins. It seemed to work just fine for all of them. On Sep 30, 2011, at 9:55 AM, Ed Pozharski wrote: On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote: Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Wait, isn't Rosetta optimized for mammalian genes, not yeast (but maybe codon bias in yeast matches that)? A sideways suggestion would be to express in yeast. Extra bonus - it smells like beer :) -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] is codon optimization worth it?
We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal, 2009) paper below. The optimisation is specifically for overexpression in BL21 (DE3). The optimised gene increased protein expression by at least a factor of 10, and changed (somewhat reduced) the degradation pattern we observed. Unfortunately it didn't do anything to improve the folding (ie. we ended up with lots of half-folded, semi-soluble protein). With other neisserial derived proteins we have had an almost undetectable effect. You can't win 'em all. Cheers, Tim Design Parameters to Control Synthetic Gene Expression in Escherichia coli Welch et al, PlosONE 2009 Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -Original Message- From: CCP4 bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] Postdoctoral Fellow Positions in Baltimore, Maryland, USA
INSTITUTE OF HUMAN VIROLOGY UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE A postdoctoral positions are available immediately for a highly motivated candidates in the Institute of Human Virology http://www.ihv.org at the University Of Maryland School Of Medicine (UMSOM; http://medschool.umaryland.edu ) in Baltimore, Maryland. IHV is the first center in the United States - perhaps the world - to combine the disciplines of basic science, epidemiology and clinical research in a concerted effort to speed the discovery of diagnostics and therapeutics for a wide variety of chronic and deadly viral and immune disorders - most notably HIV, the cause of AIDS. Our laboratory focuses on the molecular basis of function of proteins involved in the anti-HIV-1 immune responses, human immune defense in general, and cancer prevention (http://www.ihv.org/research/bio_recognition ). Successful candidate will utilize the established high-throughput structural biology platform and biochemical/biophysical techniques to study novel targets on HIV-1 Env that are exposed during viral attachement/entry and are exclusively responsible for Fc mediated effector function (ADCC). Studies will focus on structural characterization and epitope definition of ADCC-mediating anti-HIV-1 Env mAbs, as well as the structure-based studies guiding development of protein-based therapeutics and novel vaccines. The position requires a Ph.D. in biochemistry, molecular biology, or a closely related discipline with practical experience in molecular biology, antibody/glycoprotein engineering and protein science techniques including surface plasmon resonance, isothermal titration calorimetry and X-ray crystallography. Candidates need to be highly motivated individuals who enjoy working as part of a young, dynamic, collaborative and multidisciplinary team. Excellent oral and written communication skills are essential. Interested parties should submit electronically a CV, a statement of research interests and previous experience, and contact information of three references to mpazg...@ihv.umaryland.edumailto:mpazg...@ihv.umaryland.edu Review of completed applications will begin immediately.
Re: [ccp4bb] Linux vs MacOS for crystallographic software
opinion on the virtues of different OS environments for two days It might be of interest to look back on the original poster's question, because all she asked were a few questions about a specific computer (HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) running OS X 10.7. Although she asked if the latter was platform advisable for crystallographic software for the coming years, there wasn't any question about the merits of various operating systems. Presumably, she can determine that as well as anyone else, assuming accurate answers to her questions. No one ever suggested operating system monogamy was a virtue. Besides, both are simply unix variants, and are far more alike than evangelists for either Linux or OS X seem to want to admit. If you like or dislike the iCandy apps, then there might be a compelling reason for/against OS X vs. Linux. Likewise, if you refuse to use closed-source, proprietary operating systems and software on principle, as advocated by Richard Stallmann, there is a compelling reason to use strict GNU/Linux (albeit without the NVidia proprietary driver). But then, you probably wouldn't be using much apart from COOT and other GPL software. OS X users, in that respect, are kind of like vegetarians who eat fish. --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
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Bill Thanks for focusing the thread to the original poster: If you're going to go OSX I would wary away from the iMac. The all-in-one desktop solution in small form factor has its downfalls, particularly when the mechanical disk (undoubtedly) fails. I have an iMac from 2007 and the hard drive needs to be replaced. The rest of the computer is fine and will probably work for the next 3-5 years for light desktop work (at least for the wife and kiddos). However, I expect the disassembly just to replace this component to be a nightmare. F On Sep 30, 2011, at 9:44 AM, William Scott wrote: she asked were a few questions about a specific computer (HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] is codon optimization worth it?
In theory, if the rare codons are all covered by Rosetta's extra tRNAs, codon optimization should not make any difference. In practice it does because frequently it's not codon optimization per se but changing local mRNA structure. - Dima
Re: [ccp4bb] is codon optimization worth it?
To me, the key question would seem to be, if I can't win them all, how many more do I win if I go to the trouble? Brent From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys Sent: Friday, September 30, 2011 8:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal, 2009) paper below. The optimisation is specifically for overexpression in BL21 (DE3). The optimised gene increased protein expression by at least a factor of 10, and changed (somewhat reduced) the degradation pattern we observed. Unfortunately it didn't do anything to improve the folding (ie. we ended up with lots of half-folded, semi-soluble protein). With other neisserial derived proteins we have had an almost undetectable effect. You can't win 'em all. Cheers, Tim Design Parameters to Control Synthetic Gene Expression in Escherichia coli Welch et al, PlosONE 2009 Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -Original Message- From: CCP4 bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] is codon optimization worth it?
Is there a general consensus that this is true? I’ve heard exactly the opposite, i.e., that codon optimization rarely gives you dramatically improved yields of soluble protein. Are there any published studies on this topic? This seems like something that might come out of one of the SG centers. Brent From: Anastassis Perrakis [mailto:abba...@gmail.com] On Behalf Of Anastassis Perrakis Sent: Friday, September 30, 2011 10:08 AM To: Segelke, Brent W. Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? Well, codon optimization is not really trouble, it's money. The money are worth it usually anyway, since the optimized genes are easy to clone if you make many constructs out of one gene, as you better do anyway ... Compared with downstream expenses, optimized genes are these days almost always worth the trouble... A. Sent from my iPad On 30 Sep 2011, at 19:02, Segelke, Brent W. segel...@llnl.govmailto:segel...@llnl.gov wrote: To me, the key question would seem to be, if I can’t win them all, how many more do I win if I go to the trouble? Brent From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys Sent: Friday, September 30, 2011 8:29 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal, 2009) paper below. The optimisation is specifically for overexpression in BL21 (DE3). The optimised gene increased protein expression by at least a factor of 10, and changed (somewhat reduced) the degradation pattern we observed. Unfortunately it didn't do anything to improve the folding (ie. we ended up with lots of half-folded, semi-soluble protein). With other neisserial derived proteins we have had an almost undetectable effect. You can't win 'em all. Cheers, Tim Design Parameters to Control Synthetic Gene Expression in Escherichia coli Welch et al, PlosONE 2009 Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -Original Message- From: CCP4 bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edumailto:pat.l...@drexelmed.edu
Re: [ccp4bb] is codon optimization worth it?
Well, codon optimization is not really trouble, it's money. The money are worth it usually anyway, since the optimized genes are easy to clone if you make many constructs out of one gene, as you better do anyway ... Compared with downstream expenses, optimized genes are these days almost always worth the trouble... A. Sent from my iPad On 30 Sep 2011, at 19:02, Segelke, Brent W. segel...@llnl.gov wrote: To me, the key question would seem to be, if I can’t win them all, how many more do I win if I go to the trouble? Brent From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys Sent: Friday, September 30, 2011 8:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal, 2009) paper below. The optimisation is specifically for overexpression in BL21 (DE3). The optimised gene increased protein expression by at least a factor of 10, and changed (somewhat reduced) the degradation pattern we observed. Unfortunately it didn't do anything to improve the folding (ie. we ended up with lots of half-folded, semi-soluble protein). With other neisserial derived proteins we have had an almost undetectable effect. You can't win 'em all. Cheers, Tim Design Parameters to Control Synthetic Gene Expression in Escherichia coli Welch et al, PlosONE 2009 Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -Original Message- From: CCP4 bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] is codon optimization worth it?
We recently published something really old-related about it: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021035 My two cents. Best, Alfredo. Alfredo Torres-Larios, PhD Assistant Professor Instituto de Fisiologia Celular, UNAM Mexico
Re: [ccp4bb] is codon optimization worth it?
Have a look at this paper: http://www.ncbi.nlm.nih.gov/pubmed?term=18289875 the bottom line appears to be that, in most cases, co-transforming with plasmids expressing rare tRNAs is just as good as codon optimizing the gene for your protein of interest. In addition to the financial aspects already touched upon by Tassos, we even had cases where codon optimizing a gene actually completely abolished its expression, presumably by causing havoc at the mRNA level. This obviously won't happen if you co-express rare codon tRNAs... HTH, Luca Luca Jovine, Ph.D. Assistant Professor EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.524-81136 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org On Sep 30, 2011, at 19:13 , Segelke, Brent W. wrote: Is there a general consensus that this is true? I’ve heard exactly the opposite, i.e., that codon optimization rarely gives you dramatically improved yields of soluble protein. Are there any published studies on this topic? This seems like something that might come out of one of the SG centers. Brent From: Anastassis Perrakis [mailto:abba...@gmail.com] On Behalf Of Anastassis Perrakis Sent: Friday, September 30, 2011 10:08 AM To: Segelke, Brent W. Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? Well, codon optimization is not really trouble, it's money. The money are worth it usually anyway, since the optimized genes are easy to clone if you make many constructs out of one gene, as you better do anyway ... Compared with downstream expenses, optimized genes are these days almost always worth the trouble... A. Sent from my iPad On 30 Sep 2011, at 19:02, Segelke, Brent W. segel...@llnl.gov wrote: To me, the key question would seem to be, if I can’t win them all, how many more do I win if I go to the trouble? Brent From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys Sent: Friday, September 30, 2011 8:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is codon optimization worth it? We codon optimised a poorly expressed gene from neisseria meningitides based on a codon usage table derived from the Welch (etal, 2009) paper below. The optimisation is specifically for overexpression in BL21 (DE3). The optimised gene increased protein expression by at least a factor of 10, and changed (somewhat reduced) the degradation pattern we observed. Unfortunately it didn't do anything to improve the folding (ie. we ended up with lots of half-folded, semi-soluble protein). With other neisserial derived proteins we have had an almost undetectable effect. You can't win 'em all. Cheers, Tim Design Parameters to Control Synthetic Gene Expression in Escherichia coli Welch et al, PlosONE 2009 Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -Original Message- From: CCP4 bulletin board on behalf of Patrick Loll Sent: Fri 30.09.2011 16:49 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] is codon optimization worth it? Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] Linux vs MacOS for crystallographic software
I would disagree about the disk issue. That's not the failure mode we have seen in the iMacs. Fwiw. Anyway, if it were to fail you could just attach an external disk and continue merrily along - macs will boot from external FireWire (and I assume thunderbolt?) disks. We are putting money where my mouth is. Our last five purchases have been i7 iMacs. It seems like quite a nice amount of oomph for the money. Adrian Goldman Sent from my iPhone On 30 Sep 2011, at 19:46, Francis E Reyes francis.re...@colorado.edu wrote: Bill Thanks for focusing the thread to the original poster: If you're going to go OSX I would wary away from the iMac. The all-in-one desktop solution in small form factor has its downfalls, particularly when the mechanical disk (undoubtedly) fails. I have an iMac from 2007 and the hard drive needs to be replaced. The rest of the computer is fine and will probably work for the next 3-5 years for light desktop work (at least for the wife and kiddos). However, I expect the disassembly just to replace this component to be a nightmare. F On Sep 30, 2011, at 9:44 AM, William Scott wrote: she asked were a few questions about a specific computer (HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
[ccp4bb] Postdoctoral position – University of British Columbia, Canada
Postdoctoral position – University of British Columbia, Canada We are seeking a self-motivated postdoctoral researcher with experience in protein crystallography to investigate the structural biology of natural product biosynthetic enzymes. The successful candidate will optimize expression and crystallization conditions for targeted proteins, solve structures in complex with purified substrates and products, and prepare manuscripts for publication. Previous experience in enzymology and synthetic chemistry would be an asset. Please send your CV (including contact information for three referees) and a statement of interest to ksr...@chem.ubc.ca. UBC hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply. However, Canadians and permanent residents of Canada will be given priority. Katherine S. Ryan, Assistant Professor Department of Chemistry University of British Columbia 2036 Main Mall Vancouver, BC Canada V6T 1Z1 Website: http://www2.chem.ubc.ca/personnel/faculty/ryan/group/Home.html
Re: [ccp4bb] Linux vs MacOS for crystallographic software
On Sep 30, 2011, at 12:07 PM, Adrian Goldman wrote: I would disagree about the disk issue. That's not the failure mode we have seen in the iMacs. Fwiw. Anyway, if it were to fail you could just attach an external disk and continue merrily along - macs will boot from external FireWire (and I assume thunderbolt?) disks. Yes, but I treasure my desktop and USB/Firewire port space ;) My point is that replacing anything (video card, logic board, display card, drive) within an iMac is difficult. If the OP (like me) plans on keeping your computer for more than 5-7 years, then he/she might want to get something where replacing the hardware is easy. I still have several fully functional dual processor PowerPC G5 from 2004 that work wonderfully for general desktop use. And it will still run most (CCP4/Phenix/Coot) crystallographic software. We are putting money where my mouth is. Our last five purchases have been i7 iMacs. It seems like quite a nice amount of oomph for the money. Core i7? Then your macs are still quite young (i7's were introduced in 2010). I'm talking a core 2 duo mac from 2007 (the iSight G5). Time will tell if the drives in 2010 were any better than then drives from 2007. I doubt it though. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
[ccp4bb] Phenix version 1.7.2 released
The Phenix developers are pleased to announce that version 1.7.2 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: - phenix.data_viewer added under Reflection Tools - New GUIs: HySS, phenix.cut_out_density, phenix.reciprocal_space_arrays General: - New commands: phenix.cut_out_density, phenix.data_viewer, phenix.morph_model - Default map output format changed to CCP4 - Native support for CIF-format reflection files (e.g. from PDB) in many commands and GUI Refinement: === - New Xray/restraints weight optimization. Keywords optimize_wxc and optimize_wxu replaced with optimize_xyz_weight and optimize_adp_weight, respectively. - Grid searches parallelized: use 'nproc' parameter to set number of CPUs to use - this affects bulk solvent mask optimization, and XYZ and ADP weight optimization (in addition to TLS identification) - can reduce runtime by 75% or more depending on settings (see manual for details) - Modified non-bonded parameters resulting in improved geometry, especially at low resolution - Rigid-body refinement mode defaults to grouping by chain - Printout of validation statistics during coordinate refinement - Bug fix in phase-combined map calculation results in significantly improved maps - Bug fix in X-ray/ADP restraints weight calculation results in smaller B-factors deviations for bonded atoms - Experimental feature (still in testing): - Torsion-space NCS (ncs.type=torsion), automatic parameterization, similar to reference model restraints - Uses top-out potential to allow deviations between NCS related atoms New commands: = - phenix.cut_out_density: - carve out a region from map coefficients (MTZ file) - density may be specified as a sphere, a box, or masked around a PDB file - phenix.data_viewer: - visualization of reciprocal-space reflection data - 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph) - phenix.morph_model: - Use after molecular replacement to improve model for rebuilding - Morphs model to match a prime-and-switch map Molecular Replacement: == - Phaser (and AutoMR wizard): - significant speedup of fast rotation function Miscellaneous: == - phenix.reel: - better integration with main GUI, especially eLBOW - phenix.fobs_minus_fobs_map: - option to disable strict unit cell isomorphism check - phenix.ramalyze: - optional output of PNG images of Ramachandran plots; add --plot to command line arguments - phenix.fetch_pdb: - new flags: --all fetches PDB, CIF, and FASTA files simultaneously --mtz runs phenix.cif_as_mtz on downloaded CIF file For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] detect dsDNA
Hi all, . recently,I got a crystal of protein-DNA crystal.i used silver stainto prove that it is a protein crystal.Does anyone have method to detect if there is DNA in the crystal. any suggestion will be appreciated. Regards, deng
Re: [ccp4bb] detect dsDNA
Try the program DIBER to evaluate the likelihood your crystal contained ordered nucleic acid in addition to protein. See Acta Cryst. (2010). D66, 643-653 “DIBER: protein, DNA, or both?” by G. Chojnowski M. Bochtler. Good luck, Pete From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of zq deng [dengzq1...@gmail.com] Sent: Friday, September 30, 2011 8:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] detect dsDNA Hi all, . recently,I got a crystal of protein-DNA crystal.i used silver stainto prove that it is a protein crystal.Does anyone have method to detect if there is DNA in the crystal. any suggestion will be appreciated. Regards, deng
