[ccp4bb] Postdoc Position in NanoMEGAS SPRL, Belgium
Dear Colleagues, Postdoctoral associate in NanoMEGAS SPRL, Belgium Description: We are looking for an outstanding and highly motivated individual to start immediately in a European funded postdoctoral position based in Brussels (www.nanomegas.com) on analysis of nanomaterials by Electron and X-Ray diffraction. Candidates must hold (or soon expect to hold) a recent Ph.D. (preferably less than 1 year) in crystallography, materials science, Transmission Electron Microscopy (TEM) or a related field and have a number of publications in the field. A strong background in crystal structure solution and refinement from X-ray/electron diffraction is essential. Familiarity with Synchrotron X-Ray experiments, TEM microscopy and related sample preparation and basic knowledge in programming is preferred. He/she must be capable of working independently and as part of a collaborative team. The candidate must have a good knowledge of oral and written English. The candidate can be of any Nationality (m/f) and he/she has to travel quite frequently within Europe for performing experiments. After the application deadline the short listed applicants will be called for an interview. Selected applicant is expected to join after May 2015. The position will be available for 2 years. Application deadline: 15 April 2015 Applicants should send by email a full CV in English (2 pages maximum) along with a summary of previous research experience and interests in less than 500 words and arrange to have 2 reference letters, e-mail can be send at mailto:sel...@nanomegas.com sel...@nanomegas.com. -- With best regards Partha -- --- Dr. Partha Pratim Das (Director) Electron Crystallography Solutions, Spain www.ecrystsolutions.com and NanoMEGAS SPRL (Application Specialist) Blvd Edmond Machtens 79 B-1080 Brussels Belgium Phone: 0032-25881690 (Direct) http://www.nanomegas.com/ www.nanomegas.com ---
Re: [ccp4bb] Enigmatic electron density attached to Cys residue
Hi Bernhard, It is difficult guess with two dimensional images. Is it possible a metal coordinated by Cys-Sulfur and one or two acetate ions? HTH, Partha Sent from my iPhone On Aug 19, 2014, at 10:12 AM, Bernhard Loll l...@chemie.fu-berlin.de wrote: Dear all, We are currently working on a small GTPase. The structure has been solved to 1.4 A with two molecules in the ASU. In the difference electron density we can clearly see difference density (in one monomer) attached to a Cys residue. The protein has been expressed in E. coli. For crystallization experiments the GTPase was incubated with GMPPNP, that had been dissolved in 20 mM HEPES pH 7.5 and 50 mM NaCl. Prior to crystallization the protein was stored in a buffer composed of 20 mM HEPES pH 7.5, 200 mM NaCl, 5 mM, Mg acetate, 2 mM DTT and 2% (v/v) glycerol. The protein crystallized under the following conditions: 28% (v/v) PEG 200, 5% (w/v) PEG 3000 and 100 mM MES buffer at pH 6.0 The anomalous signal is too weak to judge the positions of the sulphur atoms. We have performed MS analysis on the protein before crystallization and on dissolved protein crystals. MS revealed a mass difference of about 135 Da, indicating that some chemistry must have went on in the crystallization drop. The extra electron density has a planar shape and is quite symmetric. We have placed some dummy water molecules in the density. Distances are given in A in the PNG file. Attached files coot1.png: 2FoFc electron density map (blue) @ sigma=1 and FoFc electron density map (blue) @ sigma=+3 after phenix.refine coot2.png: same electron densities as in coot1.png, with dummy atoms placed coot3.png: same electron densities as in coot1.png, side view Thanks for your time and efforts. Cheers, Bernhard -- Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und Biochemie AG Strukturbiochemie Takustr. 6 D-14195 Berlin Germany Phone: +49 (0) 30 838-57348 Fax: +49 (0) 30 838-457348 Email: l...@chemie.fu-berlin.de Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/ coot1.png coot2.png coot3.png
[ccp4bb] Izit dye stained crystal
Dear all, We did some Izit dye staining to test our crystal (salt or protein) and we observed that the crystal didn’t take up the dye well. But, showed nice protein diffraction (home source KCr 2.2909 A) and we collected a dataset (360 frames, 1o osc, 5 min exposure) on this dye stained crystal. The data collection statistics looks great and most interestingly we saw some anomalous signal for this data (see attached XSCALE.LP). This protein was crystallized in 0.2 M Ca acetate, 30 % PEG 400 pH 4.5. Izit dye is basically methylene blue which contains a sulfur atom (phenothiazine ring) and also has some basic dimethylamio groups. Our protein has many acidic residues that could enhance binding of this basic dye.We think the anomalous signal could be from this dye and the heavy atom search with autoSHARP and Phenix autosol is suggestive of 4 sulfur atoms. Did anyone come across similar situation with using this dye and also welcome any suggestions about using this data for S-SAD phasing. Thanks, Sarathy XSCALE.INP Description: Binary data
Re: [ccp4bb] Izit dye stained crystal
Dear all, Here is the XSCALE.LP output after scaling for the izit dye stained crystak. Sorry for attaching the .INP file. Sarathy On Fri, Nov 30, 2012 at 4:19 PM, Sarathy Karunan Partha sarathyus...@gmail.com wrote: Dear all, We did some Izit dye staining to test our crystal (salt or protein) and we observed that the crystal didn’t take up the dye well. But, showed nice protein diffraction (home source KCr 2.2909 A) and we collected a dataset (360 frames, 1o osc, 5 min exposure) on this dye stained crystal. The data collection statistics looks great and most interestingly we saw some anomalous signal for this data (see attached XSCALE.LP). This protein was crystallized in 0.2 M Ca acetate, 30 % PEG 400 pH 4.5. Izit dye is basically methylene blue which contains a sulfur atom (phenothiazine ring) and also has some basic dimethylamio groups. Our protein has many acidic residues that could enhance binding of this basic dye.We think the anomalous signal could be from this dye and the heavy atom search with autoSHARP and Phenix autosol is suggestive of 4 sulfur atoms. Did anyone come across similar situation with using this dye and also welcome any suggestions about using this data for S-SAD phasing. Thanks, Sarathy XSCALE.LP Description: Binary data
Re: [ccp4bb] Assay of enzyme from thermophile
You can do it without having to do an assay at high temperature, because the substrate stability would also change at higher temperature. What you could do is the following: 1. Use a PCR machine to heat the enzyme, and then cool it down. 2. Keep one fraction at 4C / RT separately. 3. Do the assays and take the ratio (residual activity). 4. Make sure you normalize against protein concentration if you are checking different mutations. 5. Do it at different pH and duration of heating. HTH, Partha On Tue, Oct 18, 2011 at 3:48 PM, Kayashree M ka...@ssl.serc.iisc.in wrote: Dear users, Pardon me for the non-crystallography related question, Can anyone provide some papers regarding the assay of enzymes from hypertherphilic /thermophilic organisms? ie, assays at high temperatures.. Thanking you With Regards M. Kavyashree -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean.
Re: [ccp4bb] Off topic: Beryllium chloride
Hi Peter, Both BeF3(-) and AlF4(-) need to be made fresh, or used from frozen. It should not be stored at room temperature. While using, you may wish to keep it on ice. If you are using Vanadate, that should be fresh (Methods in Enzymology). Also kindly note that unlike AlF4(-), which is a single species; BeF3(-) is a mixture of BeF3.(H2O)-, BeF2(OH)- etc. It can make a difference in kinetics of binding (usually a two step binding is observed). Look at old ATPase and GTPase papers such as: Characterization of the aluminum and beryllium fluoride species which activate transducin. Analysis of the binding and dissociation kinetics.http://www.ncbi.nlm.nih.gov/pubmed/1551879 Antonny B, Chabre M. J Biol Chem. 1992 Apr 5;267(10):6710-8. PMID: 1551879 Cheers, Partha On Tue, Oct 4, 2011 at 5:05 AM, Peter Hsu hsuu...@u.washington.edu wrote: Sorry for the very off topic and dumb question, but does anyone know if BeCl2 needs to be prepared fresh for use (making BeF3) or can it be stored as a solution stock at room temperature/frozen? Thanks, Peter
Re: [ccp4bb] Cadmium sites and co-ordinations in structure
Hi Sandeep, if someone sends one, kindly share the references. In general, Ca2+ could have more Asp, Asn kind of coordination and distorted pentagonal bipyramidal geometry with waters (about 2.5A), Cd can also have S- since it is softer, I guess Co might have N/O/S (i.e all three with paired electrons). An inorganic chemistry textbook like Greenwood Earnshaw or Cotton Wilkinson could be handy.. or a bioinorganic chemistry book. HTH, Partha On Fri, Aug 26, 2011 at 7:24 PM, Sandeep s.talapa...@beatson.gla.ac.ukwrote: Hi, I crystallised a protein in the presence of Calcium, Cobalt, and Cadmium and determined its structure. It turns out that I see several metal sites in the structure, mostly cadmiums. Is there any information published (preferably a review) which summarises data on cadmium sites in proteins such as for example the possible coordination numbers of cadmium, distances, type of side chains found to coordinate with cadmium, etc.? I could extract all this from the PDB, but a nice review would be simpler to start with. Thank you in advance for your help Sandeep
[ccp4bb] Off Topic: Seeking references / reviews on Enzyme engineering
Dear BBusers, Could you point me to a few classic reviews on enzyme engineering? In particular: a) pH, thermal pressure stability b) de novo design c) increasing low temperature activity Regards, Partha
Re: [ccp4bb] Fwd: Could Biological Negative Results be published?
What if the negative results contradict some recent papers in big journals? Would the PI risk his / her contacts connections? Of course for the PhD student or postdoc, it matters a lot to get it 'published'.. On Mon, Jul 11, 2011 at 4:27 PM, Bosch, Juergen jubo...@jhsph.edu wrote: http://www.jnrbm.com/ Might this be what you are looking for ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 11, 2011, at 6:03 AM, F.Xavier Gomis-Rüth wrote: Dear CCP4ers, I think this is a very interesting initiative and it could potentially lead to a discussion within the board. Best, Xavier Mensaje original Asunto: Could Biological Negative Results be published? Fecha: Sun, 10 Jul 2011 21:39:52 -0500 De: David Alcantara listmas...@mail.arjournals.comlistmas...@mail.arjournals.com Para: f...@ibmb.csic.es Dear colleague, As you are well aware it is common in our field that many of our endeavors do not lead to the results we want or expect. Numerous tests and experiments have outcomes that we share with our immediate colleagues during informal meetings, but that we are not considering material for publication. As a result a wealth of information is never brought to the attention of the greater public, which is not only unfortunate, but also has others repeating similar studies to produce the same negative results. Not only are a lot of resources like time and money wasted in this way, but it also leads to frustration that could have been prevented if only the scientists would have been aware of the negative results of earlier studies. My name is David Alcantara and, on behalf of our editorial board, I’d like to invite you to submit your articles to The All Results Journals: Biology, a new journal that focuses on publishing the grey literature that has never been published. It is our goal to compile and publish those experiments that led to negative results or to outcomes that were not expected and were not before considered for publication. We of The All Results Journals feel that it is equally important to publish these results together with interpretations of the scientists involved and in this way offer a solution to the problem that publication bias is causing, because of a strong emphasis on positive results. The All Results Journals:Biol is a peer-reviewed journal dedicated to publishing articles with negative results and outcomes that were not expected and were not before considered for publication in all areas of Biology (pure and applied). The Journal is TOTAL Open Access (no fees to publish and read) and is being indexed by well-known scientific databases such as Web of Knowledge, Scirus, and Pubmed This will assure maximum exposure of your articles. We expect to publish articles within four to six weeks of submission, and our award-winning OJS Publications Web Editions Platform will showcase your important findings to the international scientific community. Please check our info for authors to submit your articles at: http://www.arjournals.com/ojs/index.php?journal=Biolpage=informationop=authorshttp://arjournals.com/ojs/index.php?journal=Biolpage=informationop=authors http://arjournals.com/ojs/index.php?journal=Biolpage=informationop=authors Thank you very much for your time and we look forward to hearing from you.. With kind regards, David Alcantara -- David Alcantara, Ph.D Managing editoralcant...@arjournals.com Phone: 001 617 575 9152 The All Results Journals:Biol (ISSN: 2172-4784)http://www.arjournals.com/ojs/index.php?journal=Biol Follow us onhttp://www.facebook.com/pages/The-All-Results-Journals/53410901726 --- This e-mail is from The All Results Journals. The e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorized dissemination or copying of this e-mail or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this e-mail in error, please notify or telephone and delete it from your system. -- If you do not want to receive any more e-mails from us visit, http://mail.arjournals.com/?p=unsubscribeuid=7f58f771c3b6364a657dc5f086f8962f -- Powered by PHPlist, www.phplist.com --
[ccp4bb] Question about mathematical modeling of membranes, pores and transporters
Hello, From experimental crystallography kinetics background, I have arrived at a situation where I need to model certain membrane related phenomena and correlate it to experimental (metabolonomic) data. In particular, I am looking for mathematical expressions and derivations for: a) Change of properties of the lipid membrane upon chemical reactions, such as oxidation b) ATP-ion co transporters c) Voltage gated pores. Could someone suggest me any source for such information? Regards, Partha
[ccp4bb] Off topic: Monitoring kinetics of multiple enzymes in living cell / lyset
Dear all, Apologies for a off topic question. I could not think of a better place to ask this. Suppose, we have four enzymes turning over five molecules, either in the living cell, or in fresh mammalian cell lyset. The molecules could be as simple as ATP, GTP, NADP, GSH etc. Now, one can add a inhibitor / drug Y to this mixture and that might change the dynamics. I am wondering how could someone measure the concentration of these metabolites.. ! It can not be done on purified enzyme, it has to be done when everything else is present. All I can think of are: a) Using mass spec on the metabolites: Quench the reaction at different time points, remove whatever possible by centrifugation and a spin filter (similar to QIAGEN kit), and do mass spec. b) Use some sort of a focused optical method (IR/UV laser?) on living cell that could excite multiple molecules (but I have no clue beyond this..) Has anybody seen something that addresses the question? Any suggestion would be highly appreciated. Cheers, Partha
Re: [ccp4bb] Refining residues as rigid bodies
Hi Jason, Instead of doing rigid body refinement of each residue, you may consider rigid.inp of CNS or an equivalent strategy in Phenix which will do SA, rigid body and B factor refinement, followed by either composite omit (CNS) or 'prime switch' of phenix (rather resolve) to fix the side chains. Cheers, Partha On Wed, Dec 2, 2009 at 2:00 AM, Jason Porta jpo...@unmc.edu wrote: Hi everybody, I am currently refining a 3 ang structure and would like to do rigid body refinement treating each residue as a separate rigid body. I have looked through several refinement packages, but do not see a way to do this without having to type each residue in manually (there are 512 residues total). Preferably, I would carry out the refinement in Refmac5, but any advice pertaining to any program would be greatly appreciated. Thanks in advance for any help. Jason Porta Graduate Student Eppley Structural Biology Facility Dept. Biochemistry Molecular Biology University of Nebraska Medical Center Omaha, NE 68198 (402) 559-5533
[ccp4bb] Regarding Open Source
Dear BBusers, I initially did not want to post this in the BB. With all due respect, could we use the word open source for those programs where the latest build or source code are available to the community? Regards, Partha
Re: [ccp4bb] multi-domain protein with identical tertiary structure
Hi Shankar, Another fascinating example might be Dscam (Down Syndrome cell adhesion molecule) with multiple Ig like domains and Fibronectin type III domains. Different splice isoforms are expressed in different nerves, and it serves as a recognition module, same repels, different ones attract. Not all the domains have been solved yet, and looking at the functional diversity, it is the small differences which are interesting in such case. There are also examples of tandem SH2, FHA, BRCT repeats, but it depends on how strict you are with the identical. Cheers, Partha On Thu, Jul 2, 2009 at 6:39 AM, Shankar Prasad Kanaujia spkanau...@gmail.com wrote: Dear CCP4 users, Is there any multi-domain protein (with at least two domains) which has identical tertiary structure of each domain ? Thanking you. -regards shankar -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Off-topic: unidentified density for N-terminal Thr modification
Hi Jonathan, This is purely a chemistry guess, but if you have a PEG400 derived compound like: (HO)-CH2-CH2-O-CH2-CHO, i.e, part oxidised, then the CHO might form a N,O acetal ring with the free amine and side chain. Five membered ring formation is kinetically favourable, though the chemistry might be a bit unlikely at your pH. Cheers, Partha On Tue, Jun 23, 2009 at 3:10 PM, Jonathan Elegheert jonathan.eleghe...@ugent.be wrote: Dear bb, I have a high resolution dataset showing that the N-terminal threonine of my protein has been modified and cyclized, with the main chain N and side chain OG1 now involved in a non-planar 5 membered ring sugar-like structure. The molecule seems to be 5-6 atoms long with some 'head group'. http://studwww.ugent.be/~jeleghee/ccp4/coot_front.pnghttp://studwww.ugent.be/%7Ejeleghee/ccp4/coot_front.png http://studwww.ugent.be/~jeleghee/ccp4/coot_side.pnghttp://studwww.ugent.be/%7Ejeleghee/ccp4/coot_side.png http://studwww.ugent.be/~jeleghee/ccp4/coot_angle.pnghttp://studwww.ugent.be/%7Ejeleghee/ccp4/coot_angle.png Modification must have occurred in the drop since N-terminal sequencing through Edman degradation after it came from the column gave a signal, i.e. the N-terminal Thr amine was free. This also confirmed that the initiator Met is definitely cleaved off. The crystallization condition is as follows; - 0.1 M Tris pH 8.2 - 1.65 M (NH4)2SO4 - 2 % PEG400 - 0.25 % (v/v) β-octyl glucoside It is worthy to mention that in the periphery of the protein, ethylacetate is bound (the reaction product of the ethanol and acetate impurities/breakdown products of the PEG400 stock solution). I don't know whether any PEG400 breakdown products or others derived from some of my crystallization components could show that sort of reactivity. Many thanks in advance if anyone has any pointers, Jonathan -- Jonathan Elegheert Ph.D. Student Ghent University jonathan.eleghe...@ugent.be -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
[ccp4bb] Refmac specific questions
Hi, Sorry to sound stupid, could someone explain what does refmac do if one chooses mixed (bref MIXED) or overall (bref OVER) B factor refinement in the context of TLS refinement? Is it something like: Isotropic for the main chain and/or waters and anisotropic for the side chain? Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Computer hardware and OS survey
For Linux, there is also a program called Bibus, which works with either MS office or open office.. it is like endnote, just a little less.. It is in the Fedora repo, possibly also Ubuntu.. On Mon, May 4, 2009 at 10:48 PM, Donnie Berkholz dberkh...@gentoo.orgwrote: On 14:02 Mon 04 May , Paul Paukstelis wrote: Openoffice with Zotero/Firefox works very nicely for refs. I've found the OpenOffice plugin for Zotero to be very flaky on my Linux system. In my experience, it's crash-prone, slow, and likely to corrupt my document and totally screw up references to the point of being unfixable. My current workflow involves switching to Endnote in OS X as a final step for adding references after writing the rest in Google Docs. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Computer hardware and OS survey
Cygwin has problems with Vista.. you need to run it as administrator.. works fine with XP though. Moreover, Cygwin is not very well supported anymore, as the developer works for Red Hat now. If it is just the X, there are other free programs.. XMing is quite good. You can indeed install Ubuntu under a virtual machine, and sun virtual box is free for example.. but model building would be much slower. Cheers, Partha On Fri, May 1, 2009 at 4:42 PM, Jacob Keller j-kell...@md.northwestern.eduwrote: I have found that cygwin works quite well for doing unix-type things on windows--one can use whatever shell one likes, run perl scripts, etc. Have people had problems with cygwin? I used to run CNS on it all the time. Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: ha...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, May 01, 2009 10:23 AM Subject: Re: [ccp4bb] Computer hardware and OS survey Hi Most of the software for macromolecular crystallography data analysis will run happily on Linux, OS X or Windows. However, Windows is much more GUI-based and much less open to shell scripting than UNIX based systems like Linux or OS X (DOS-Shell is very inflexible, even compared to sh or csh, let alone tcsh, zsh or bash). Even Python scripts are often not 100% portable (some of the older scripting languages like Tcl are better inthis respect, in my experience). Having said that, nearly half the downloads of Mosflm are for the Windows version - but I have no figures on how many people actually use it, having got hold of a copy! In my hands, it works as well as on the other platforms. YMMV. If your home institution really wants you to drop Macs, then I think you have to insist on Linux with proper support - but that costs salaries! Just my two ha'porth. My home institution, in effort to cut costs, is making an effort to push those of us on Macs onto PCs. Up till now they have been very generous via a lease program for computer hardware, but that is changing given the current economics. The institution currently does not support Linux so we are limited to Mac and Windows OS. We certainly make use of William Scotts crystallography on OS X (thanks so much!) so our main argument is that we would have far more support out there for crystallography on the Mac than we would have for on Windows. But to be fair (and hopefully bolster our argument) I should find out if that is true. I did not find an equal web support page for Windows. A volunteer survey will be distorted (probably by Mac fanboys like me) so I am asking for peoples best guesstimate as to what % use of Mac, Windows, or Linux is out there for data processing and model building. Our core programs are coot, o, pymol, cns, and ccp4 but we certainly make occasional use of other crystallography programs out there (solve, epmr...) Also what are the relative crystallography support for Mac vs. Windows. Thanks in advance. Todd -- Todd M. Link Assistant Professor MD Anderson Cancer Center Univ. of Texas (713) 834-6394 -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
[ccp4bb] Off topic: Coot and shared libraries
Hi, I am running a 64 bit Fedora 10 machine and having problems with coot, if i say ldd coot-real linux-gate.so.1 = (0x5000) libguilegtk-2.0.so.0 = not found libgthread-2.0.so.0 = /lib/libgthread-2.0.so.0 (0x00df8000) librt.so.1 = /lib/librt.so.1 (0x005f) libguile.so.17 = not found libgmp.so.3 = not found libcrypt.so.1 = /lib/libcrypt.so.1 (0x55572000) libltdl.so.3 = not found libclipper-ccp4.so.2 = not found libclipper-cif.so.2 = not found libclipper-phs.so.2 = not found libclipper-contrib.so.2 = not found libclipper-minimol.so.2 = not found libclipper-cns.so.2 = not found libclipper-mmdb.so.2 = not found libclipper-core.so.2 = not found libccp4c.so.0 = not found librfftw.so.2 = not found libfftw.so.2 = not found libz.so.1 = /lib/libz.so.1 (0x00769000) libssm.so.0 = not found libmmdb.so.0 = not found and so on. There were similar problems with imosflm which got fixed after installing compat-libstdc++-33.i386 following a suggestion of Kay Diederichs. Is there something similar for this case? Or have I forgotten to set up some path correctly? Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli
Just to add couple of things to what Artem said.. If it is something similar to a mammalian kinase or malaria protein for example, 1. Recodonizaton can change expression from near zero to substantial amounts, however, a) ideally, it needs to be recodonized separately for each target expression system (E. coli / yeast / IC) b) Expression does not guaranty solubility. One thing which sometimes works is coexpression of a phosphatase, if the non phospho form is of any interest. Similar things have been done by Src related kinases.. YopH or Lambda might be a good starting point. See: http://www.ncbi.nlm.nih.gov/pubmed/16260764?ordinalpos=3itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum HTH, Partha On Tue, Feb 24, 2009 at 3:48 PM, Mo Wong mowon...@gmail.com wrote: I thought I'd post this to the CCP4bb, as judging by previous posts, it seems I could get some useful insight into my problem... This is question has probably been asked by people for a long as molecular biology has been around, but hopefully my question isn't a complete rehash of other peoples: I am trying to express a human protein in bacteria where the only modified amino acids are 3 phosphorylated serines. I’ve gone through the usual hoopla of trying to get it expressed in E. coli (Rosetta/Codon+ cells, varying IPTG, low temperature, etc). Sequencing confirms my insert is correct, but from coomassie gel inspection, I appear to get near zero induction (I need to do a Western to get a clearer assessment). I’ve heard about custom gene synthesis, and it appears Mr. Gene (https://www.mrgene.com/) would be a good avenue to look into as they optimize the ORF taking into account codon usage in E. coli (though I’m not sure they examine putative mRNA substructure formation like some companies do). It’s only 49c per base pair, so doesn’t seem too cost prohibitive. My only concern is that if this protein is toxic, I could be wasting money. So I was wondering, has anyone seen the expression for a particular protein change from zero in Rosetta/Codon+ cells using native sequeneces to being largely overexpressed in BL21(DE3) cells using codon optimized sequences? For folks who have had a similar problem to the one I've described, would you recommend that I first try using a codon optimized sequence in E. coli over testing protein expression in yeast/insect cells, or the other way round? Thanks! -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
[ccp4bb] Off topic: (Addressing more than 2GB RAM with NVidia 9 series)
Hi, Sorry for the off topic question. It seems that for some of the new laptops that have more than 2 GB RAM and Nvidia 9 series, graphics is a serious problem. I have tried recompiling the graphics driver with kernel headers etc., no success. Was wondering if someone knows a fix, such as recompiling kernel with details of memory. I am not fussy about distro, any of CentOS / Ubuntu / OpenSuse.. (32 bit / 64 bit) will do. It runs Vista perfectly by the way.. Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
Chris, Try this: sudo apt-get install envyng sudo apt-get install envyng-gtk fire the envyng-gtk interface from the command line or menu and see if it finds a solution.. HTH, Partha On Wed, Jan 7, 2009 at 10:49 AM, Chris Ulens chris.ul...@med.kuleuven.be wrote: Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++ -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Protein folding pattern schematic
Hi Charu, Indonesia is one option, system independent but you need Java for that. http://xray.bmc.uu.se/dennis/ Cheers, Partha On Mon, Nov 10, 2008 at 6:53 PM, Charu Chaudhry [EMAIL PROTECTED] wrote: Hello, Does anyone know of a program that can automatically generate a folding pattern schematic diagram showing the arrangement of secondary structure elements for a protein ? Presumably one would have to feed it a PDB file with secondary structure assigned from DSSP. Thanks! Charu Mayer lab/NIH -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] For a laugh.. ( Ratio of Number of Reflections to Number of restrained )
Since we learn a lot from this BB, here is a new view.. ;) -- Forwarded message -- From: Rajan Pillai [EMAIL PROTECTED] Date: Mon, Sep 8, 2008 at 6:46 PM Subject: Re: [ccp4bb] Ratio of Number of Reflections to Number of restrained Parameters To: Partha Chakrabarti [EMAIL PROTECTED] Dude no offense, your response is just another classic example where people try to prove knowing much, without even knowing what they know and what they don't. As a request, please do not assume this scientific newsgroup as any other newsgroups on yahoo or orkut for your past time. It helps to maintain the purpose of this newsgroup. On Mon, Sep 8, 2008 at 1:11 PM, Partha Chakrabarti [EMAIL PROTECTED] wrote: Dude, no offenses.. but I believe that person is a native speaker and a developer in CCP4.. people who usually understand York if you say Y.. and teach people for free.. if you care to read, there is a refinement program called restrain.. also probably regarding rotation function etc.. check out the acknowledgment of Blundell Johnson.. It helps to keep that arrogance at the doorstep.. On Mon, Sep 8, 2008 at 5:52 PM, Rajan Pillai [EMAIL PROTECTED] wrote: The question was well crafted. It behooves on part of the respondent to understand the question or clarify before answering. On Fri, Aug 29, 2008 at 2:24 PM, Ian Tickle [EMAIL PROTECTED] wrote: Agreed - but it wasn't entirely clear from the original question that this was the purpose of the calculation. Assuming that is the case then it surely behoves subscribers as far as possible to ask the right questions, or at least explain their reasons for needing to perform the calculation: it should not be assumed that others will understand what you meant to say, as opposed to what you did say!
[ccp4bb] Running Resolve after Sharp?
Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would appreciate any input.. I am confused with the eden file.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] Building NCS mate in Coot
Hi While building from scratch in Coot (3A resolution), if I can supply NCS operators in CCP4 format, is it possible to display NCS related molecules in the same way as crystallographic symmetry related ones? External scheme script is fine if that is the way.. (I worked out the operators using NCS6D and IMP (Uppsala) and refined it in DM.) Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Missing space group in ?.mtz file
what happens if you type: env | grep SYMINFO Does it show the path? Either Solve or CCP4? On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko [EMAIL PROTECTED] wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Restraints in Refmac5
One question is, why do you want to fix that and from what literature are you expecting the values? BeF3- is often a ground state analogue for GTP binding proteins for example.. and the depending on the coordination state, the bond angle and length might change a bit I would have thought.. for example, if you have an oxygen from a ligand and a water close enough to the Be, then the bond order of the B-F is lower.. if you have good resolution, this might be interesting in the other way around.. Cheers, Partha On Thu, Jun 26, 2008 at 3:26 PM, [EMAIL PROTECTED] wrote: Hi everyone, I am refining a protein structure containing a Beryllium Fluoride (BeF3) ligand. I am using Refmac5 in ccp4i. The distances between the Be and the F atoms are slightly longer than what I would expect (1.7A instead of ~1.5A). Does anyone know how I can fix the distances and restrain the bond lengths for the BeF. Thanks, Yael. -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] Question about map cutting..
Hi, Is it possible to cut out a spherical map around a heavy atom site directly without having to make bones or building something? I want to place that in a larger P1 cell and use that for phased molecular replacement (Phaser / Molrep).. can someone point me how to do that? Regards, Partha
Re: [ccp4bb] Two off-topic questions
Or, make sure that you don't post it on Monday, some people, sometimes are in very bad mood on Mondays, I am not going to explain why.. :P On Mon, May 12, 2008 at 5:57 PM, Yong, Wei [EMAIL PROTECTED] wrote: Sorry that I missed a letter. I wanted to extract mRNA from pig liver. Thank you, Frank, for having taught me a lesson. I will carefully check my emails before I send them to ccp4bb. I am looking forward to getting suggestions. Best wishes Wei Yong From: Frank von Delft [mailto:[EMAIL PROTECTED] Sent: Mon 5/12/2008 11:12 AM To: Yong, Wei Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Two off-topic questions only tried once). Does any body have ideas about how to extract mRNA from pig live (or animal tissue in general)? From pig live? Yeah sure, toss it in a blender -- you can tell whether it's alive by the squealing. You may need quite a large blender, though, and a crane to lift it, pigs are deceptively large. It's trickier to keep the pig alive even after extracting the mRNA. The subject was dealt with at some length as far back as the late 16th century by a well-known English dramatist, although he framed the problem in more general terms. But do you really need a pound of the stuff? phx. -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] HKL2000 and gcc4
I had similar problem with Mosflm due to odd combination of Suse and AMD-64. Copied those files from a different installation, everything runs just fine.. would agree with James.. lol.. On Mon, May 5, 2008 at 8:32 PM, Chris Waddling [EMAIL PROTECTED] wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] Off topic, CNS language related
Hi, Apologies for the off topic question. I am curious if the CNS/Explore language is a derivative of Lisp. In that case, how does it invoke C/Fortran routines? There seems to be something called Lush which does it inline and supports GPL/maths libraries.. Cheers, Partha
Re: [ccp4bb] too good R/Rfree with resolve
Hi, Just a newbie question: Could someone explain what might have gone wrong in this case? I guess the structure factors should not change anyway! I am a bit confused because I have used solve resolve several times for experimental phasing, never had such a problem, on the other hand, have not heard about density modification for MR apart from one posting (from Prof. Lawrence Perl I think). Is it by any chance that the FOMs were highly overestimated and that creates a problem with Maximum likelihood? That sort of reminds me of what I had heard for SHARP-solomon in a couple of instances.. Any insight would be highly appreciated.. Regards, Partha On Fri, Mar 28, 2008 at 2:35 PM, Garib Murshudov [EMAIL PROTECTED] wrote: make sure that you are using the original observation (Fobs and corresponding sigmas) not that produced by density modification (e.g. solve resolve) programs. Garib On 28 Mar 2008, at 10:43, stefano ricagno wrote: Dear CCP4bb readers, this is my problem: I solved a structure by MR: the solution was easily found (molrep, phaser and balbes found always the same one), density looked generally reasonable (however in several places it was dubious) but R/Rfree were stuck at 42/47%. Then I tried some density modifications, resolve worked spectacularly the density became wonderful and several parts which were not in the model appeared. So I finished to build the model and everything looked good. The problem is now for a structure at 2.8 Å resolution I have R/ Rfree of 8/9.5% respectively, which is clearly too good. Checking refmac log file it looked to me that refmac uses all the reflections in the .mtz file (that is as many reflections as before the resolve run). Ideas? thanks Stefano ps this is my last refmac: 2 mol in the AU, no NCS used, weighting term 0.01, no tls. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.0943 0.1051 0.937102149.5673.2 0.0070 0.298 1.202 0.546 0.077 1 0.0910 0.1024 0.940101442.5642.4 0.0058 0.252 1.091 0.481 0.073 2 0.0898 0.1019 0.940101221.5634.0 0.0055 0.238 1.061 0.461 0.072 3 0.0891 0.1016 0.941101080.5628.8 0.0052 0.226 1.045 0.451 0.072 4 0.0884 0.1011 0.942100947.5622.7 0.0050 0.217 1.033 0.445 0.071 5 0.0877 0.1006 0.942100824.5617.0 0.0049 0.211 1.024 0.440 0.071 6 0.0872 0.1001 0.943100708.5611.4 0.0047 0.205 1.016 0.436 0.070 7 0.0866 0.0997 0.943100593.5606.5 0.0047 0.202 1.008 0.432 0.070 8 0.0861 0.0992 0.944100483.5601.5 0.0046 0.199 1.002 0.429 0.069 9 0.0857 0.0989 0.944100391.5597.5 0.0045 0.196 0.996 0.426 0.069 10 0.0852 0.0985 0.944100313.5593.5 0.0045 0.193 0.990 0.423 0.068 _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+worldmkt=en- USform=QBRE -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] question about processing data
Hi Melody, There was a nice discussion in this year's ccp4 study weekend. In general, one needs to consider several factors.. If you were at 3A, or low symmetry, you would of course try to get the maximum out of it, on the other hand, there are requirements for experimental phasing.. in general, judge it from: 1. Completeness 2. Redundancy 3. I / Sigma 4. R merge statistics Not just one of them. If you are pushing it too far, you will see the effect in later refinement step.. With 74% completeness, how does the other parameters look like? HTH, Partha On Mon, Mar 17, 2008 at 10:06 AM, Melody Lin [EMAIL PROTECTED] wrote: Hi all, I have always been wondering... for a data set diffracting to say 2.15 Angstrom but in the highest resolution shell (2.25-2.15) the completeness is 74%, should I use merge all the data and call it a 2.15 A dataset or I should cut the data set to say 2.25 A where the highest resolution shell has better completeness (85%)? What is an acceptable completeness value for the highest resolution shell? Thank you. Best, Melody -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] question about processing data
Looks ok I guess.. for the highest shell, if Rmerge is less than 0.45 and I/sigma is about 2, it is worth a try.. as James said, completeness might be from why it is incomplete.. is it something like C2? experts might tell us more.. Best, Partha On Mon, Mar 17, 2008 at 11:03 AM, Melody Lin [EMAIL PROTECTED] wrote: well, redundancy for the highest shell is 4.8, I/sigma is 3, Rmerge for overall is 0.08 for highest shell is 0.336. I/sigma and Rmerge don't seem quite nice... thanks. On Mon, Mar 17, 2008 at 11:51 AM, Partha Chakrabarti [EMAIL PROTECTED] wrote: Hi Melody, There was a nice discussion in this year's ccp4 study weekend. In general, one needs to consider several factors.. If you were at 3A, or low symmetry, you would of course try to get the maximum out of it, on the other hand, there are requirements for experimental phasing.. in general, judge it from: 1. Completeness 2. Redundancy 3. I / Sigma 4. R merge statistics Not just one of them. If you are pushing it too far, you will see the effect in later refinement step.. With 74% completeness, how does the other parameters look like? HTH, Partha On Mon, Mar 17, 2008 at 10:06 AM, Melody Lin [EMAIL PROTECTED] wrote: Hi all, I have always been wondering... for a data set diffracting to say 2.15 Angstrom but in the highest resolution shell (2.25-2.15) the completeness is 74%, should I use merge all the data and call it a 2.15 A dataset or I should cut the data set to say 2.25 A where the highest resolution shell has better completeness (85%)? What is an acceptable completeness value for the highest resolution shell? Thank you. Best, Melody
Re: [ccp4bb] phenix.refine and refmac
One point which I don't understand is how can someone compare the two different programs when they don't use the same numbers for xray:geometry terms? Taking the default settings for a given resolution might not be enough.. ! On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides [EMAIL PROTECTED] wrote: Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of refinement cycle. Some of the early publications from Axel Brunger on crystallographic cross-validation address the need for enough reflections (500) in the test-set. In addition, the presence of even a handful of strong but inaccurately measured/integrated low-resolution reflections in a limited test-set can aggravate abnormal behavior in R-free. Best wishes Savvas toQuoting yang li [EMAIL PROTECTED]: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Codon Optimized Expression
Hi Andrea, We have seen examples where it can make a dramatic difference, no expression even with codon plus strains, but really good expression with the daughter constructs as already pointed out. It is particularly true for parasite proteins where the percentage of AT is higher than bacteria. Also for mammalian kinases etc. However, it can become a maximisation and not optimisation, hence can lead to trouble regarding toxicity or solubility. But there are expression system other than IPTG induced where one can fine tune these things. Regards, Partha On Feb 1, 2008 3:29 PM, Looney, Andrea Lynn (Andrea Hevrdeys) [EMAIL PROTECTED] wrote: Dear All, I am getting very little (not zero) expression of my protein. I am curious to know if it is worthwhile to codon optimize my gene, which is ~1200bp, for E.coli. Can you have too much of a good thing? Can codon optimizing overwhelm the cell or in some way cause death or lowered expression? Thank you all, Andrea L. Hevrdeys -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file
Hiya, I used shelex C/D/E on a SAD data, and wanted to refile the positions in MLPHARE before going for AddSOLVE. Confused with the output of two shelex files. shelx1.pdb file says CRYST1 50.050 65.520 105.180 90.00 90.00 90.00 SCALE1 0.019980 0.00 0.000.0 SCALE2 0.00 0.015263 0.000.0 SCALE3 0.00 0.00 0.0095080.0 HETATM1 S HAT 1 13.301 15.247 9.244 1.000 20.00 HETATM2 S HAT 2 11.528 28.067 11.167 0.803 20.00 HETATM3 S HAT 3 15.167 5.763 19.810 0.613 20.00 HETATM4 S HAT 4 13.307 30.233 13.293 0.599 20.00 HETATM5 S HAT 5 12.792 19.519 4.781 0.572 20.00 HETATM6 S HAT 6 13.273 15.312 20.083 0.373 20.00 END shelxd_fa.res file says: REM TRY 37 CC 37.28 CC(weak) 19.64 TIME 56 SECS REM TITL eba28_4_shelxc_fa.ins SAD in C2221 CELL 0.98000 50.05 65.52 105.18 90.00 90.00 90.00 LATT -7 SYMM -X, -Y, 1/2+Z SYMM -X, Y, 1/2-Z SYMM X, -Y, -Z SFAC SE UNIT 128 SE01 1 0.265762 0.232712 0.087886 1. 0.2 SE02 1 0.230339 0.428368 0.106166 0.8032 0.2 SE03 1 0.303047 0.087959 0.188342 0.6130 0.2 SE04 1 0.265884 0.461433 0.126384 0.5992 0.2 SE05 1 0.255577 0.297905 0.045451 0.5723 0.2 SE06 1 0.265198 0.233696 0.190944 0.3728 0.2 HKLF 3 END I have only 4 Se atoms, as judged from cell content analysis, so I guess I do see some Sulphurs. What should I do with atom identifiers in MLPHARE? Cheers, Partha
Re: [ccp4bb] FreeR flag value swap
Hi, The assumption is hard to understand. We are thankful to the community who are developing the great programs (and teaching), and with limited experience, I think it is good to have choices. So, thanks also to people who provide such scripts. If we have to convert file formats, then whats wrong with good old CNS? Requires less memory to run on a laptop [:P]. Best, Partha On 9/27/07, Pavel Afonine [EMAIL PROTECTED] wrote: Hi, Just to explaine: it is assumed that if you came from using phenix AutoSol and AutoBuild then for refinement you use phenix.refine (refinement program in PHENIX). phenix.refine uses 1 for TEST and 0 for WORK (similar to CNS). It is not clear to me at all why you need to do the swap. Pavel. Petra Lukacik wrote: I have a mtz file (output from phenix AutoSol and AutoBuild) where the FreeR flag for the test set has a value of 1 and and the working set has value 0. This is opposite to the ccp4 default where the FreeR set used within refinement is flagged as 0. Is there a way to swap the two around so that my file has the ccp4 default arrangement? Preferably I would like to avoid conversion to ASCII reflection file formats (and back to mtz). Many thanks Petra -- Dr Petra Lukacik NIDDK, NIH Building 50, Room 4507 50 South Drive Bethesda MD 20892 USA Tel: 301 594 9231 - -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
