Hi, Please unsubscribe me from this list as the posts are not relevant to my research profile. Kind Regards, Shivam On 28 Mar, 2013, at 12:32 AM, CCP4BB automatic digest system <[email protected]> wrote:
> There are 9 messages totaling 164114 lines in this issue. > > Topics in this special issue: > > 1. ./configure problem (2) > 2. High number of clashes with high TFZ score (2) > 3. off topic, BN PAGE > 4. IUCr Travel Grants Available - (11th International Conference on > Biological Synchrotron Radiation (BSR), Hamburg, Germany, 8-11 Sept 2013) > 5. Rec- variant of E coli B (2) > 6. refinement protein structure > > ---------------------------------------------------------------------- > > Date: Tue, 26 Mar 2013 20:16:12 -0400 > From: A K <[email protected]> > Subject: ./configure problem > > Hi there, > I am trying to install ccp4 on a scientific linux system. I've got stuck in > the step where I need to configure the system. After sourcing ccp4.setup, I > go to the main ccp4 folder and try ./configure help, but I get the error > "bash: ./configure: No such file or directory". It looks as if the > configure script has not been included in my tar file. The file I unzipped > was called ccp4-6.3.0.1-arp-linux-x86_64.tar.gz. Any suggestion is highly > appreciated. > Alex > > ------------------------------ > > Date: Tue, 26 Mar 2013 21:55:38 -0400 > From: Zhijie Li <[email protected]> > Subject: Re: ./configure problem > > Hi Alex, > > The CCP4 package you downloaded seems to be a prebuilt binary package for the > X86_64 architecture. You do not need to compile yourself - and you can't > without the source code. Running ./configure is for configuring the > compilation environment before running "make" to compile source codes, which > dose not apply to binary packages. > > I guess you probably was following this page: > http://www.ccp4.ac.uk/dist/INSTALL.html. The information on that page is for > compiling the source code, not for the binary packages. The layout of that > page is a little confusing: it does mention how to download the binary > packages and started to say "then first you need to decide where you want to > put the software", but then it suddenly jumps to how to build the CCP4 from > source code. I think this might be something the authors want to fix. > > For prebuilt binary packages, please take a look at the INSTALL file in the > unpacked CCP4 directory for installation instructions. The CCP4 binary > installation is very simple: run the BINARY.setup in the unpacked CCP4 > directory. After it is done, append this line to /etc/bashrc (assuming your > default shell is bash): > > source /path_to_ccp4/ccp4.setup-sh > > Then open a new shell, type ccp4i, you should see the CCP4 user interface. > > Zhijie > > > > > > From: A K > Sent: Tuesday, March 26, 2013 8:16 PM > To: [email protected] > Subject: [ccp4bb] ./configure problem > > > Hi there, > I am trying to install ccp4 on a scientific linux system. I've got stuck in > the step where I need to configure the system. After sourcing ccp4.setup, I > go to the main ccp4 folder and try ./configure help, but I get the error > "bash: ./configure: No such file or directory". It looks as if the configure > script has not been included in my tar file. The file I unzipped was called > ccp4-6.3.0.1-arp-linux-x86_64.tar.gz. Any suggestion is highly appreciated. > Alex > > ------------------------------ > > Date: Wed, 27 Mar 2013 17:32:46 +0900 > From: Rojan Shrestha <[email protected]> > Subject: High number of clashes with high TFZ score > > Hello, > > > > I am trying phasing using homology models with Phaser. We obtained very high > TFZ scores with many clashes. The number of clashes are around more than > 100. The space group is P321. We tried two other space groups P3121 and > P3221 but both gave same problem. Can you help on this problem? > > > > Regards, > > > > Rojan > > ------------------------------ > > Date: Wed, 27 Mar 2013 08:42:19 +0000 > From: Randy Read <[email protected]> > Subject: Re: High number of clashes with high TFZ score > > In such circumstances, one of the most common issues is that the space group > is incorrect, which is often because twinning gives higher apparent symmetry. > If (for example) the true space group is P3, there will be solutions in P321 > that place the molecules correctly around the 3-fold axis (so they give a > better than random score in the translation search), but the extra symmetry > causes clashes. Have you looked at the results of twinning tests? > > If that doesn't explain your problem, you could send me the log file from one > of the Phaser runs (probably offline) and I could see if there are any hints > of other explanations in the output. > > Best wishes, > > Randy Read > > On 27 Mar 2013, at 08:32, Rojan Shrestha <[email protected]> wrote: > >> Hello, >> >> I am trying phasing using homology models with Phaser. We obtained very high >> TFZ scores with many clashes. The number of clashes are around more than >> 100. The space group is P321. We tried two other space groups P3121 and >> P3221 but both gave same problem. Can you help on this problem? >> >> Regards, >> >> Rojan > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: [email protected] > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > ------------------------------ > > Date: Wed, 27 Mar 2013 02:24:49 -0700 > From: Careina Edgooms <[email protected]> > Subject: off topic, BN PAGE > > Hi > > Has anyone found the coomassie in a BN PAGE to be interfering with the > oligomeric structure of their protein? If so, how did you deal with this? > Thanks > > ------------------------------ > > Date: Wed, 27 Mar 2013 15:26:54 +0100 > From: margret <[email protected]> > Subject: IUCr Travel Grants Available - (11th International Conference on > Biological Synchrotron Radiation (BSR), Hamburg, Germany, 8-11 Sept 2013) > > *IUCr Travel Grants Available!! * > *APPLY NOW!!* > > *11th International Conference on Biological Synchrotron Radiation (BSR)* > *Hamburg, Germany* > *8th - 11th September 2013* > > We are pleased to announce that we have a number of travel awards > available for young scientists, kindly provided by the International > Union of Crystallography (IUCr). Up to 450 Euros will be awarded to > outstanding students for supporting travel costs. Applicants must be > graduate students, post-graduate students or post doctoral fellows under > the age of 30 (exceptionally 35). If you are eligible and wish to apply, > please indicate this when you register for the conference. Successful > applicants will be notified in the summer. > > The 11th International conference on Biological Synchrotron Radiation > (BSR) aims to bring together scientists involved in the methodical > developments on synchrotron and laser sources with a broad community of > biologists with an ambition to make the best use of the most advanced > infrastructures in structural biology. > > Topics include: > > Biological small angle X-ray scattering > > Macromolecular X-ray crystallography > > Biological X-ray imaging and spectroscopy > > Biological sample preparation > > Free electron laser applications > > Synchrotron instrumentation > > Industrial applications > > Structural biology hybrid methods > > Ultimate storage rings > > > For more information and to register, please go to: www.bsr2013.org > <http://www.bsr2013.org> > > > Looking forward to seeing you in Hamburg! > > Margret Fischer on behalf of > > Matthias Wilmanns, Dmitri Svergun (EMBL Hamburg) > > ------------------------------ > > Date: Wed, 27 Mar 2013 16:13:28 +0100 > From: Mark J van Raaij <[email protected]> > Subject: Rec- variant of E coli B > > Dear All, > we were wondering if knows of an Escherichia coli B strain that is Rec > deficient (Rec-). > We want to compare certain properties of E coli B and K12, and for the > experiment it would be best to use a Rec- variant. > We have TOP10, which is a K12 derivative that is Rec-, but derivatives of B > like BL21 are Rec+. > Have a happy Easter, > Mark > > Mark J van Raaij > Lab 20B > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > ------------------------------ > > Date: Wed, 27 Mar 2013 15:20:36 +0000 > From: Marko Hyvonen <[email protected]> > Subject: Re: Rec- variant of E coli B > > Hi Mark, > > BLR(DE3) should be what you are after. > > http://www.emdmillipore.com/life-science-research/blrde3-competent-cells/EMD_BIO-69053/p_yYub.s1Ol18AAAEjORl9.zLX > > hth, Marko > > On Wed, 27 Mar 2013, Mark J van Raaij wrote: > >> Dear All, >> we were wondering if knows of an Escherichia coli B strain that is Rec >> deficient (Rec-). >> We want to compare certain properties of E coli B and K12, and for the >> experiment it would be best to use a Rec- variant. >> We have TOP10, which is a K12 derivative that is Rec-, but derivatives of B >> like BL21 are Rec+. >> Have a happy Easter, >> Mark >> >> Mark J van Raaij >> Lab 20B >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> c/Darwin 3 >> E-28049 Madrid, Spain >> tel. (+34) 91 585 4616 >> http://www.cnb.csic.es/~mjvanraaij >> > > > _____________________________________ > > Marko Hyvonen > Department of Biochemistry, University of Cambridge > [email protected] > http://www-cryst.bioc.cam.ac.uk/groups/hyvonen > tel: +44-(0)1223-766 044 > mobile: +44-(0)7796-174 877 > fax: +44-(0)1223-766 002 > -------------------------------------- > > ------------------------------ > > Date: Wed, 27 Mar 2013 16:22:25 +0000 > From: Tom Van den Bergh <[email protected]> > Subject: refinement protein structure > > Dear members of ccp4bb, > > I need some help with the refinement of my structure of a variant of mRFP > (monomer red fluorescent protein, sequence in attachment). I have done > molecular replacement with phaser with model 2VAD of protein database. Then i > have done some model building phenix.autobuild. (2 pdb's (overall...), freeR > flags and log file attached) When i refine with phenix.refine my structure i > get a R-value of 0,42 which is still way too high. (redfluorescent > protein.pdb, .mtz and logfile attached) When i look at the structure in coot > i find many unmodelled blobs and many outliers in density analysis and > rotamer analysis. The problem is that there are so many problems with my > structure, that i dont know where to begin. Could you try some refinement for > me, because this is first structure that i need to solve as a student and i > dont have too many experience with it. > > Greetings, > > Tom > > ------------------------------ > > End of CCP4BB Digest - 26 Mar 2013 to 27 Mar 2013 - Special issue (#2013-90) > ****************************************************************************
