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 <[log in to unmask]> 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 <[log in to unmask]>
> 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 <[log in to unmask]>
> 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: [log in to unmask]
> 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 <[log in to unmask]>
> 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 <[log in to unmask]>
> 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 <[log in to unmask]> 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: [log in to unmask]
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
> ------------------------------
>
> Date: Wed, 27 Mar 2013 02:24:49 -0700
> From: Careina Edgooms <[log in to unmask]>
> 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 <[log in to unmask]>
> 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 <[log in to unmask]>
> 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 <[log in to unmask]>
> 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
> [log in to unmask]
> 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 <[log in to unmask]>
> 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)
> ****************************************************************************
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