Re: [ccp4bb] all of a sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac laptop

Hi Pietro, I guess this might be a GTK gsettings [1] problem; do you have a ~/.config/dconf/user [2] file in your home directory? If so, maybe move this somewhere else for now and see of Coot opens OK (Is this a $home directory that has also been used via NFS or similar on a Linux

[ccp4bb] Positions available at Evotec

thanks, Mark [cid:image002.png@01D514C2.B80E8D30] Dr. Mark Brooks Project Leader, mark.bro...@evotec.com<mailto:mark.bro...@evotec.com> www.evotec.com<http://www.evotec.com/> Evotec (U.S.) Inc Building 303B, College Road East, Princeton, NJ 08540, USA. STATEMENT OF CONFIDENTIALITY.

Re: [ccp4bb] Dimer in SDS-PAGE

Dear Amit, Maybe try adding an equal volume of 8M urea to your sample before adding the SDS-PAGE sample buffer. Then I'd test boiling and not boiling that sample prior to loading on the gel. Good luck, Mark On 21 February 2017 at 17:22, amit gaur wrote: > Hi all,

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

Hi Marc, I have an Intel Iris Pro graphics chip on a Late 2013 MacBook Pro which works impressively well with all these programs, even on a 15 inch Retina display. I don’t know if the Nvidia one is better though... Bonne chance, Mark On 17 Mar 2015, at 16:12, Marc Graille

Re: [ccp4bb] A Moleman alternative?

baverage for atom numbers (protein/ligand/water), B factors http://www.ccp4.ac.uk/html/baverage.html Mark On 17 Nov 2014, at 19:55, Yong Tang liutan...@gmail.com wrote: Dear all, I have no access to Moleman now but I need to compile a statistics table for a structure, more specifically,

Re: [ccp4bb] [phenixbb] [ot]: nedit on Mac 10.10 yosemite

Try reinstalling X-quartz. IIRC, /usr/X11R6 is deleted during MacOS upgrades. Mark On 29 October 2014 14:45, Sebastiano Pasqualato sebastiano.pasqual...@gmail.com wrote: Hi folks, sorry for the off-topic and slightly ‘demodée’ question, but, since I updated to Yosemite on my Mac, nedit

Re: [ccp4bb] moleman2 install problem

Jul 2014, at 13:39, Mark Brooks mark.x.bro...@gmail.com wrote: Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I

Re: [ccp4bb] Non-catalytic Rossmann fold domain

DprA, from the Streptococcus pneumoniae transformasome, is one, I believe: http://www.ncbi.nlm.nih.gov/m/pubmed/22904190/ On 22 Apr 2014, at 14:26, Tanner, John J. tanne...@missouri.edu wrote: Does anyone know of a protein that has a Rossmann dinucleotide binding domain that does not

Re: [ccp4bb] ipmosflm not connecting to XQuartz on Mac.

I had a similar problem with CCP4 generally after a recent computer upgrade. Re-installing xquartz worked for me, because some components had seemingly become deleted. HTH Mark On 15 Apr 2014, at 21:54, Francis Reyes francis.re...@colorado.edu wrote: Hi all, Anyone having issues

Re: [ccp4bb] Convert DSSP to PDB format

Hi Wenhe, One answer to Q#2 is James Stroud's dssp2pdb to take the output of DSSP write HELIX and SHEET lines etc. http://www.jamesstroud.com/software/dssp2pdb/ Mark P.S. I believe the answer to question #1 is DSSP but I suspect the answer is more complex. On 1 March 2014 13:50, Wenhe

[ccp4bb] Off topic: Scientist Position in Protein Production and Expression at Evotec, near Oxford

Dear all, Please forward this job posting to any appropriate candidates. If interested, plese don't reply to me, but instead apply using the website below. Yours, Mark *Scientist* *Protein Production and Expression within our Structural Biology Department* *Location:

Re: [ccp4bb] SA-omit map

Maybe try CNS or SFCheck: http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720 To improve Phenix maps, maybe try increasing the number of boxes (the parameter IIRC n_box_target= ) http://www.phenix-online.org/documentation/autobuild.htm In CNS, you can decrease the starting

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

Tim has the more modern answer, but PDBSET http://www.ccp4.ac.uk/html/pdbset.html is quite simple and scriptable. If I recall correctly, the SYMGEN keyword may be of use. From the example in the documentation: Expand dimer to tetramer, rename chains, transform

Re: [ccp4bb] writing scripts-off topic

Hi Yuri, If you don't like Python, like myself (and I'm not alone, it would seem), you could try Ruby (http://www.ruby-lang.org/en/). Some examples of PDB file manipulation are below (taken from [1]). The language is a great improvement in Perl and Python in my opinion, but the downside

Re: [ccp4bb] adxv

Dear Rajesh,                   Are you using the Openmotif library? If so, do you have an XKeysymDB file installed? In as shell, issue: $ locate XKeysymDB You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is elsewhere [1]. I suspect you're not the only one to have seen this [2]. I

Re: [ccp4bb] Akta Prime

Dear Mike,                At Evotec (a UK site), we gave up using GE to service our GE instruments (!) due to problems with their bureaucracy. Agilent offer service contracts for Aktas that are competitively priced and are a work-alike in our experience. For call-outs, they sub-contract the usual

Re: [ccp4bb] PYMOL installation in openSUSE 11.3 (64 bit)

Hi, If you're missing Python.h (since your compiler complains about it), I guess you're missing the development package of python, whatever that's called in SUSE. Probably python-devel, according to this: http://www.novell.com/products/linuxpackages/opensuse/python-devel.html Good luck,

Re: [ccp4bb] Protein sequencing service?

Jeff Keen is good, but just to add to the list Cambridge Peptides http://www.cambridgepeptides.com/proteinsequencing.html based in Birmingham (!), is fast and efficient from either membrane or directly from gel slices. Yours, Mark On 24 September 2010 16:46, Rex Palmer rex.pal...@btinternet.com

Re: [ccp4bb] pdf to text

For OCR without installing software, Free OCR http://www.free-ocr.com/ works quite well for me, but beware that you may need to do corrections afterwards. Just upload your file to this web site, as long as it isn't secret! The OCR in Adobe Acrobat works better for me though, and is worth the

Re: [ccp4bb] database-assisted data archive

Dear Andreas, If you really want to do this, and want to define what is the data is, it's not _so_ difficult to do it yourself, with Ruby on Rails ( http://rubyonrails.org/) You have to know how to script a bit, and know a bit about Model/View/Controller frameworks.

Re: [ccp4bb] software for predicting protein solubility, stabililty and disorders

Hi, My favourite is Phyre: http://www.sbg.bio.ic.ac.uk/~phyre/ A benefit of this is that it predicts your domains, makes sequence alignments with the similar proteins, and makes homology models which are sometimes good enough to start building with when you've phased the structure! Another

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Dear Nasos Hailiang, Gerard Kleywegt's MAPMAN calculates the RSR, discussed here: http://xray.bmc.uu.se/usf/mapman_man.html#S41 Mark On 21 May 2010 23:54, Athanasios Dousis ndou...@rice.edu wrote: Hello all, I'm forwarding a question from my labmate

Re: [ccp4bb] ncsfind

Hello,         If you have Phenix, try phenix.find_ncs (sorry for the non-CCP4 answer). The example run in the PHENIX documentation is: phenix.find_ncs anb.pdb mlt.mtz This will then write out the NCS operators in various flavours. Basically if you have a list of Se sites it calls RESOLVE, but

Re: [ccp4bb] control of nucleation

Dear Zq Deng, I've had success with the dilution method as described by Dunlop and Hazes: http://scripts.iucr.org/cgi-bin/paper?en5016 For me it worked for a couple of projects, and gives you a bit more to permutate than just varying the protein:mother liquor ratios, as Thomas

Re: [ccp4bb] align DNA structures

: Hi all, I will highly appreciate your help regarding following: How to align  two  DNA structures in Pymol or Coot or any other softwares? ( I tried regular align in Pymol, but it doesn't work for DNA; it works great for protein structures.) Thanks a lot in advance ! Mike -- Mark

Re: [ccp4bb] NADP - ADP binding

     Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks

Re: [ccp4bb] Regarding CCP4 on mac

the GUI, and the programs are definitely present and run in the ccp4 bin directory. Does anyone know what could be going wrong? Thanks, Mohinder -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype

Re: [ccp4bb] phaser troubles

are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud

Re: [ccp4bb] song CRT Multiscan E540 monitor for stereo view

the stereo view? Thanks, Eric -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks

Re: [ccp4bb] OT: VectorNTI alternatives

, both free and paid. Any experience? Thanks, Darren EMBL Grenoble ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. -- Mark Brooks

Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10

+++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++ -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay

Re: [ccp4bb] to extract protein sequence from a rebuilt pdb file

by sequence alignment. Any ideas about this? thanks Best Jane -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks

Re: [ccp4bb] regarding cloning

here.http://in.rd.yahoo.com/tagline_messenger_7/*http:/in.messenger.yahoo.com/win/ -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks

Re: [ccp4bb] crystallisation

/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique

Re: [ccp4bb] CCP4 for bioinformatics?

fax : 01 45 82 75 77 mobil: 06 07 23 51 16 [EMAIL PROTECTED] * -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE UMR8619 - Bât 430 - Université de

Re: [ccp4bb] upgrading ccp4 broke my Coot stereo

what it is. Any ideas? -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE UMR8619 - Bât 430 - Université de Paris-Sud 91405 ORSAY CEDEX

Re: [ccp4bb] Stereo setting in program O with stereo-ready graphic card in x86_64

technology fusion Tel) 82-2-450-4090 E-mail) [EMAIL PROTECTED] -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE UMR8619 - Bât 430 - Université de Paris-Sud 91405 ORSAY CEDEX