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 computer?

[ccp4bb] Positions available at Evotec

Many 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 CONFIDENTIA

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, > I am trying to pu

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 wrote: > > Dear all, I have no access to Moleman now but I need to compile a statistics > table for a structure, more specifically, for its atom numb

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, "ne

Re: [ccp4bb] moleman2 install problem

ciation SIG9 (Crystallographic > Computing) > > On 24 Jul 2014, at 13:39, Mark Brooks 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,

Re: [ccp4bb] moleman2 install problem

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 don't know that Snow Leopard binaries are compatible with Maveric

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." wrote: > > Does anyone know of a protein that has a Rossmann dinucleotide binding domain > that does not participate in cofact

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 wrote: > > Hi all, > > Anyone having issues getting ipmosflm to connect

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: *Oxford

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 temp

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 #!/bin/cs

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 h

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, M

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 wrote: > Can anyone p

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 mo

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. http://www.yout

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 bene

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 wrote: > Hello all, > > I'm forwarding a question from my labmate Hailiang Zhang reg

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 ha

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

nd : > 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.) &g

Re: [ccp4bb] NADP - ADP binding

any rules that dominate these two >> cofactors to select the surface istead of typical Rossmann fold. >> >> Thank you >> >> Sajid >> >> >> >>      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] amino acid analysis for SeMet incorporation

Any suggestions would be highly appreciated! > > Best, > > Marija > > > Marija Backovic, Ph.D. > > Pasteur Institute > Department of Virology > 25 rue du Dr Roux > 75015 Paris > France > > +33 (0)1 45 68 82 87 > -- Mark Brooks, IBBMC, UMR8619 - Bât

Re: [ccp4bb] Regarding CCP4 on mac

al/ccp4-6.1.2/bin/ccp4.setup-sh > > before running 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, Univers

Re: [ccp4bb] phaser troubles

in the personal > views and opinions of the author, which 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

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

n order to get > 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

iles 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, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks

Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10

> 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.

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

that I could see clearly which part need to be > rebuilt 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

he vector at 3.7kb ,for the ligation i am using the > ratio of vector to insert is 1:3,1:2,getting the colony after the > transformation but some how when i used to confirm my clone through double > digestion i am not getting my insert at the correct position.Some time in > the gel only the size of the vect

Re: [ccp4bb] crystallisation

03.JPG (720k bytes) > Phoebe A. Rice > Assoc. Prof., Dept. of Biochemistry & Molecular Biology > The University of Chicago > phone 773 834 1723 > > http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/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 Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks

Re: [ccp4bb] CCP4 for bioinformatics?

> > > > > > > -- > * > Dr Claudine MAYER > MCF Université Paris 6 > LRMA Equipe 12 UMR S 872 > Laboratoire de Bactériologie (5ème étage gauche) > Faculté de Médecine PITIE-SALP

Re: [ccp4bb] upgrading ccp4 broke my Coot stereo

ppear that an environmental variable involving a library > path is missing or wrong but I have not been able to figure out 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

s, > > Lin-Woo Kang, Ph.D. > > Assistant professor > Konkuk university > Dept. of advanced 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

Re: [ccp4bb] oxidised cys

ust didn't find them. > > Second question: > > How could I "explain" to refmac that there is the OO bond? > > I tried to write a line similar to the one for SSBOND in the pdb header > > OOBOND 1 CEA A 42CEA D 42 > > but refmac couldn&#x