[ccp4bb] Postdoc Position in NanoMEGAS SPRL, Belgium

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

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

[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

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

Re: [ccp4bb] Assay of enzyme from thermophile

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

Re: [ccp4bb] Off topic: Beryllium chloride

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

Re: [ccp4bb] Cadmium sites and co-ordinations in structure

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

[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:

[ccp4bb] Question about mathematical modeling of membranes, pores and transporters

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

this..) Has anybody seen something that addresses the question? Any suggestion would be highly appreciated. Cheers, Partha

Re: [ccp4bb] Refining residues as rigid bodies

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

[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

. 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

Re: [ccp4bb] Off-topic: unidentified density for N-terminal Thr modification

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

[ccp4bb] Refmac specific questions

, 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 ,

Re: [ccp4bb] Computer hardware and OS survey

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

[ccp4bb] Off topic: Coot and shared libraries

= 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

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

://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

[ccp4bb] Off topic: (Addressing more than 2GB RAM with NVidia 9 series)

, 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

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

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

[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

[ccp4bb] Running Resolve after Sharp?

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

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

Re: [ccp4bb] Restraints in Refmac5

.. 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

[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,

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

[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

.. 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

Re: [ccp4bb] question about processing data

, 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

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

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]

Re: [ccp4bb] Codon Optimized Expression

. 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

[ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file

do see some Sulphurs. What should I do with atom identifiers in MLPHARE? Cheers, Partha

Re: [ccp4bb] FreeR flag value swap

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