Re: [ccp4bb] Assay of enzyme from thermophile

You can do it without having to do an assay at high temperature, because the substrate stability would also change at higher temperature. What you could do is the following: 1. Use a PCR machine to heat the enzyme, and then cool it down. 2. Keep one fraction at 4C / RT separately. 3. Do the

Re: [ccp4bb] Off topic: Beryllium chloride

Hi Peter, Both BeF3(-) and AlF4(-) need to be made fresh, or used from frozen. It should not be stored at room temperature. While using, you may wish to keep it on ice. If you are using Vanadate, that should be fresh (Methods in Enzymology). Also kindly note that unlike AlF4(-), which is a

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

Hi Sandeep, if someone sends one, kindly share the references. In general, Ca2+ could have more Asp, Asn kind of coordination and distorted pentagonal bipyramidal geometry with waters (about 2.5A), Cd can also have S- since it is softer, I guess Co might have N/O/S (i.e all three with paired

[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

Hello, From experimental crystallography kinetics background, I have arrived at a situation where I need to model certain membrane related phenomena and correlate it to experimental (metabolonomic) data. In particular, I am looking for mathematical expressions and derivations for: a) Change of

[ccp4bb] Off topic: Monitoring kinetics of multiple enzymes in living cell / lyset

Dear all, Apologies for a off topic question. I could not think of a better place to ask this. Suppose, we have four enzymes turning over five molecules, either in the living cell, or in fresh mammalian cell lyset. The molecules could be as simple as ATP, GTP, NADP, GSH etc. Now, one can add a

Re: [ccp4bb] Refining residues as rigid bodies

Hi Jason, Instead of doing rigid body refinement of each residue, you may consider rigid.inp of CNS or an equivalent strategy in Phenix which will do SA, rigid body and B factor refinement, followed by either composite omit (CNS) or 'prime switch' of phenix (rather resolve) to fix the side

[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

Hi Shankar, Another fascinating example might be Dscam (Down Syndrome cell adhesion molecule) with multiple Ig like domains and Fibronectin type III domains. Different splice isoforms are expressed in different nerves, and it serves as a recognition module, same repels, different ones attract.

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

Hi Jonathan, This is purely a chemistry guess, but if you have a PEG400 derived compound like: (HO)-CH2-CH2-O-CH2-CHO, i.e, part oxidised, then the CHO might form a N,O acetal ring with the free amine and side chain. Five membered ring formation is kinetically favourable, though the chemistry

[ccp4bb] Refmac specific questions

Hi, Sorry to sound stupid, could someone explain what does refmac do if one chooses mixed (bref MIXED) or overall (bref OVER) B factor refinement in the context of TLS refinement? Is it something like: Isotropic for the main chain and/or waters and anisotropic for the side chain? Regards,

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

Cygwin has problems with Vista.. you need to run it as administrator.. works fine with XP though. Moreover, Cygwin is not very well supported anymore, as the developer works for Red Hat now. If it is just the X, there are other free programs.. XMing is quite good. You can indeed install Ubuntu

[ccp4bb] Off topic: Coot and shared libraries

Hi, I am running a 64 bit Fedora 10 machine and having problems with coot, if i say ldd coot-real linux-gate.so.1 = (0x5000) libguilegtk-2.0.so.0 = not found libgthread-2.0.so.0 = /lib/libgthread-2.0.so.0 (0x00df8000) librt.so.1 = /lib/librt.so.1 (0x005f) libguile.so.17

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

Just to add couple of things to what Artem said.. If it is something similar to a mammalian kinase or malaria protein for example, 1. Recodonizaton can change expression from near zero to substantial amounts, however, a) ideally, it needs to be recodonized separately for each target expression

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

Hi, Sorry for the off topic question. It seems that for some of the new laptops that have more than 2 GB RAM and Nvidia 9 series, graphics is a serious problem. I have tried recompiling the graphics driver with kernel headers etc., no success. Was wondering if someone knows a fix, such as

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 a

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?

Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification ( maybe NCS / building) directly with the sharp output? If so, I would

[ccp4bb] Building NCS mate in Coot

Hi While building from scratch in Coot (3A resolution), if I can supply NCS operators in CCP4 format, is it possible to display NCS related molecules in the same way as crystallographic symmetry related ones? External scheme script is fine if that is the way.. (I worked out the operators using

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

One question is, why do you want to fix that and from what literature are you expecting the values? BeF3- is often a ground state analogue for GTP binding proteins for example.. and the depending on the coordination state, the bond angle and length might change a bit I would have thought.. for

[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

Hi, Just a newbie question: Could someone explain what might have gone wrong in this case? I guess the structure factors should not change anyway! I am a bit confused because I have used solve resolve several times for experimental phasing, never had such a problem, on the other hand, have not

Re: [ccp4bb] question about processing data

Hi Melody, There was a nice discussion in this year's ccp4 study weekend. In general, one needs to consider several factors.. If you were at 3A, or low symmetry, you would of course try to get the maximum out of it, on the other hand, there are requirements for experimental phasing.. in general,

Re: [ccp4bb] question about processing data

[EMAIL PROTECTED] wrote: well, redundancy for the highest shell is 4.8, I/sigma is 3, Rmerge for overall is 0.08 for highest shell is 0.336. I/sigma and Rmerge don't seem quite nice... thanks. On Mon, Mar 17, 2008 at 11:51 AM, Partha Chakrabarti [EMAIL PROTECTED] wrote: Hi Melody

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

Hi Andrea, We have seen examples where it can make a dramatic difference, no expression even with codon plus strains, but really good expression with the daughter constructs as already pointed out. It is particularly true for parasite proteins where the percentage of AT is higher than bacteria.

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

Hiya, I used shelex C/D/E on a SAD data, and wanted to refile the positions in MLPHARE before going for AddSOLVE. Confused with the output of two shelex files. shelx1.pdb file says CRYST1 50.050 65.520 105.180 90.00 90.00 90.00 SCALE1 0.019980 0.00 0.000.0

Re: [ccp4bb] FreeR flag value swap

Hi, The assumption is hard to understand. We are thankful to the community who are developing the great programs (and teaching), and with limited experience, I think it is good to have choices. So, thanks also to people who provide such scripts. If we have to convert file formats, then whats