Re: [ccp4bb] Extra electron density

r a fatty acid of an appropriate length. If it is truly spurious density as I suspect it is, you'll see negative density lighting up your screen despite using appropriately low occupancy. Good luck! Sangeetha. On Sun, Nov 4, 2012 at 8:17 PM, Sangeetha Vedula wrote: > Could it be a fat

Re: [ccp4bb] protein cleavage

Do you see the same MBP band (or corresponding to the same MW, in case it isn't MBP) before cleavage, at the same total concentration of protein? If not, your protein could be crashing out. Even so, if you use SDS and heat up the sample, I am surprised that your protein just disappeared. TEV protea

Re: [ccp4bb] Extra electron density

Could it be a fatty acid? It looks like it has a (hydrophobic?) tail with a (charged?) head. Partially occupied perhaps, as they're so close together. On Sun, Nov 4, 2012 at 7:38 PM, yogesh khandokar wrote: > Dear All > > I am working on an enzyme which involved in fatty acid biosynthesis. We >

Re: [ccp4bb] Enhancing Crystal Quality

Lucas, if your crystals diffract worse at room temp than cryoprotected, it looks like there may be radiation damage at room temperature, so you may need to cryoprotect. The change in osmotic pressure may be too much for your crystals when you're cryoprotecting the crystals by a sudden dunk. Also, d

[ccp4bb] determination of oligomerization state of protein

Hello all, I am working with a protein that is probably a hexamer based on homology with other proteins but when I ran it on an analytical size gel filtration column, I see multiple peaks. I would like to determine the exact oligomerization state of the mixture and have considered blue native gel

[ccp4bb] Desalting columns

Dear bb users, I am trying to crystallize a ~320 kDa protein that crashes out if concentrated past about 3 mg/mL. I would like to try to exchange it into various buffer-salt-additive combinations to see which buffer works. For a starting point, I'd like to use desalting colums. Does anyone have

Re: [ccp4bb] Very high B-factors of some atoms of ligand in Refmac

on damage (are those high-B > atoms on the ligand maybe I or Br?) ... decarboxylation on side-chains > etc etc. > > Just some ideas ... > > Cheers > > Clemens > > On Thu, Jan 28, 2010 at 11:04:52AM -0500, Sangeetha Vedula wrote: > > Dear all, > > >

Re: [ccp4bb] Biorad Profinia vs GE AKTAPrime Plus, for affinity tagged proteins

AM, Edward Collins wrote: > personally, I don't know why you would want to limit yourself to just using > affinity tags to purify your proteins. For my money the flexibility of the > AKTA is critical. > good luck > -ed > > On Jan 28, 2010, at 11:08 AM, Sangeetha Vedula wrot

[ccp4bb] Biorad Profinia vs GE AKTAPrime Plus, for affinity tagged proteins

Dear all, My lab is looking into buying a protein purification system. The AKTA is more versatile, but does anyone know if the Profinia is in any way superior to the AKTA for purification of affinity-tagged proteins? If it is, I would really appreciate if you can tell me in what way it is superior

[ccp4bb] Very high B-factors of some atoms of ligand in Refmac

Dear all, I am refining a crystal structure with two enantiomers of the ligand lying on a two-fold crystallographic axis (making the density an average of 4 orientations/optical identity). The ligand fits pretty well over all in the density, but some atoms stick out of density. While B-factors for

Re: [ccp4bb] hairpin formation in gene

- > > *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of > *Sangeetha > Vedula > *Sent:* Friday, November 20, 2009 8:03 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] hairpin formation in gene > > > > Dear bb-ers, >

[ccp4bb] hairpin formation in gene

Dear bb-ers, I am trying to have a gene synthesized and found out that it forms an 11-bp hairpin. Does that complicate expression? Would it be better to try and disrupt it by altering codon usage to improve expression? Thank you in advance, Sangeetha.

Re: [ccp4bb] XDS Viewer

I am using a MacBook Pro running OS 10.4.11. I downloaded XDSViewer from: http://sourceforge.net/project/platformdownload.php?group_id=239755 On Thu, Jun 11, 2009 at 1:23 PM, Sangeetha Vedula wrote: > I moved the program to /Applications as well. > > When I start XDSviewer giving it

Re: [ccp4bb] XDS Viewer

I moved the program to /Applications as well. When I start XDSviewer giving it the whole path, it errors out, saying: /Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer: line 6: 818 Bus error "$CURRENT_DIR/xds-viewer-bin" If I double-click on XDS-Viewer.app icon, it begins to

Re: [ccp4bb] xds undefined data_range error

> -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > On Thu, 11 Jun 2009, Sangeetha Vedula wrote: > > I checked: >> >> 1. I did name it XDS.INP; no problem there. >> 2. The p

Re: [ccp4bb] xds undefined data_range error

image number for finding spots > > and instead define the spot range only in one line e.g. SPOT_RANGE=1 50 > > That should fix your problem I think. > > Jürgen > > On 11 Jun 2009, at 11:27, Sangeetha Vedula wrote: > > I checked: > > 1. I did name it XDS.INP;

Re: [ccp4bb] xds undefined data_range error

range?). I am attaching the file, XDS.INP that I am using. Thank you so much in advance for taking the time. Regards, Sangeetha. On Thu, Jun 11, 2009 at 3:23 AM, Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Sangeetha Vedula schrieb: > > Hello all, >> >>

[ccp4bb] xds undefined data_range error

Hello all, Apologies for the non-CCP4 question. I am trying to process some data collected at X6A in March. I edited the XDS.inp file for ADSC detector. When I try to run xds, however, it gives an error immediately: !!! ERROR !!! UNDEFINED DATA_RANGE= I checked the data range and the image path

Re: [ccp4bb] libcheck merge monomer library

Thank you, Sridhar. For some reason, that gives an error, saying that it couldn't execute libcheck. Instead, I tried using the keyworded input format. Do you know what could be wrong with that? I tried to install libcheck but apparently my computer can't figure out what the "make" function is (ma

[ccp4bb] libcheck merge monomer library

Hello all: I am trying to merge library files for 2 molecules using libcheck dialogue. But it only writes out the first library file that I read in. FILE_L 1.cif FILE_L2 2.cif It writes out a file called libcheck.lib which contains only lines from 1.cif. What am I doing wrong? Is there somethin

[ccp4bb] arp/warp ligand

Hi all, I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite 6.0.2 on CCP4interface 1.4.4.2. I get an error message telling me to look for the error in a "##_warp_ligand_details.log". _ Running Refmac5 to refine

Re: [ccp4bb] VOIDOO average volume report

Hi Manish and everyone, If one uses the volume on the plot grid size, volume is biased by the plot grid size one chooses and not the converged volume. In short, one isn't even using the results of volume refinement because one'd get the same answer from the same grid size for the same orientation

Re: [ccp4bb] VOIDOO average volume report

Hi Manish, But then volume is biased by the plot grid size one chooses and not the converged volume. In short, one isn't even using the results of volume refinement because one'd get the same answer from the same grid size for the same orientation (given the same probe radius). Using the final con

[ccp4bb] VOIDOO average volume report

Hello all I am comparing the probe-occupied volumes of a protein cavity with and without several ligands. Which cavity volume is used for the comparisons? I found an FAQ link: http://www.imsb.au.dk/~mok/o/ofaq/Q.507.html Q.507 - Which VOIDOO cavity

Re: [ccp4bb] Preventing close contact between protein and ligand

;wrote: > You're probably better off trying to change the restraints in the > ligand .cif file. It sounds like you have some torsion angle or > chiral center set wrong. > -bob > > On Tue, Jul 29, 2008 at 10:24 AM, Sangeetha Vedula > <[EMAIL PROTECTED]> wrote: > > De

Re: [ccp4bb] Preventing close contact between protein and ligand

if you could suggest anything else. I'll try anything! Thanks, Sangeetha. > > regards > Garib > > > On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: > > Dear bb users, > > I am refining a protein-ligand complex (at 1.68 A resolution) in which the > lig

[ccp4bb] Preventing close contact between protein and ligand

Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps

[ccp4bb] error running refmac version 5.4.0073

*** #CCP4I TERMINATION STATUS 0 error in dsyev_mo Could someone tell me what this means and how I can fix it? Thanks, Sangeetha Vedula.