[ccp4bb] RE-anomalous difference fourier maps

Thank you guys, All of your suggestions were great. It worked. I can see the electron density of zinc, but now the problem is that it is not where I was expecting but at a very near but not superimposable position with the calcium. So I am wondering what would be the best way to rectify my structu

Re: [ccp4bb] phi/psi angle display in coot

On Thursday 18 February 2010 14:48:57 Paul Emsley wrote: > Ursula Schulze-Gahmen wrote: > > I am a new user of Coot and I haven't found an easy way of displaying the > > phi/psi angle of a specific residue while I am rebuilding. I found of course > > the Ramachandran plot, but i would like a way to

Re: [ccp4bb] anomalous difference fourier maps

Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 out

[ccp4bb] anomalous difference fourier maps

Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular repla

Re: [ccp4bb] Expression of a protein of 43KDa

The maltose binding protein is one possibility. Some collaborators did provide us with very pure MBP instead of the protein of interest... Mass spec eventually identified it after we wasted some time on it... Fred > I am trying to overexpress a His-tagged protein of 29KDa in E.coli > (BL21-codon

Re: [ccp4bb] phi/psi angle display in coot

Ursula Schulze-Gahmen wrote: I am a new user of Coot and I haven't found an easy way of displaying the phi/psi angle of a specific residue while I am rebuilding. I found of course the Ramachandran plot, but i would like a way to display the main chain geometry of a specific residue. You can'

[ccp4bb] coot distributed by ccp4-6.1.3 and python scripting

Hi, I noticed that the coot distributed by ccp4-6.1.3 does not have python built into it. Is there anyway to add in the python support post installation ? I am running the ccp4 supplied coot on OSX Leopard 10.5.8 I am cc-ing the coot mailing list as well . Thanks Hari

[ccp4bb] error in dtrek2mtz

Hi, I got the following error: DTREK2MTZ: Normal termination Times: User: 0.3s System:0.1s Elapsed: 0:00 #CCP4I TERMINATION STATUS 0 Error from script /sw/share/xtal/ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read "dataset_name": no such variable #CCP4I TERMINAT

[ccp4bb] phi/psi angle display in coot

I am a new user of Coot and I haven't found an easy way of displaying the phi/psi angle of a specific residue while I am rebuilding. I found of course the Ramachandran plot, but i would like a way to display the main chain geometry of a specific residue. Ursula

Re: [ccp4bb] Expression of a protein of 43KDa

I see the issue now, sorry... I agree with Jurgen. Did you get it DNA sequenced before overexpression? Size of tag? Jon On 02/18/2010 03:06 PM, Jürgen Bosch wrote: Well that it's not his protein which he has crystallized but an over expressing contaminant :-) Or the alternative would be alt

Re: [ccp4bb] Expression of a protein of 43KDa

Well that it's not his protein which he has crystallized but an over expressing contaminant :-) Or the alternative would be although it's supposed to be 29kDa it runs funny and appears larger in the SDS gel, in that case it would be OK. If we only had some confirmation that the 43kDa band is

Re: [ccp4bb] Expression of a protein of 43KDa

You should mass spec your samples to determine what has crystallized, possible e coli contaminant. M. Gordon Joyce, Visiting Fellow, Structural Immunology Section, Laboratory of Immunogenetics, NIH/NIAID, 12441 Parklawn Drive, Rockville, MD 20851 Phone: 301 594 0242 Office 301 496

Re: [ccp4bb] Expression of a protein of 43KDa

Maybe I am not getting it, but I don't see your problem or question? What I understand from your message is that you have a protein that overexpresses, purifies, and crystallizes... where's the problem? We all wish we had that problem... Jon On 02/18/2010 11:49 AM, Armando Albert de la Cr

[ccp4bb] RNA 3D Modeling & Simulation Meeting at the 2010 Biophysical Society Annual Meeting

Simbios invites you to attend its ancillary meeting on RNA 3D Modeling & Simulation, to be held as part of the 2010 Biophysical Society Annual Meeting. We have lined up 6 diverse presentations on RNA computational tools, which will be followed by an informal discussion on the technical challenges

Re: [ccp4bb] Expression of a protein of 43KDa

EF-Tu Poul On 18/02/2010, at 18.49, Armando Albert de la Cruz wrote: I am trying to overexpress a His-tagged protein of 29KDa in E.coli (BL21-codon plus) and I end up with a highly expressed product that of 43KDa that binds to the Ni-column. I also have nice crystals. Does anyone have any

[ccp4bb] Neutron Protein Crystallography Call for Proposals

PROTEIN CRYSTALLOGRAPHY STATION AT LANSCE -- CALL FOR PROPOSALS for Run Cycle Beginning the June 2010 You are invited to apply for beam time on the neutron Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center. The

[ccp4bb] Expression of a protein of 43KDa

I am trying to overexpress a His-tagged protein of 29KDa in E.coli (BL21-codon plus) and I end up with a highly expressed product that of 43KDa that binds to the Ni-column. I also have nice crystals. Does anyone have any experience on this. Armando

[ccp4bb] Neutron Protein Crystallography Call for Proposals

PROTEIN CRYSTALLOGRAPHY STATION AT LANSCE -- CALL FOR PROPOSALS for Run Cycle Beginning the June 2010 You are invited to apply for beam time on the neutron Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center. The

Re: [ccp4bb] Protein crystallizes while concentration

A cheaper solution than buying the dialysis buttons would be just to make your own out of the top of a microtube. Depending on what volume you want to dialyse you can use either a PCR tube (~35 uL per lid) or larger 1.5 mL tube (~250 uL). Just cut the top off the tube using a hot scalpel, you th

Re: [ccp4bb] xds and cell refinement in cP

Hi Jan, there is now a new version of XDS at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ The old versions of XDS had a very low radius of convergence for the cell refinement in high-symmetry spacegroups. This is fixed in the latest version, and it has other enhancements, too. best, Kay Ja

Re: [ccp4bb] Protein crystallizes while concentration

Dear Rajkumar, I would use dialysis buttons. E.g. http://hamptonresearch.com/product_detail.aspx?cid=10&sid=63&pid=111 Put your protein to the button and seal it with a piece of dialysis membrane. Place this to a linbro plate (easy to look with a microscope), fill the well with low salt buff

Re: [ccp4bb] Distinguishing Between Na+ and H2O

It is my feeling that the surface binding sites for ions are not so rigid as to be unable to accommodate the larger ionic radii of heavy metal compounds. In part this is why halide soaks, particularly iodide salts, are so successful as heavy atom derivatives (Dauter, et al., 2000, Nagem et al.,

[ccp4bb] Protein crystallizes while concentration

Dear All I am Rajkumar, working on the protein which has unusual behavior while concentration. When I kept protein in 15 mM Tris 7.5, 150 mM NaCl and 5 mM DTT, the solubility of the protein is decreases drastically and tend to crystallize while concentration. Protein cannot be concentrated mor

Re: [ccp4bb] Distinguishing Between Na+ and H2O

The deposition 3fiy from the start of last year might be of interest: FORMUL 2 NA199(NA 1+) FORMUL 20 HOH *256(H2 O) It is annoying that the periodic table offers such a discrete range of sizes for 1+ ions; I hoped the lanthanide c

Re: [ccp4bb] Distinguishing Between Na+ and H2O

This may be true for many structures but in general I am not a friend of massive changes made to already deposited structures - it more likely produces more errors than better structures. 2.4 Angstrom hydorgen bonds for water are probably not entirely impossible and on the other hand some close dis

Re: [ccp4bb] hkl into mtz using f2mtz

This may also be a job for 'convert2mtz', which I think will pick up the complex columns automatically. Only available from the command line though. Kevin Eleanor Dodson wrote: I am no expert on CNS files, but do the entries for F_BULK and F_MODEL correspond to an amplitude and a phase - it ce

Re: [ccp4bb] hkl into mtz using f2mtz

I am no expert on CNS files, but do the entries for F_BULK and F_MODEL correspond to an amplitude and a phase - it certainly looks like that.. If so you can read both in: I havent checked the format but your script would look like this title [No title given] format '(6X,3F5.0,6X,F10.0,6X,F10.

[ccp4bb] silverstaining of 15% Tris-Tricine Gels

Hi everyone, I'm encountering problems with silverstaining of 15% Tris-Tricine Gels. I'm using a standard protocol: 1. Fixation 50% MeOH 12% Acetic acid (1 hour - overnight) 2. Washing in 50% EtOH (3x 10 min) 3. 1min 0,2% Sodiumthiosulfate 4. 3x 20min H20 5. Impregnation 2g/L AgNO3 (+150µL Form

[ccp4bb] Silverstaining of Tris-Tricine (15%) Gels

Hi everyone, I'm encountering problems with silverstaining of 15% Tris-Tricine Gels. I'm using a standard protocol: 1. Fixation 50% MeOH, 12% Acetic acid (60min - overnight) 2. Washing 50% EtOH (3x 10min) 3. 0,2% Sodium thiosulfate (1 min) 4. Washing H20 (3x 20 min) 5. Impragnation AgNO3 (2g/L)