[ccp4bb]

I think you have solved it! That is an excellent LLG and if you can't see anything else in the map, then there s prob. not another molecule. Does it refine? If you look at the maps following refinement any missing features should become more obvious. Solvent content of 65% is not uncommon.

[ccp4bb] superposing multiple structural segments between two PDBs

Dear All, Is there a way to superpose multiple, discontinuous stretches of residues between two protein chains ? Dali output shows that there are discontinuous stretches between the PDBs that are being aligned. But I can not find any option to download the superposed PDB. The

[ccp4bb] AW: [ccp4bb] Add an atom in Coot

In this case, editing the pdb file is probably the best approach. However, my favorite approach is Validate Difference Map Peaks. By pressing . (next peak) or , (previous peak), one can quickly go through all problems (red density) or unexplained peaks (green density). The pointer will be

Re: [ccp4bb] Add an atom in Coot

didn't know about the trick to move the pointer (and for some reason it doesn't work on my computer at home but does at work). and yes, editing pdb files by hand has to be done carefully - however, I find that editing the pdb file (before refinement), is sometimes the quickest way for me, and

Re: [ccp4bb] superposing multiple structural segments between two PDBs

Dear Sreetama, For this, Gesamt from ccp4 should do the work. Run gesamt without parameters to get instructions, they are basically the same as for ccp4's superpose. HTH, Eugene On 19 Mar 2014, at 07:34, sreetama das wrote: Dear All, Is there a way to superpose multiple,

[ccp4bb] a couple of doubts: phaser and something else

Dear CCP4 users, I am doing a molecular replacement with Phaser and I am using more than one ensemble for the search. How could I, once that one of them has been placed, fix it as a solution in order to be able to provide an additional fragment for further MR search? I have a second doubt about

Re: [ccp4bb] superposing multiple structural segments between two PDBs

You can have a look at the pair_fit function in PyMOL (see http://www.pymolwiki.org/index.php/Pair_fit) Cheers Jose On 19/03/14 08:34, sreetama das wrote: Dear All, Is there a way to superpose multiple, discontinuous stretches of residues between two protein chains ? Dali

[ccp4bb] BCA/CCP4 Summer School in Protein Crystallography at Diamond

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is

[ccp4bb]

Yes in the first couple of rounds of refinement it refines very well for a 3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs contiguously except for a donut hole in between six dimers that are related by symmetry. Trying to put a molecule there disrupts the symmetry and leads to

[ccp4bb] minimum acceptable sigma level for very small ligand and more

Hello, My protein is 26 kDa and the resolution of the data is 1.90 angs. My ligand is 174 Daltons. and it was soaked into the crystal. Ligand is colored and the crystal after soaking takes up intense color. However if we soak more than optimum, the color deepens in intensity but the crystal

Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more

Before putting in the ligand, there is a clear density for three extra atoms at more than 3 sigma in the Fo-Fc map but for other atoms the density appears around those 3 peaks in the 2Fo-Fc map only and not in the Fo-Fc. Thanks for your reply. Amit On Wed, Mar 19, 2014 at 8:57 PM, Sampson,

[ccp4bb]

Thank you to everyone for their input. I am posting a picture to some of the symmetry related molecules shortly. There are six dimers related by symmetry (60 degrees) with a donut hole in the middle. This was troubling to me as I have solved mostly tighter packing structures (monoclinic or

[ccp4bb]

How pretty - I love circular molecules! Eleanor On 19 March 2014 15:58, Yarrow Madrona amadr...@uci.edu wrote: Thank you to everyone for their input. I am posting a picture to some of the symmetry related molecules shortly. There are six dimers related by symmetry (60 degrees) with a donut

Re: [ccp4bb] minimum acceptable sigma level for very small ligand and more

Hi, First, there is nothing magical about contouring a map at 1 rms. The standard deviation of the electron density values really has no relationship to the rms of those values, and appears to generally be much smaller. This is discussed quite brilliantly in the recent paper

[ccp4bb]

Very reasonable structure, I guess in the direction perpendicular to your picture you will have next donut etc. You can call this - nan-pore ;-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978,

[ccp4bb]

Dear Yarrow your toroidal structure suggests that the protein may actually have the propensity to assemble as such in solution, hinting a connection to a biologically relevant state. Do you have any experimental information that it does so? e.g. via SAXS, MALS, native PAGE etc.? best regards

[ccp4bb]

Hi Yarrow, That solution looks very reasonable to me. If you are worried about the size of your doughnut-hole, look at the packing of the latest structure we solved. :) https://dl.dropboxusercontent.com/u/5116503/4J05.png best -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group