Re: [ccp4bb] Calcium ions in enzymes

Hi Liu, A complex example is oxygen envolving complex of photosystem II.. Biochemistry 2003, 42, 6209-6217 http://www.rsc.org/chemistryworld/News/2011/August/05081101.asp -Vandu... On 5/31/13, Patrick Loll wrote: > staph nuclease > > On 31 May 2013, at 6:25 AM, Wei Liu wrote: > >> Dear all, >

Re: [ccp4bb] pdb sequence search

Hi Ed, What about submitting the uniprot accession number of your protein to the PDB?. As you know, this will just list the all entries where your protein sequence is there.. -Vandu murugan.. On 6/23/12, Ed Pozharski wrote: > Silly question. > > Say I want to find every str

[ccp4bb] Defining an ellipse around a protein structure

Dear all, Is there a program or server that would define a ellipsoid around a given protein molecule? I would also like to calculate the axis components of the defined ellipse. Thanks in advance.. cheers, wandu

[ccp4bb] Crystal structure and NMR structure

Dear all, I would like to get some information on proteins where there is conformation/structural change between the crystal structure and solution structure of the same protein. Do anybody came across such situations? Thanks in advance.. cheers, Vandu

[ccp4bb] MR with MD trajectories

Dear all, I have a protein molecule with two flexible domains. For a 2.8 angstrom data, I could get MR solution for the larger domain but not for the smaller domain (around 80 aminoacids). The second domain appears as extra density showing its presence , but does not allow manual model build

[ccp4bb] Psedo-translation detected

Dear all, Recently I collected a data for my 20Kda protein in C2 space group, and ran SFcheck in ccp4 suite. It is giving an indication for pseudo-translation as 'Pseudo-translation is detected: 17.6% Pseudo-translation vector: 0.000 0.000 0.078. Is it a significant amount? Any commen

[ccp4bb] MR with polysaccharide

Dear all, I am seeing some bulk extra denisty near my protein molecule, in a 2.7 angstrom map. The crystallization condition condition has a sulfated polysaccharide. If I want to perform a MR with this polysaccharide, in presence of the refined protein model in the cell, which program shoul

[ccp4bb] FT of fo-fc.coeff

Dear all, With a fo-fc.coeff file, which came out after running model_map.inp using cns 1.1, i like to do a fourier tranform and calculate the structure factor. I need to run a MR with the resulting file. could some one tell me how to do this FT with the available fo-fc coeff file. Thanks in

[ccp4bb] MR from fo-fc

Dear all, I have calculated a fofc map using model_map.inp of cns1.1 and I have a fofc.coeff file. It has following coloums as INDE 600 MAP_FOM= 1.000 MAP_PHASE= 180.000 MAP_SCALE= .225 MAP_COEFF= 606.623 180.000 Presently (r and rfree are 35

[ccp4bb] Wilson B and Mean B factors

Dear all, If one could find a difference of more than 15 between Wilson B factor of the data ( 55) and Mean B factor of the structure, (30) what could be the possible reasons? I am seeing it in my structure. Could someone tell me why it could be?? Thanks in advance. Yours faithfully, Murug

[ccp4bb] measure of anamolous signal

Dear all, I have collected a 2.7 angstrom home source data with Cu-Kalpha source for a protein with 6 cysteines, with a multiplicity of around 23. I need to know, is there any significant anamolous signal present in the data set, since there is no good model for my protein. Can any one tell, w

[ccp4bb] Contact betwen multiple chains

Dear all, I like to calculate contact between one target chain, and 6 other different chains in a complex model at a time. Could you tell me how to do this? also, what is the different between contact and Ncontact programs in ccp4? Thanks in advance. cheers, V. Murugan