[ccp4bb] How to manually dock the rigid molecule into the active site
Dear All, I have a protein crystal co-crystallized with a rigid molecule (solved by small-molecule X-ray method). The color of that crystal is orange (native is colorless) after 2d cocrystallization experiment. Then I collected synchrotron data with a resolution at 1.25 Ang. I can solve it by MR. After I re-build slightly the protein and add some known ions/water, i found there are +ve connected blobs in the known active site of that protein. At first I suspect they are water/ion/EDO but many of them are partially connected within C-C/C-O distances (1.4-1.6 Ang) and in some part, i may imagine some broken six-membered ring, that are presumably found in that rigid molecule. How can I dock or confirm that rigid molecule using CCP4 software or COOT smartly? I tried to look at all density regions bit by bit, but the density for the protein atoms always interfere with my vision. Is it possible to mask out the density of protein atoms, leaving the residue density of interest for the rest atoms (maybe the rigid molecule)? many thanks in advance. stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] Distinguish NH4 from Na?
Dear JPK, I think the coordination geometry of Na is a key, normally it adopts octahedral geometry with Na---O distances of 2.1-2.2 ang, whereas water molecule is h-bonded with H-acceptor or H-donor with the distances between 2.6-3.3 ang. I am not sure it is correct, as i used to be small-molecule X-ray worker. stephen Quoting Steiner, Roberto roberto.stei...@kcl.ac.uk: Bond valence sum Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A) R On 16 Nov 2011, at 18:20, Jacob Keller wrote: Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.uk -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] Convert Bruker X8 sfrm to Mosflm format
Dear all, I know somebody had asked such question before, can anyone of you can remind me the way of converting Bruker in-house data (*.sfrm) to the format readable by MOSFLM in CCP4i by using the GUI version of FrmUltility.exe? When I input the sfrm, and choose the tab MSOFLM, i did not change any setting, and it asked for P4P or SPIN, then I choose LINEAR. Also for the tab _IX, I also select LINEAR. Finally I pressed Unwarp, Flip Convert button to convert it, the following message come: FATAL dimensions of correction frame(s)different than data frame Spatial table is 0x0, while data frame is 1024x1024 Please kindly advise, many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] REMARK REMARK 3 OVERALL ANISOTROPIC B VALUE.
Dear all, can anyone tell me how to obtain the B11, B22, B33 values? After i performed the anisotropic refinement of the dataset at 1.6 A using REFMAC5, i can't read these values from the output PDB. thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] Monomers in COOT
Dear All, For all monomers (3 letter) used in COOT, where can i find the full names of the whole library? Many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] Monomer_lib_cif from PDB (Sketcher)
Dear CCP4 users, I just wonder if this problem can be solved using Sketcher. When i use Sketcher (PC or linux) in the CCP4 GUI to generate the monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of this ligand change (see V3Oand the attached files are used. Any comment is highly appreciated. stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) V3OAc.pdb Description: Protein Databank data V3O_bondlist.cif Description: CIF chemical test V3O_libcheck.pdb Description: Protein Databank data V3O_mon_lib.cif Description: CIF chemical test
[ccp4bb] A quick question - monomer lib cif
Dear all experts, Just a simple question, how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? If i have a CCDC cif file. many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] About using COOT
Dear all, My protein has two chains A B. The space gp is P212121. If I want to have a new PDB file containing the symmetry-equivalent molecule of B (x+1/2, -y+1/2, z+(0 -1 0)), and keep the chain A (x,y,z) unchanged. How can I do this COOT? many thanks for this help. stephen -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] Unexplained density
Dear Daniel Is the omit map for the model with and without the zinc ions possible to confirm its existence? I am curious. What is the resolution of dataset? stephen Quoting Daniel Bonsor bon...@bbri.org: Hello again I currently have some unexplained density in my structure. As you can hopefully see from the images (see file), the density is dumbbell shaped. Whatever it is, it is coordinated by Asp and Glu residues. To me it looks like each lobe is a ring structure. The crystallization condition was: 6.5% PEG 8K, 10mM ZnSO4, 100mM sodium cacodylate pH 6.5, 100mM Am2SO4, 1% glycerol, with 20% glycerol as cryo. Protein was originally in 50mM Tris, 50mM NaCl pH 7.5. I originally placed a single Zn at the center of each lobe. Though after refmac, the Zn was displaced to one side. Two zincs in each dumbbell may have worked, but I am dubious about two zinc atoms being 4A apart and there is still some unexplained density. Are there any possible cyclization reactions of Tris, cacodylate or glycerol may have undergone to explain the density? Or is it simply a highly ordered water network? Or is there some other explanation? Thanks in advance Dan -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] HKL-MTZ conversion
Dear All, can anyone of you using Bruker PROTEUM X8? How can I convert HKL to MTZ in CCP4i? I want to do data analysis (TRUNCATE) for the dataset. Many thanks! stephen -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
[ccp4bb] Purchase of Protein Samples
Dear all CCP4 experts, Hello, I'm not molecular biologist and quite new in this field. I would like to know what companies (i.e. Sigma/Aldrich) are possibe for me to purchase purified protein samples. Any suggestion is welcomed. Many thanks in advance. stephen -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
