Re: [ccp4bb] Freezing crystal
Hi Theresa, Once I had crystals in 3.5 M Amm. Sulfate. I used Paraffin oil and Paraton-N-oil (in 1:1 ratio). I also used 30% Xylatol. Best, Vineet On Sun, Feb 5, 2012 at 5:49 PM, Theresa H. Hsu theresah...@live.com wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
[ccp4bb] JLigand: Handedness related issue
Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using JLigand. The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue? I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur
[ccp4bb] JLigand: Handedness related issue
Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using JLigand. The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue? I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur
Re: [ccp4bb] Beginning crystallography text
Hi, I found Crystal, X-rays and Proteins by Dennis Sherwood very helpful in understanding the basic concepts of crystallography. However, it seems that the book is out of print. It would be great, If anyone here is having an E-copy of this book and can share with us. Thanks, Vineet
Re: [ccp4bb] molecular replacement
Also check if you have correctly estimated no. of molecules in asymmetric unit. On Fri, May 21, 2010 at 4:58 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear intekhab, a few suggestions: - are you sure of the space group or might there be alternatives? - is you protein globular or modular, i.e., is it worth running MR with stable subdomains one after the other? - try a poly-alanine model (e.g. chainsaw can do this for you, pdbset probably, too) - did you get overloads? If so, collect a low resolution pass to get correct intensities even at the poor resolution end. - what is your low resolution limit? Did you use the default or could you extend it? - did your crystal(s) suffer from radiation damage? It might be worth collection only a complete data set with not too high multiplicity. Good luck, Tim On Fri, May 21, 2010 at 08:01:10PM +0900, intekhab alam wrote: Hi all I am trying to do molecular replacement with low resolution (4Å) using Molrep and Phaser. Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95. Identities between my protein and templates were more than 80%. I couldn’t get correct solution. Rotation function, translation score, and contrast were low, and they had no significance, though I changed the range of resolution. Molrep suggested solution coordinates clashed with symmetry molecules. I tried MR after remove clashed regions, but another clashes happened. In the case of phaser, there were many clashes, too. Please, give me any suggestion. Should I concern about any options when I run MR programs? Hope you guys will be interested to answer!! Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFL9m5wUxlJ7aRr7hoRAnJRAJkBglzDPgqcJ07lOf8wLpGTornFyACeMxwB XCPdN9n9Km6Gdn2SK+jv8WY= =ncth -END PGP SIGNATURE-
[ccp4bb] composite omit map calculation
Hi All, Sorry for a non CCP4 querry. I am using CNS for composite omit map calculations. the structure is having a ligand for which parameter and topology files have been generated using PRODRG server. however while running composite_omit_map.inp i m getting the following torsion topology error (where chain D is the ligand): ERROR: There are no suitable base groups. This problem can be caused by isolated bonding networks with undefined or weak dihedral force constants. The atoms that cannot be placed in a tree are listed below: %atoms D -242 -AMG -O4 %atoms D -242 -AMG -C4 %atoms D -242 -AMG -C3 %atoms D -242 -AMG -O3 %atoms D -242 -AMG -C2 %atoms D -242 -AMG -O2 %atoms D -242 -AMG -C1 %atoms D -242 -AMG -O1 %atoms D -242 -AMG -C7 %atoms D -242 -AMG -O5 %atoms D -242 -AMG -C5 %atoms D -242 -AMG -C6 %atoms D -242 -AMG -O6 %TORSION:TOPOLOGY error encountered: Fatal Topology Error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. topology and parameter files have been attached to this posting. Kindly suggest if there is any problem with topology or parameter file or i am missing on something else. with best regards Vineet Gaur mam.param Description: Binary data mam.top Description: Binary data
[ccp4bb] .cif file
Hi all I am using COOT for model building and refinement. i have to introducea ligand in my model i have downloaded .cif file from RCSB. However while importing the cif file i m getting the warning message of having No restraints in the CIF file is there any problem in the format of the following cif file data_SPM # _chem_comp.idSPM _chem_comp.name SPERMINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAI _chem_comp.formula C10 H26 N4 _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date2007-08-16 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight202.340 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SPM _chem_comp.pdbx_model_coordinates_details? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code1DPL _chem_comp.pdbx_processing_site ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_ordinal SPM N1 N1 N 0 1 N N N -1.386 5.560 25.140 -0.292 0.012 7.961 1 SPM C2 C2 C 0 1 N N N -2.248 4.344 25.282 0.514 -0.023 6.734 2 SPM C3 C3 C 0 1 N N N -1.844 3.214 24.376 -0.408 0.014 5.515 3 SPM C4 C4 C 0 1 N N N -2.834 2.063 24.495 0.432 -0.022 4.237 4 SPM N5 N5 N 0 1 N N N -2.313 0.871 23.720 -0.453 0.013 3.066 5 SPM C6 C6 C 0 1 N N N -3.235 -0.310 23.760 0.411 -0.024 1.880 6 SPM C7 C7 C 0 1 N N N -2.669 -1.391 22.871 -0.451 0.011 0.617 7 SPM C8 C8 C 0 1 N N N -3.306 -2.753 23.219 0.450 -0.028 -0.617 8 SPM C9 C9 C 0 1 N N N -2.886 -3.777 22.188 -0.412 0.006 -1.880 9 SPM N10 N10 N 0 1 N N N -3.212 -5.172 22.585 0.453 -0.031 -3.066 10 SPM C11 C11 C 0 1 N N N -2.084 -5.778 23.391 -0.433 0.005 -4.237 11 SPM C12 C12 C 0 1 N N N -2.443 -7.162 23.912 0.407 -0.032 -5.515 12 SPM C13 C13 C 0 1 N N N -1.448 -8.158 23.367 -0.515 0.005 -6.734 13 SPM N14 N14 N 0 1 N N N -0.553 -8.726 24.427 0.292 -0.029 -7.961 14 SPM HN11 1HN1 H 0 0 N N N -1.660 6.326 25.754 -0.739 0.916 7.988 15 SPM HN12 2HN1 H 0 0 N N N -1.355 5.869 24.168 0.354 -0.014 8.735 16 SPM H21 1H2 H 0 1 N N N -2.281 4.005 26.343 1.181 0.838 6.713 17 SPM H22 2H2 H 0 1 N N N -3.322 4.602 25.135 1.105 -0.939 6.715 18 SPM H31 1H3 H 0 1 N N N -1.722 3.550 23.320 -1.074 -0.847 5.536 19 SPM H32 2H3 H 0 1 N N N -0.796 2.883 24.565 -0.999 0.930 5.534 20 SPM H41 1H4 H 0 1 N N N -3.061 1.809 25.556 1.098 0.839 4.215 21 SPM H42 2H4 H 0 1 N N N -3.862 2.355 24.178 1.023 -0.938 4.217 22 SPM HN5 HN5 H 0 1 N N N -1.378 0.612 24.037 -0.976 -0.849 3.071 23 SPM H61 1H6 H 0 1 N N N -3.427 -0.667 24.798 1.078 0.838 1.889 24 SPM H62 2H6 H 0 1 N N N -4.284 -0.042 23.493 1.002 -0.940 1.891 25 SPM H71 1H7 H 0 1 N N N -2.780 -1.142 21.789 -1.117 -0.851 0.608 26 SPM H72 2H7 H 0 1 N N N -1.555 -1.427 22.916 -1.042 0.927 0.607 27 SPM H81 1H8 H 0 1 N N N -3.068 -3.077 24.258 1.117 0.833 -0.608 28 SPM H82 2H8 H 0 1 N N N -4.414 -2.687 23.323 1.041 -0.944 -0.607 29 SPM H91 1H9 H 0 1 N N N -3.319 -3.536 21.189 -1.079 -0.855 -1.889 30 SPM H92 2H9 H 0 1 N N N -1.802 -3.675 21.945 -1.003 0.922 -1.891 31 SPM HN0 HN0 H 0 1 N N N -3.451 -5.748 21.778 0.976 0.831 -3.071 32 SPM H111 1H11 H 0 0 N N N -1.133 -5.797 22.808 -1.099 -0.857 -4.215 33 SPM H112 2H11 H 0 0 N N N -1.767 -5.101 24.219 -1.023 0.921 -4.217 34 SPM H121 1H12 H 0 0 N N N -2.512 -7.194 25.024 1.074 0.830 -5.536 35 SPM H122 2H12 H 0 0 N N N -3.497 -7.443 23.683 0.998 -0.948 -5.534 36 SPM H131 1H13 H 0 0 N N N -1.964 -8.969 22.803 -1.181 -0.856 -6.713 37 SPM H132 2H13 H 0 0 N N N -0.851 -7.712 22.537 -1.105 0.921 -6.714 38 SPM HN41 1HN4 H 0 0 N N N 0.119 -9.398 24.058 -0.354 -0.003 -8.735 39 SPM HN42 2HN4 H 0 0 N N N -1.099 -9.133 25.186 0.814 0.833 -7.990 40 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2
[ccp4bb] coot: Show Symmetry
Hi All i want to display symmetry molecules in COOT, but regularly getting the following warning: There are no model molecules that can display symmetry (Cryst1 problem). How to troubleshoot this Cryst1 problem thanks in advance Vineet gaur
[ccp4bb] assigning water molecules to monomers
Hi All i am solving a structure with four molecules in asymmetric unit. Initially i was refining the structure with four fold NCS, which now i have removed. i have picked some of the water molecules after removing the NCS. now i m facing the problem of assigning these water molecules to individual protein monomers. is there any program available by which i can identify the water molecules w.r.t protein monomers. thanks in advance Vineet Gaur
[ccp4bb] alternate confirmations of residues
Hi all Sorry for a non CCP4 question. I m using CNS for structure refinement. The structure is having few residues in alternate confirmations. i can see the density for those alternate confirmations. i m defining those alternate confirmations in the pdb but while generating the topology file, the information of alternate confirmations is getting lost. how can i define the alternate confirmations in generate.inp n minimize.inp. the way i m defining the alternate confirmations in pdb : ATOM 6101 1N LYS D 9383.029 39.489 93.510 0.50 42.90DN ATOM 6101 2N LYS D 9383.028 39.495 93.498 0.50 42.90DN ATOM 6102 1CA LYS D 9382.366 40.672 93.101 0.50 41.09DC ATOM 6102 2CA LYS D 9382.391 40.686 93.075 0.50 41.09DC ATOM 6103 1CB LYS D 9383.019 41.834 93.797 0.50 41.27DC ATOM 6103 2CB LYS D 9383.119 41.836 93.691 0.50 41.27DC ATOM 6104 1CG LYS D 9382.331 42.627 94.824 0.50 43.61DC ATOM 6104 2CG LYS D 9382.419 42.747 94.517 0.50 43.61DC ATOM 6105 1CD LYS D 9381.797 42.040 96.162 0.50 43.24DC ATOM 6105 2CD LYS D 9382.004 42.209 95.769 0.50 43.24DC ATOM 6106 1CE LYS D 9382.265 40.647 96.659 0.50 43.68DC ATOM 6106 2CE LYS D 9380.982 43.099 96.495 0.50 43.68DC ATOM 6107 1NZ LYS D 9382.884 40.390 97.999 0.50 43.36DN ATOM 6107 2NZ LYS D 9380.832 44.665 96.562 0.50 43.36DN ATOM 6108 1C LYS D 9382.478 40.825 91.578 0.50 39.28DC ATOM 6108 2C LYS D 9382.477 40.826 91.567 0.50 39.28DC ATOM 6109 1O LYS D 9382.412 41.847 91.106 0.50 38.72DO ATOM 6109 2O LYS D 9382.408 41.844 91.093 0.50 38.72DO Thanks in advance vineet gaur
[ccp4bb] calculating molecular dimensions
Hi All is there any programme available that can calculate the parameters like length of longest and shortest axis passing through the center of mass of a protein mlecule thanx in advance vineet gaur
[ccp4bb] REFMAC and Hetroatoms
Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refinement with REFMAC i m getting following warnings: I am reading library. Please wait. mon_lib.cif WARNING : residue: CA994 chain:XX different element name: file:C dict:CA WARNING : residue: CL995 chain:Xa different element name: file:C dict:CA how can i rectify this problem thanx in advance vineet gaur
[ccp4bb] Rfree and unaccounted density
Hi all i m solving a structure at 2.2 A using MIR. rt now my Rfree is 30.55% and Rcryst is 28.51%. i have already carried out B factor refinement n water has also been picked up to 2.3 sigma cut off. now i m not able to refine the structure any further. The protein has been purified directly from the source. At this pt of refinement i m able to see lot of unaccounted densities, far bigger to b accounted by water or sugar, as we don't have any information abt the possible molecules that can interact with this protein. . is this unaccounted density be the reason why i m not able to refine the strucure? thanx in advance Vineet Gaur
[ccp4bb] intel Xeon vs AMD Opteron for crystallographic applications
Hi all we r planning to upgrade hardware in the lab. just curious to know weather anybody has tested a dual core xeon vs dual core opteron for standard crystallographic applications. Also wanted to know weather programs compiled on a xeon will have problems executing on an opteron. regards vineet
[ccp4bb] TFT monitors n stereo
Hi all i have a non CCP4 query. pls tell me how to view stereo images on a TFT monitor. thanx vineet gaur
