[ccp4bb] deposition related question

dear all, i am trying to deposit a protein structure to PDB, for which data was scaled and merged using AUTOMAR program. But i could not find the log file to be deposited alongwith generated by AUTOMAR. it generates all the files separately (like AUTOMAR. index, .join, .marScale etc) but not one

Re: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

Edward A. Berry wrote: I'm helping set up crystallography programs on a ubuntu system, and we're stuck because one program (scalepack) needs the library libg2c.so.0 . Maybe compat-libf2c I understand this is absent from modern distributions because gcc discontinued support for g77 and f2c in

[ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

I'm helping set up crystallography programs on a ubuntu system, and we're stuck because one program (scalepack) needs the library libg2c.so.0 . I understand this is absent from modern distributions because gcc discontinued support for g77 and f2c in recent releases. However on fedora there are co

Re: [ccp4bb] help with pymol error message

I know people sometimes have good reasons, but people should be very careful about "carving" a map so close to the atoms - one could end up seriously misrepresenting the quality of the map. = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The Unive

Re: [ccp4bb] help with pymol error message

Hi Rakesh, My guess is that PyMOL is getting confused by your map's name when loaded into PyMOL as an object. When you call isomesh/isosurface the 2nd parameter is the name of the map object loaded into PyMOL, not the filename you loaded from. I made some slight modifications to that set of comm

[ccp4bb] help with pymol error message

Hi all, I am trying to get a model-density figure made where selected residues are shown with their densities whereas the nearby unmodeled densities are removed. I tried the "isomesh mesh" command as suggested by the tutorial: 1. Loading PDB file File -> Open -> 1w2i.pdb 2. Load the map file

Re: [ccp4bb] Cys auxotroph

I would also try non-auxotrophic strains. We have recently had successful double SeCys + SeMet using BL21. Paper has just been accepted in Acta D, should be published soon. Paula On 18 October 2010 16:05, Yogesh Gupta wrote: > Does anyone know a commercial source of Cys-auxotroph strain of E.

Re: [ccp4bb] JAC (2010), 43,1242-1249

Thank you all for not sharing the pdf. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fa

Re: [ccp4bb] JAC (2010), 43,1242-1249

It is available online at http://www.stat.ucla.edu/history/essay.pdf Michel Fodje Staff Scientist Canadian Macromolecular Crystallography Facility Canadian Light Source Tel: 306 657 3758 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]

Re: [ccp4bb] Reg. PATCH-ERR in CNS

Dear Thangavelu, I have looked in my old files and I think you did not specify things correctly. The way I did it was: 1) in the PRESidue definition: delete the lines with "1=Cys" and "GROUP". Read this file in in the block where you read in the topology files. 2) add the following patch statem

[ccp4bb] Reg. PATCH-ERR in CNS

Dear CCP4BB We are having some problem in maintaining the covalent bond between the Cys "Sulphur" and the inhibitor molecule during the CNS refinement. We have used the below given patch statement in the inhibitor topology file and included the appropriate bond length angles and dihedral angl

Re: [ccp4bb] Refinement

I second that. Incorrect space group assignment usually causes this behaviour of having R and R-free stuck at very high values. It is useful to go back to the data processing stage and carefully consider all Bravais lattices (and associated space groups) that the autoindexing routine finds cons