Re: [ccp4bb] How to generate a complete viirus PDB

Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one : http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this r

[ccp4bb] phasing with EM map using Amore

structure factors ? Or am I proceeding in the wrong direction? I tried to use Phaser and Molrep but it did not give a solution. Any help would be highly appreciated. Thank you. -Sujata Halder

Re: [ccp4bb] strict structure based alignment

Hi, SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver) will do a structure based alignment and outputs a table of rmsd but will not give you a alignment file as such. -Sujata On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth < christian.r...@bbz.uni-leipzig.de> wrote: > Dear

Re: [ccp4bb] color for metal ions

> Sent: Sun, May 20, 2012 2:54 pm > Subject: Re: [ccp4bb] color for metal ions > > As long as you are considerate of the needs of colorblind people, I > would vote that anything goes. > Artem > On May 20, 2012 3:17 PM, "sujata halder" wrote: > >> Hi all, &g

[ccp4bb] color for metal ions

Hi all, I was wondering if there is a rule for coloring metal ions a specific color. I am using pymol and was not sure if I have to use a specific color for calcium or magnesium ions for publication figures. Thanks, Sujata

Re: [ccp4bb] Sodium ion vs. Water

Hi, I decided to give the server a try...and the output is: FILE NOT FOUND: /prod/tmp/individual_validation/output_wasp/25854/bindividual6Na.ion Either my pdb does not have any metal ions or this server is currently not working. Sujata On Tue, Aug 2, 2011 at 5:04 PM, Sean Seaver wrote: > > Hi

Re: [ccp4bb] Library description for Pentacoordinated phosphate.

Hi, phenix.elbow might work... from the phenix website: To run eLBOW on a PDB file (containing one molecule) phenix.elbow input_file.pdb To run eLBOW on a PDB file containing protein and ligands. This will only process the ligands that are unknown to phenix.refine. phenix.elbow input_file.pdb -

Re: [ccp4bb] how convert SF to intensities

Hi, Use SFALL to convert coordinates to structure factors...and then use mtz2various to convert to intensities...use the scalepack format under mtz2various. On Thu, May 12, 2011 at 3:13 PM, Fulvio Saccoccia < fulvio.saccoc...@uniroma1.it> wrote: > Dear ccp4 users, > I need to generate intensitie