[ccp4bb] How to generate a complete viirus PDB

Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang

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

Hi Hong, you can usually download the 'biological assembly' from the PDBe, be warned that for viruses this is rather large, cheers, Matt. On 25/04/2013 08:19, Guan Hong Hsiang wrote: Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to

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

Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already

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

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

Hi Hong, In your PDB file if the BIOMT transformation matrix (under remark 350) is provided, you can use this script to generate the biological assembly : http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ Greetings, Abhi On Thu, Apr 25, 2013 at 9:31 AM, sujata halder

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

Hi all, There's also a tool available for converting PDB files into the viper format available at http://viperdb.scripps.edu/pdbToViper.php Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology

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

Would PISA not do this? -- Eugene On 25 Apr 2013, at 09:20, abhimanyu singh wrote: Hi Hong, In your PDB file if the BIOMT transformation matrix (under remark 350) is provided, you can use this script to generate the biological assembly : http://watcut.uwaterloo.ca/cgi-bin/makemultimer/

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

Dear Hong, As Eugene mentioned, you should be able to build the full virus assembly using PISA. Another option is to use the multiscale model menu of UCSF Chimera (default setting is Biological Assembly) to generate the complete virus assembly from PDB BIOMT records. If this is a new

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Re: [ccp4bb] salt or not?

Careina, One thing to try if other ideas don't work or are too difficult, is covalently (therefore unambiguously) labelling a little of your protein with a fluorescent dye. If you add 20 nL of this to the drop *after the crystals have grown*, protein crystals will light up, but salt crystals

[ccp4bb] Curious electron density associated with Asp sidechain

Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is

Re: [ccp4bb] Curious electron density associated with Asp sidechain

Call EBI, consider some kind of chemical modification. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel:

[ccp4bb] Factor 10a protease

Dear colleagues, i hope every one doing well. i am trying to remove the 10x his tag , as i tried to crystallize with the tag but i didn^t obtain crystals unless some salt crystals , very small crystals and some precipitant. i want to use factor 10a protease but i didn^t tried it before. this is

Re: [ccp4bb] Curious electron density associated with Asp sidechain

Hello Tony is that Asp-Gly? If so, it could be prone to succinimide formation. Check out this paper:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323960/ and references therein! Good luck Jon.Cooper --- On Thu, 25/4/13, Antony Oliver antony.oli...@sussex.ac.uk wrote: From: Antony Oliver