Re: [ccp4bb] Protein-Protein Interactions

evidence to cross check results obtained from other method. Hope it helps Manish Manish Chandra Pathak, Ph.D. Indian Institute of Science Education and Research ITI (Gas Rahat) Building Govindpura, Bhopal 462023 India tel: +91-750-4092340 -- On Thu, Aug 2, 2012 1:28

Re: [ccp4bb] modeling thioester bond

  C4A PLP A 400 >> >> >>OR >> >>You need a dictionary file to tell the COOT that the two residues are >> >>connected. If an instance already exist in PDB, then you can download >> >>the refmac dictionary from  http://xray.bmc.uu.

Re: [ccp4bb] sequence format conversion

Guess, you are looking for ReadSeq; with GenBank|gb set as output format. http://www.ebi.ac.uk/cgi-bin/readseq.cgi However, no idea how to get only 10 residues in a line, if you are specific. best Manish > > From: K Singh >To: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] Self-rotation Patterson maps

Hello John, In my struggle with self-rotation function, I found this extremely useful to start with. Specially the fig 4 on page 107. "Characterizing a Crystal From an Initial Native Dataset" by Michael R. Sawaya http://www.springerlink.com/content/k024q83484477j42/ The peaks in the log fil

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Hi Bashir, In Pymol: 1. Show---Surface (will generate surface around the protein) 2. Setting-Surface---Cavities & Pockets Only. (will show only Cavities inside) 3. Use cavity_cull command to set the filter for cavities. (eg. set cavity_cull, 40) Manish -- Manish Chandra Pa

Re: [ccp4bb] sequence from pdb

Hi Rex, I like this simple and quick server to extract pdb seq. http://swift.cmbi.ru.nl/servers/html/soupir.html Manish -- Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 USA Tel: +1-404-727-2563

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

Hi Peter, I think, instead of tightening the weighing term, giving it slight freedom would have helped. If data quality is good at 1.8 ang, then it certainly deserves more freedom. What do you think. best wishes Manish Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory

Re: [ccp4bb] Regarding BMCD

It is due to your local computer's or LAN's firewall denying access to the port 8060. Is it correct? all the best Manish From: Nishant Varshney To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, June 12, 2009 3:08:14 AM Subject: [ccp4bb] Regarding BMCD Dear all, I

Re: [ccp4bb] PDB protein strucutrues as screen saver

For mac, a screen saver (structure) is already available. moreover it's free and displays couple of structural information exactly the way Jayashankar wants. http://www.sourcecod.com/structure/ I hope their is something like this for Linux/Windows also. F

Re: [ccp4bb] Setting drops with proteins that are hard to concentrate

Dear Matt, In one of our project, the protein of interest used to elute from Ni-column with ~20 other proteins. I also guessed it due to surface Cysteines. Addition of 2mM free Cys in the protein sample helped, which competed with free Cys on the protein surface and, ultimately, gave happy

Re: [ccp4bb] refinement problem of labelled RNA complex

Hi, It's much easier to begin with the cif file created by Refmac5 itself, but this cif file needs to be checked and corrected manually for the restrains. Certainly, Iodine is not happy with the current restrains. Most of the time, i have found problems beginning with the protonation and th

Re: [ccp4bb] .cif file

Hello Vineet, This seems old one and doesn't have all restraints. you may use refmac dictionary for spermine. I am sure this will work in coot also. you may find it at /ccp4-6.0.2/lib/data/monomers/s/SPM.cif thanks Manish Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all I am using COOT for