A Postdoctoral Research position is currently available at the University of
North Carolina under the direction of Dr. Edward Collins. A person with a
Ph.D. and experience in protein crystallography is preferred, but others with
similar credentials will be considered. The project is a collab
Dear Remie,
the first A is the segment identifier and the second A is the chain
identifier. You might have missed it but there was an email today from
Thomas Holder solving exactly this problem. See below:
On 07.08.2014 19:40, Thomas Holder wrote:
Hi Remie,
PyMOL by default sorts atoms base
Dear Remie,
May be you have saved the coordinates as A.pdb? In that case the first /A/ will
be the file name followed by the second /A/ for the protein chain. Else,
somewhere in the pdb you may have an empty atom record, which is very unlikely.
Best regards,
Avinash
Thanks for all the valuable comments.
In fact, chain “A” shows up first in my pdb, then comes “B” then “C”.
Also the atom/hetatm number are in order starting from the first atom all the
way to the end.
And resSeq number is in order, protein (which is chain A) 9-694, then ligand
starts at 836.
Hello,
My apologies for sending the previous post to the wrong BB.
Zhijie
-Original Message-
From: Zhijie Li
Sent: Friday, August 08, 2014 11:10 AM
To: R.D. Oeffner ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [phenixbb] local BLAST server
Hi Rob,
The BLAST nr database (fasta format) can b
Hi Rob,
The BLAST nr database (fasta format) can be downloaded from the NCBI ftp:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
As I remember it is the nr.gz file. When unzipped the file is called "nr".
According to BLAST the nr database does contain PDB entries.
http://blast.ncbi.nlm.nih.gov/Blast
Dear Remie,
PyMol considers both chain identifier (chainID, column 22 in a PDB file) as
well as the Residue sequence number (resSeq, columns 23-26 in a PDB file) to
show the order of arrangement. So, simply renaming chainID’s will not work. In
addition to that you will also have to renumber the
Dear Prem,
Defaults are very useful, but I also get very annoyed if it is not possible to
overrule them, even if it is just to test some hypothesis. In your case I would
try another program to generate the restraints, e.g. Grade from Global Phasing.
The PKa’s from active site residues can be ve
