In the past I remember using a simple program or webserver to check whether
modelled water molecules might be metal ions, especially sodium, magnesium etc.
as they do not differ much in density to waters. Based on coordination.
However, I can't remember the name and can't find it in google or
turns out some people indeed have better memory than me:
WASP inside STAN server
http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
thanks!
On 14 Feb 2014, at 12:49, Mark van Raaij wrote:
In the past I remember using a simple program or webserver to check whether
modelled water molecules
Coot:
Extension - Modelling - Residues with Missing Atoms...
Or watch out for the blue bars in the rotamer validation graph in Coot.
B
Dear all,
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
Many thanks in
Dear all,
Does anyone know a program that will check a PDB file for missing atoms and
output a list of the corresponding residues?
Many thanks in advance,
Tiago
***
Tiago Barros, PhD
Kuriyan lab - Molecular and Cellular
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote:
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
REFMAC reports a (truncated?) list in the log file. Coot can also
identify missing atoms. I would be pretty sure
Hi Tiago,
easy, two steps:
1) Save the lines between *** into a file say called run.py:
***
import os,sys
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import monomer_library
import mmtbx.monomer_library.server
from cStringIO import StringIO
def exercise(args):
file_name =
According to the PDB Format document, entries with missing
atoms should have a parsable REMARK 470. You might want
to write some quick code to look for that REMARK.
The PDB staff could comment about the accuracy of REMARK
470 in its entries.
Frances Bernstein
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tiago Barros
[ti...@me.com]
Sent: Tuesday, August 23, 2011 2:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Check
check
check mail ...
Sorry, I just figured out how to post to the CCP4bb instead of sending a
private email.
Here are two missed messages that I think should appear on the board:
- Original Message -
From: Miles Pufall [EMAIL PROTECTED]
To: Zhijie LI [EMAIL PROTECTED]
Sent: Tuesday, February 19, 2008
Dear All experts,
I want to check the conformation of one important amino acid in the structure
by looking the difference density map. Should I just omit that amino acid in
the refinement or should I also omit its flanking amino acids? Which one is
better?
Thank you very much for
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