Dear All,
I normally refine my structure without the hydrogens until the final
stages. But today I'm facing a real trouble with phenix.refine!! It
seems phenix.refine does not recognize the hydrogen atoms and writes out
this message: "Fatal problems interpreting PDB file: number of atoms
with unkno
Dear All,
I'm looking for a free program that I can use to measure the geometric
surface complementarity of protein-protein interfaces. I have created
inhibitor mutants that possess different binding affinities to their
cognate enzyme and it would be very helpful if I can quantify the shape
complem
Thank you all for very helpful suggestions, I used the software STRAP,
Espript is also user friendly and effective. Many recommended ALINE, but
unfortunately I had troubles with the download. Thanks again, Mohd
Dear All,
I'm trying to prepare an alignment figure of 2 proteins that highlight
conserved and similar residues and probably secondary structures; I will
greatly appreciate it if anybody can recommend a software that I can
use. Thanks, Mohd
Pablo Rd
Jacksonville, FL 32224
Tel: (904) 953-0046
Fax: (904) 953-0277
salameh.m...@mayo.edu
**
-Original Message-
From: Phil Jeffrey [mailto:pjeff...@princeton.edu]
Sent: Friday, March 12, 2010 12:37 PM
To: Salameh, Mohd A., Ph.D.
Subject: Re: [ccp4bb
Dear All,
In every refinement round the wxc and wcu are out of control, although I
modify the def file and change the values of wxc=1 and wxu=1 so they
are tightly restrained, but it failed to fix the problem, wxc and wxu
values keep fluctuating, in my latest refinement round wxc=256!! wxu=3.
T
ancer Research building,Rm 331
4500 San Pablo Rd
Jacksonville, FL 32224
Tel: (904) 953-0046
Fax: (904) 953-0277
salameh.m...@mayo.edu
**
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Salameh, Mohd A., Ph.D.
Dear all,
I'm about to deposit a structure into the protein data bank and I'm
encountering a disturbing problem, I have a protein site where the
peptide bond is not properly linked, the distance of C-N bond is 2.23
Angstrom, I tried to restrain that site by modifying my def file but the
problem p
Road
Jacksonville, FL 32224
Tel:(904) 953-0046
Fax:(904) 953-0277
salameh.m...@mayo.edu
-Original Message-
From: Eleanor Dodson [mailto:c...@ysbl.york.ac.uk]
Sent: Wednesday, September 16, 2009 5:14 AM
To: Salameh, Mohd A., Ph.D.
Cc: C
Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon and/or the backbone atoms and I wonder if somebody knows a module
or software that I can use, I tried the structure analysis/Temperature
factor analysis module in CCP4 but it plots the average b-factor of all
ato
Thank you all, it was very, very helpful discussion. However, I
collected crystal data and the Rmerge overall was very high around 0.17
at 2.6A resolution and I'm wondering what is the acceptable value
(range) of R-merge that worth the time to continue processing! Very
anxious to hear your thoughts
Hi everybody!
I will appreciate it if anybody can clarify to me the differences
between Rmerge and Rsym. Many thanks, M
Mohammed A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32
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