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
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
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
work either (phenix.refine refine.def fix_wxc=1.0). I will
certainly appreciate any help. Thanks, Mohd
**
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research building,Rm 331
4500 San Pablo Rd
Jacksonville, FL 32224
Tel: (904) 953-0046
Fax: (904
Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in
this case if the weights need to be tightly restrained, I should not use
tls refinement!
**
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research building,Rm 331
4500 San
I'd like to thank you all, the problem is resolved. Apparently, in the
pdb file, the carbonyl oxygen should be listed right after the carbonyl
carbon not after the side chain atoms! M
**
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer
persist after refinement. I wonder if anybody can help resolving
this problem. Thanks and happy holidays! Mohd
**
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research building,Rm 331
4500 San Pablo Rd
Jacksonville, FL 32224
Tel: (904) 953-0046
Fax
Many thanks to all of you who replied, many great suggestions and I'll
try to utilize some of your ideas very soon. Thanks, Mohd
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
atoms which I'm not interested in. appreciate your help. Thanks, Mohd
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32224
Tel:(904) 953-0046
Fax:(904) 953-0277
salameh.m
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
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