[ccp4bb] Phenix refine has a problem with the added H, plz help

2011-04-26 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] measuring shape complementarity

2010-12-06 Thread Salameh, Mohd A., Ph.D.
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

Re: [ccp4bb] Alignment software

2010-05-25 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] Alignment software

2010-05-21 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] phenix target weight refinement

2010-03-12 Thread Salameh, Mohd A., Ph.D.
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

Re: [ccp4bb] phenix target weight refinement

2010-03-12 Thread Salameh, Mohd A., Ph.D.
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

Re: [ccp4bb] phenix refinement peptide bond poor geometry

2009-12-21 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] phenix refinement peptide bond poor geometry

2009-12-18 Thread Salameh, Mohd A., Ph.D.
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

Re: [ccp4bb] backbone b-factor

2009-09-16 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] backbone b-factor

2009-09-15 Thread Salameh, Mohd A., Ph.D.
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

[ccp4bb] differences between Rsym and Rmerge

2008-01-18 Thread Salameh, Mohd A., Ph.D.
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