Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

Just to add to the outliers in Refmac - careful when some of your atoms have zero occupancy. The bond restraints are not applied any more to these atoms (my feeling) and CERTAINLY are NOT CHECKED FOR OUTLIERS by Refmac at the end of the refinement. Jan Dohnalek Eleanor Dodson wrote: No comme

[ccp4bb] HETATM to ATOM change, and atom identifier change in REFMAC...

Good morning/day/evening all, I have a structure that is refined, with the exception of the molybdenum (MoOOS) cofactors (there are two of them), which are square pyramidal and coordinated to 2 sulfurs in an enedithiolate of a pterin ring. I have brought up my issues with refining this before in

Re: [ccp4bb] Tough ligand to bind?

Nian, Have you considered pressure-freezing, the method developed by Sol Gruner's group at Cornell? If cryoprotectants are causing the problem, freezing under pressure reduces the need for them. It's also possible that your ligand is present but disordered in the crystal, and pressure-freezin

Re: [ccp4bb] Number of refinement parameters

Paul, Refinable parameters are the model parameters that are varied to optimize a goal function. The "number of refinement parameters" is the number of refinable parameters. If you refine: - individual coordinates only, then the number of refinable parameters = number_of_atoms * 3; - isotrop

[ccp4bb] Number of refinement parameters

A couple of basic questions concerning the number of refinement parameters: How do you come up with the number of parameters based on the number of atoms? I was under the impression it was simply the number of atoms times 4 (x,y,z,B), but I've seen some reported numbers that have left me confu

Re: [ccp4bb] Tough ligand to bind?

I am working with a protein/ligand complex that is very resistant. to getting a stable complex. The first thing to try is to go to saturating ligand concentrations, even if it seems that it is excessive. It is possible that binding affinity is significantly different. My biggest problem is precipi

[ccp4bb] Position for PSI Knowledgebase development

=== Lawrence Berkeley National Laboratory Software Developer II === Software Developer II Job ID: 20930 Division: Phy

[ccp4bb] Postdoctoral Position for PHENIX development

=== Lawrence Berkeley National Laboratory Computational Postdoctoral Fellow === Computational Postdoctoral Fellow Job ID: 2

Re: [ccp4bb] Covalently bound drug molecule

I was using X-PLOR at the time. I later switched to a PRESidue patch. I was not sure how many atoms must be added to a residue before a modified amino acid becomes a linked amino acid. The PDB seems a bit adverse to non-standard links. For example, why is NADP not two residues with a LINK? There ar

[ccp4bb] unsubscribe ccp4bb

Title: unsubscribe ccp4bb

Re: [ccp4bb] Covalently bound drug molecule

What refinement program are you using? I assume cns. Ihe idea with the non-standard residue works very good, but the usual way is to PATCH the covalently linked molecule to its respective covalently bound atom in cns or xplor. So, you do not need to alter your pdb-file. Define a PRESI entry in topo

[ccp4bb] Postdoctoral Position in Structural Enzymology, University of Michigan

Postdoctoral Position in Structural Enzymology, University of Michigan, Ann Arbor, MI, USA A postdoctoral research position is available at the University of Michigan to study enzymes that regulate chromatin structure and function. The enzymes under investigation govern gene expression and ot

[ccp4bb] post-doc position in Gif-sur-Yvette (France)

STRUCTURAL BIOCHEMISTRY OF THE INTERACTION OF THE NEURONAL PROTEIN TAU WITH TUBULIN A post-doctoral fellowship is available immediately at the Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, Gif-sur-Yvette, France. The contract will be initially for a period of one year.

[ccp4bb] unsubscribe

W. Dexter Kennedy, MD Beyond the Known Scientific Reality ۞ Discovery Associate Director, Clinical Pharmacology Merck & Co., Inc. P.O. Box 100, UG4D-48 351 North Sumneytown Pike North Wales, PA 19454 * [EMAIL PROTECTED] *267-305-7095 * (267)-305-6382 -

Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

No comment on the Auto debate, but the RMSD of bonds is a crude measure unless you check the outliers.. You can make REFMAC list these - I think it should do so by default actually.. Bad metal distances for instance can distort the number enormously. Eleanor Mark Mayer wrote: Hello all, I b

[ccp4bb] Postdoctoral position in Durham

University of Durham (UK) Department of Chemistry Postdoctoral Research Associate (fixed-term) Applications are invited for a postdoctoral position in the newly established protein crystallography group of Dr. Ehmke Pohl at the Chemistry Department of Durham University. The research projec

[ccp4bb] Deadline(19-sept ) for beamtime proposals at BM14/ESRF for Nov/Dec 2007

Dear all -in case of confusion I re-post with correct dates for beamtime deadlines and period at BM14 for last run of year at ESRF! Apologies but at least this means I get to announce this wonderful opportunity for you to come and collect great data and solve structures at BM14 during Novembe

Re: [ccp4bb] Covalently bound drug molecule

You need a LINK record in the PDB and a dictionary to describe the link. If you run the job from the GUI with Review Restraints, the program should write out a suitable dictionary to describe the link. Check the distances etc to see if you agree with them. You then use the extended pdb and tha

[ccp4bb] Deadline(19-sept ) for beamtime proposals at BM14/ESRF for Nov/Dec 2007

Dear all –in case of confusion with earlier post, I re-post with correct dates for beamtime deadlines and period at BM14 for last run of year at ESRF! Apologies but at least this means I get to announce a second time this wonderful opportunity for you to come and collect great data and solve

[ccp4bb] Deadline(19-sept ) for beamtime proposals at BM14/ESRF for Nov/Dec 2007

Dear all, please submit your proposals for next round of beamtime at BM14 to ensure you get beamtime during Nov/Dec Deadline for submission of online proposals is next Wednesday the 19th Sept. 2007 Link: http://www.esrf.fr/exp_facilit