Re: [ccp4bb] TER in PDB file

On Tue, May 13, 2014 at 9:20 PM, Felix Frolow wrote: > Phenix does even more, it adds TER after ions and ligands, so again manual > messing is needed. > However they may have a jiffy to fix it. > phenix.sort_hetatms will remove them for you, although why this "problem" was apparently beyond the c

Re: [ccp4bb] TER in PDB file

Phenix does even more, it adds TER after ions and ligands, so again manual messing is needed. However they may have a jiffy to fix it. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israe

Re: [ccp4bb] TER in PDB file

Dear Felix, I recently had the same problem. I didn't think TER records were a big deal. I never had a program that did weird thing because of missing TER records. But well, orders are orders, so we need TER records for deposition. It would be nice if all refinement programs would write those.

Re: [ccp4bb] High B-factors

On Tuesday, 13 May, 2014 22:49:15 Kgosisejo, Oarabile wrote: > Hi all, > > We have solved the structure of a protein at 2.3 A with the final R-work and > R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with > an average of 72. There are 3 molecules in the asymmetric unit

[ccp4bb] High B-factors

Hi all, We have solved the structure of a protein at 2.3 A with the final R-work and R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with an average of 72. There are 3 molecules in the asymmetric unit and the 3rd molecule is very disordered and I believe is the main cont

[ccp4bb] OFF TOPIC - zebra printer labels for SBS format plates

Hello all, Sorry for the off topic post. I am looking for alternate (and more reasonably priced) sources for label rolls for our Zebra printer for labeling crystallization experiments. We use Formulatrix rock imagers and rock maker software but am interested in hearing from anyone that uses Zebr

[ccp4bb] TER in PDB file

Community! I am in the process of PDB deposition. I have used for refinement Refmac. I enter to refinement cycle PDB file with TER separators. After refinement they disappear. PDB validation server (option 1 with geometrical parameters report ) DEMAND TER separator. In my structure there are 28 h

Re: [ccp4bb] puzzle of reference zone in HKL2000

these are symmetry alternative choices of the cell axes they sure are the same as there are 14 Bravais lattices I guess it is not space group related. they were introduced to maintain a precision of calculationI guess, so to choose and alternative orientation were trigonometric parameters are in

[ccp4bb] puzzle of reference zone in HKL2000

Hi everybody! I met with a problem when I was reading the HKL2000 online manual. It's the reference zone setup in the "Step 11: What is the reference zone? How is this useful? (page 38, figure 38)". Does anybody know the definition of reference zone, and why the reference zone setup window seems al

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Sanjit, We routinely use Protein G coupled resins for purification of monoclonals produced in the facility. On a structural level, antibodies typically recognize 5 or more residues in a protein unless the immunogen, such as a single amino acid in your case, is a hapten conjugated to a carrier mol

Re: [ccp4bb] Helix alignment and movement

Dear Mike, I think that the "old" CCP4 "superpose" program used to be able to do this ? (This was a FORTRAN program, based on code from Wayne Hendrickson's PROLSQ program). With this program you specify one set of residues to do the alignment with and another set to do the st

[ccp4bb] Helix alignment and movement

Dear Eugene and other CCP4ers The recent discussion about superposition has prompted me to ask about a different kind of superposition problem. We are working on a small dimeric protein that is entirely made up of helices. Instead of large, concerted domain movements, which I am quite familia

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Dear All I am planning to purify monoclonal antibody. In this concern I found Pseudospecific ligands such as histidine, tryptophan,phenylalanine etc. can be used to purify a wide range of bio-molecules and especially immunoglobulin. I wish to know the structural mode of binding of Hi

Re: [ccp4bb] Google Gets it Right

http://www.google.com/doodles/dorothy-hodgkins-104th-birthday has more information about the doodle... though I don't think "cryptographer" was the right word to use :-) Rich -- Richard Fearn Senior Software Engineer Diamond Light Source Ltd. Tel: +44 1235 778655 -- This e-mail and any a

Re: [ccp4bb] Google Gets it Right

Dear Felix, I now, of course. The molecule on the picture look like consisting of rather light atoms, and I would be very impressed if the instrumentation and software at that time allowed the reliable detection of the hand from that particular molecule. I don't assume Dorothy Hodgkin made a mist

Re: [ccp4bb] Google Gets it Right

Anomalous signal analysis is quite early development in structural biology. There are couple of classical papers by Bijvoet in the first issues oaf Acta Crystallographica. Presently I am out of ability to find exact references :-/ Dr Felix Frolow Professor of Structural Biology and Biotechnol

Re: [ccp4bb] Google Gets it Right

Dear Javier, without the analysis of the anomalous signal you have a 50:50 chance to get the correct configuration, and those times were too early for that. The comment may have been added later and/or from using a different type of experiment. Best, Tim On 05/13/2014 02:21 AM, Javier Gonzalez w