Re: [ccp4bb] DSSP and PDB secondary structure assignments

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mark, I was tought to always check the outcome of automated secondary structure assignment, because it is defined by hydrogren bondings, not by what some software thinks. DSSP is certainly very good, but always worth comparing the boundaries with

Re: [ccp4bb] interesting alternative to CCP4's superpose tool

Yes indeed and a very powerful tool. I'm just wondering what the difference between his old Theseus and Theseus 2.0 is. From the abstract it seemed fairly familiar with what I had been using Theseus 1.6 in conjunction with MUSCLE. Sometime BRAIN 1.0 works well too. Jürgen On Jul 25, 2012, at

[ccp4bb] interesting alternative to CCP4's superpose tool

Hello, Quite interesting article: http://bioinformatics.oxfordjournals.org/content/28/15/1972.abstract Regards, F.

Re: [ccp4bb] DSSP and PDB secondary structure assignments

OK, but you don't specify that Promotif uses DSSP for that purpose, right? -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 Nancy University, School of Medicine 9, Avenue Foret de Haye, BP 184 F-54500 Vandoeuvre-les-Nancy (France) Tel : +33 (0)3 83 68 32 73 Fax : +

Re: [ccp4bb] DSSP and PDB secondary structure assignments

I got the following response from PDB In PDB, Helix and sheet records are automatically generated by Promotif software. Authors who wish to provide their own helix and sheet records may do so; a remark will be added to REMARK 650 and REMARK 700 of the PDB entry to indicate that the helix and/or

[ccp4bb] DSSP and PDB secondary structure assignments

I've recently noticed that the Helix and Sheet records in PDB entries differ from those generated by DSSP and would like to ask if anyone can explain how the PDB makes the assignments. Until now I'd always assumed that the PDB and DSSP records were the same. As an example I've listed a few lin

Re: [ccp4bb] Refmac: ADP is non-positive

I can confirm the problem. If I take a previous successful refmac refinement, remove the initial N atom from the first residue in the input PDB file, and re-run the refinement I get: Problem with the ADP of the atom N A 33 ADP is non-positive -94.380859 Problem with the ADP

[ccp4bb] Post-doctoral Fellowship University of Michigan

  Postdoctoral Fellow Macromolecular crystallography, Biophysics and Biochemistry We are looking for a highly motivated postdoctoral research fellow to join our laboratory at the Life Sciences Institute, University of Michigan in Ann Arbor, Michigan. Synapses mediate comm

[ccp4bb] Nagoya Symposium: Frontiers in Structural Physiology

Nagoya Symposium: Frontiers in Structural Physiology Nagoya University, Nagoya, Japan January 22 - 24, 2013 Web site: http://symposium.cespi.nagoya-u.ac.jp/ Poster: http://symposium.cespi.nagoya-u.ac.jp/docs/poster.pdf Topics: Membrane Proteins Macromolecular Complexes Receptors, Channels and Tra

[ccp4bb] modeling thioester bond

No answers yet from the COOTbb (yet), so I'm cross posting this to the ccp4bb. Sorry for the double post. Hi there, I'd like to model a thioester bond, starting from protein A with an exposed Cys, and having juxtaposed the carboxyl group of a C-terminal residue of protein B. The way I would

Re: [ccp4bb] Somewhat OT: question of professional courtesy

I disagree. If the primary citation is available in the PDB it should be cited. If we allow reference solely to a database entry, eg. a PDB ID, then reference to a wikipedia entry becomes a valid reference and I don't think we should go down that road yet. I agree with Evette's earlier commen

[ccp4bb] 3rd MX User Workshop at Diamond - September 5th-6th, 2012

Dear All I quick reminder - last chance to sign up for the 3rd MX User Workshop at Diamond - the workshop is part of the Synchrotron User Meeting, September 5th-6th, 2012. Workshop sessions include presentations from staff and users on latest developments, in-situ screening, using fast detector

Re: [ccp4bb] Somewhat OT: question of professional courtesy

I concur with Mike - If the paper reproduces at least in part a result already published, then the precedent(s) should be referenced (even if the experimental approach is different) - If the paper discusses a previous experimental result or inference from the results of anot

Re: [ccp4bb] Somewhat OT: question of professional courtesy

Yes, I think this is reasonable. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of R. M. Garavito Sent: Wednesday, July 25, 2012 9:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy Evette, I think the primary issue i

Re: [ccp4bb] Somewhat OT: question of professional courtesy

Evette, I think the primary issue is what kind of analysis was being reported on. That is what I look for when I review a manuscript. If the authors are doing a broad structural analysis (homology of TIM barrels, X-ray refinement protocols, etc.), I wouldn't expect citations beyond stating th

Re: [ccp4bb] Somewhat OT: question of professional courtesy

Well, I guess that would be because when my CV and credentials are reviewed by e.g. study sections of funding agencies, institutional committees making decisions affecting my promotion and academic advancement, potential future employers, etc., many will look at metrics such as h-index and the like

Re: [ccp4bb] Somewhat OT: question of professional courtesy

I think that people who do this are not really crystallographers (at least to me) since they do not give credit to the effort that produces a structure. That is why that I always insist on proper refereeing when I review a manuscript. Maybe it is time for this community to ask journals to put i

Re: [ccp4bb] Somewhat OT: question of professional courtesy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Evette, the PDB lists the citation when you enter the PDB-ID in the search mask of any of the web-interfaces, which is much easier for the reader than typing the information from the list of references, i.e. all information is in the article by m

Re: [ccp4bb] Somewhat OT: question of professional courtesy

In the least case the PDB DOI number should have been cited. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone:

[ccp4bb] Somewhat OT: question of professional courtesy

Dear bb, This morning as I scanned an accepted manuscript from a well-respected-but-not-particularly-glamorous journal that publishes many macromolecular structures, I came across a brief mention of homology and rmsd with a published structure listed by PDB accession number, but no citation of the

Re: [ccp4bb] How to identify unknown heavy atom??

XRF or TXRF would be very quick and definitive. With TXRF you could easily identify and quantify metals present in 1-10 uL of a 10 mg/mL solution. ICP-OES will also work, but will require about 300 ug or so of protein (depending on MW). ICP-MS is maybe 10x more sensitive than -OES but is more comp

Re: [ccp4bb] Question about weird diffraction map

Hi Zhao, I would try a crystal that has not been treated with any dye. Small molecules, particularly drug like compounds, crystallise out in soaking experiments and can give diffraction similar to yours. My worry is that you have non-diffracting protein crystals coated in some small molecule cry

Re: [ccp4bb] Improvement in crystal quality

Niks Seeding often works very well with needles. But start with seeding in RANDOM SCREENS, i.e. "rMMS" References - Allan D’Arcy, Frederic Villarda, May Marsh. 'An automated microseed matrix-screening method for protein crystallization'. Acta Crystallographica section D63 (2007) 550–554. On

Re: [ccp4bb] How to identify unknow heavy atom??

Shameless self plug: http://scripts.iucr.org/cgi-bin/paper?fw5057 That was done with a crappy crystal in a relatively weak beamline. With a good crystal one can get cleaner data. Cheers. Jose. Jose Antonio Cuesta-Seijo, PhD Carlsberg Laborat

Re: [ccp4bb] 2D-bar code scanner to read Hampton pins barcodes

We use a Pepperl+Fuchs Omnitron handheld cabled reader. Our model is a cr2010_4 but this is now several years old. It looks similar to the MH200 model that I found after a quick google. It is used for every synchrotron trip, and works well. Johan On 24 July 2012 15:33, Pietro Roversi wrote: > D

Re: [ccp4bb] How to identify unknow heavy atom??

Dear All, re identifying metals, It's possible to calculate crystallographic element-specific anomalous difference maps if you can collect data on either side of the absorption edge. I have used this successfully for Sr, Zn and Mn. http://www.ncbi.nlm.nih.gov/pubmed/15858259 I have a set of