Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

R-free of 37.4% at 3.9 A resolution, could you please tell me how reliable this structure of Lambda repressor bound to DNA is? Thanks Misbha -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Misbha -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fed

Re: [ccp4bb] metal ion coordination

To find Cl its worth looking at anomalous maps, especially for home source data, since even with partial occupancy Cl is easily located. Also, for well ordered Cl ions, B-factor will often refine to lower value than coordinating atoms when its incorrectly refined as water. Finally, in a subset o

Re: [ccp4bb] somewhat off-topic: stereo on macs for building into density...

Xavier, What Mac and graphics card works for stereo on the LG display? Mut be a newish model to have HDMI output. Thanks, Mark

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

[ccp4bb] Directories & Projects Spring Cleaning

I'd appreciate suggestions about how to reorganize my My Directories&ProjectDir listing. Its currently got several years worth of work and is getting hard to work with. I'd like to archive old projects (say by year) but keep all the CCP4i files for each project intact, so that I can easily go bac

[ccp4bb] Postdoctoral Fellowship in Membrane Protein Structural Biology at NIH

publications, a brief statement of experience and scientific interests, and contact information for three references to may...@mail.nih.gov Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 --

[ccp4bb] UV microscopes for Xtal visualization

I have read the paper by Gill in Acta Crys F66: 364-372 and wonder what other peoples experience has been with the MUVIS from Formulatrix and the JANsci microscope for imaging 96 well plates. The JANsci instrument seems to have an advantage over the MUVIS in having two objectives. For detec

[ccp4bb] Deposition of riding H: R-factor is overrated

Huh? That's not a cif fragment. What file are you looking at? In my experience the PDB feeds back to you a cif format structure factor file with a name like rcsb054058-sf.cif Near the top of that file you should find a description of the data columns. The columns present depend on what you fed

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

Ethan wrote I believe that deposition of Fc Phic FOM should be required. Certainly it should be the recommended practice. For the same series of structures I just deposited, which started the the riding H discussion, my mtz file had Fc Phic FOM + other data put out by Phenix - pavel can ela

Re: [ccp4bb] Deposition of riding H

However this thread appears to have reached the point where not much new ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the

[ccp4bb] Deposition of riding H

Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better g

Re: [ccp4bb] Stereo Mac OS X - Update

1) A couple of people like the Zalman BUT when I contacted the vendor recommended on the WIKI here's the response (edited). Note that the price has gone up, and its currently not available; my guess this is a US wide lack of availability? "We are totally sold out of these and Zalman is not prov

[ccp4bb] Stereo Mac OS X - what current options?

I searched the BB and this has been discussed on and off over past year. If any one has setup a Mac for stereo with COOT using LCD with currently available hardware please post details. Thanks :)

Re: [ccp4bb] Distinguishing Between Na+ and H2O

Try USF STAN server and run WASP. http://alpha2.bmc.uu.se/usf/ It picks up waters which could be potential cations based on geometry; it works well in our hands, but misses those ions for which ligands come are generated by crystallographic symmetry; if this is important, then expand your AU

[ccp4bb] how to improve Rfree?

You can also pick thin shells with SFCHECK and with 12-fold NCS the referees will likely not be kind if you dont!!! -- Mark

Re: [ccp4bb] taming structural biology

Blow's book is excellent. Another good one is Practical protein crystallography by Duncan McRee 1999 Academic Press. Its ever so slightly out of date on software, but the basics don't change. I think its an easier read for new crystallographers. Also, check out some great web sites: The Camb

[ccp4bb] Postdoc positions available NIH Jan 2010

research experience to Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Lab web site: http://snb.nichd.nih.gov/index.htm --

[ccp4bb] Hel with library definition for Asn-NAG link

We are refining a 2.7 A structure with multiple ASN-NAG links. The torsion angle between the Asn amide and the sugar is quite variable, while from the chemistry of this link we would expect a value close to 180°, as reported in the PDB survey by Imberty & Perez (Protein Engineering 8:669-709

Re: [ccp4bb] Deglycosylation

One thing to watch out for: in addition to frustrating crystallographers those sugars play other roles in protein chemistry, and its not uncommon for the solubility of proteins to change dramatically after deglycosylation. Good luck! MLM

[ccp4bb] Slightly off-topic - silica based columns

Superdex and Superose columns. Please describe specific columns if you can. Thanks -- Mark Mayer

[ccp4bb] Postdoctoral Fellowship at NIH Structural Biology of Neurotransmitter Receptors

A postdoctoral position is available to study the structure and function of neurotransmitter receptors. Recent papers describing work from the lab include: Nat Struct Mol Biol. 2006 13:1120-7; Nature. 2006 440 :456-462; Neuron 2007 53:829-841.We are looking for a highly motivated person who

[ccp4bb] Ramachandran statistics

Hello, Is there a consensus about which program / data base most accurately reports Ramachandran statistics? I believe that PROCHECK inaccurately flags outliers because the data base was compiled many years ago, and there are now many more high resolution structures. Likewise I think I've he

[ccp4bb] Refmac B ARRAY FOR HESSIAN TABULATION

Hello, I'm running a TLS refinement with Refmac and keep getting the following output in my logfile. B ARRAY FOR HESSIAN TABULATION TOO BIG VALUE RESET TO MAXIMUM On the next round of refinment e.g below everything seems normal, but each cycle end with this warning. Can I (should I) set the

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

Hello all, I believer the suggested matrix weight for running refmac is 'auto'. I'm at the end of refinment for a data set that I've cut at 1.59 A, so maps are pretty. Here's the logfile with auto weighting ... NOTE bond rmsds !!! REMARK 3 R VALUE(WORKING SET) : .15481

[ccp4bb] Li ion scattering factor

Dear All, We have a structure under refinement with a putative Li bound to a potentially important allosteric site. I'd assumed that Li+ would lose an electron and have weaker scattering than Li Metal, but the entry for atomsf.lib has the same # of electrons for both entries while the entries

[ccp4bb] twin fraction varies between crystals?

For cases where people have had merohedral twinning, did the twin fraction vary substantially between individual crystals grown under indentical conditions? I have no prior experience with merohedral twinning, and was surprised to see that the twin fraction varied substantially as detailed be

[ccp4bb] Merohedral twinning

Hi, I'd greatly appreciate advice on how to proceed with trying to solve and refine a structure with nearly perfect merohedral twinning - or is this impossible? The SG is H3; most likely nmol is asu is 4 from Matthews coefficient - but not sure about this. Here are the twinning stats from p