[ccp4bb] HTP ligand screening

es before and after water picking. If you happen to have an automated ligand-fitting technology you can throw that in also. I use this script all the time for projects (usually cocrystals or fragment screening) where I have many data sets and I want an efficient route to the first maps. Thanks John Badger

[ccp4bb] MIFit and MIExpert v2010-10 Released

. MIFit and MIExpert will continue to be developed and improved. Feedback is welcomed. Bradley A. Smith, Ph.D., MIFit Project Manager John Badger, Ph.D., MIExpert Author

Re: [ccp4bb] [phenixbb] what to do with disordered side chains

not made very often but that is more a shame on the reviewers than the willingness of the journal at this point in time. Of course, it is a confusing situation when you only see density for a part of a ligand and it comes up all the time. Thanks John Badger

[ccp4bb] Announcement: SDsearch 2.0 released

The SDsearch software is used to search compound libraries in the form of SD files over chemical properties and chemical substructures. SDsearch 2.0 now adds multi-conformer docking to check the steric compatibility of compounds that contain positioned subfragments within protein target sites.

Re: [ccp4bb] Refining against images instead of only reflections

ol. 63 251-276, 1995. From this perspective it is quite surprising that crystallographers are so keen on using TLS models for fitting displacement amplitudes. John Badger

Re: [ccp4bb] Refining against images instead of only reflections

Hi Ethan, Your effort to play devils advocate is appreciated - I have not seen much debate on the applicability of TLS so at risk of diverging into a separate thread: I would not argue that TLS is necessarily a valid model for correlated motion in proteins because it 'works' in fitting the ava

Re: [ccp4bb] Deposition of a BUSTER refined structure

I would echo Ethan on this metric being something of a relic and add a bit more data. Several years ago I tried to get a practical solution to the questions: - when is a refinement finished? - how to detect the correctable abnormalities (errors) in a structure so they can all be corrected durin

[ccp4bb] Announcement: Fragment-based Lead Discovery Conference (FBLD2008)

are now being accepted for poster presentations. Please see http://fbld2008.com/ for more details. Individual inquiries may be address to Mary Canady at [EMAIL PROTECTED] Thanks John Badger, Director of Structural Biology, ActiveSight

[ccp4bb] Announcement:MIFit+ released

uters with Windows and LINUX operating systems. Thanks John Badger, Director of Structural Biology, ActiveSight

Re: [ccp4bb] converting structure factor files to mtz files

users. There is an installer for Windows and gzipped tar file for Linux http://mi.active-sight.com/download.html There is a lot of flexibility in rendering and image export. Thanks John Badger, Director of Structural Biology, ActiveSight

[ccp4bb] Early registration deadline for FBLD08 is Nov 15

Thursday November 15 is the early registration deadline for the Fragment Based Lead Discovery meeting to be held in San Diego over 18-20 Feb 2008. More details are available from http://fbld2008.com/ Thanks John Badger, Director of Structural Biology, ActiveSight

[ccp4bb] xtalview and mifit

A reference to Xtalview/xfit and MIFit came up in a thread without subject line. The poster is correct that MIFit is a successor to XtalView. MIFit is under active development and is free to academics. It runs on Windows and Linux. MIFit can be obtained from http://mi.active-sight.com/download.

Re: [ccp4bb] tutorial / pipeline for ligand fitting, refinement?

ds more to pipelining common tasks for typical cases. Thanks John Badger, Zenobia Therapeutics

Re: [ccp4bb] ARP/wARP and computer platforms

ws - especially as it is one of the more unique programs, perhaps without a direct substitute. As a sidebar, Windows interoperability and reduction of cost/complexity in the crystallographic computing environment is the main reason for preserving arp-waters in CCP4. Thanks John Badger, Direc

[ccp4bb] Announcement: Fragment Screening Library for X-ray Crystallography

...@zenobiatherapeutics.com or visit www.zenobiatherapeutics.com. For additional information on Zenobia's fragment library, contact Dr. John Badger at j...@zenobiatherapeutics.com. John Badger, Director of Structural Biology, Zenobia Therapeutics http://www.zenobiatherapeutics.com/

[ccp4bb] Fix for MIFit8 compatibility issue with CCP4 6.1.1

; > $CCP4/deprecated/src/arp_waters_ > > If you type "make" in $CCP4/deprecated/src you should get it back. We are examining alternatives for water-picking that workable in the context of automated refinement and are not aware of any other incompatibilities at this time. Thanks John Badger

Re: [ccp4bb] structure alignment based on the ligand

If you mean that you have many structure files for the same protein but with different ligands you can automatically align them all based on just the target site CA atoms (i.e. defined as those close to one of the ligands) using the Job/Cocrystal superposition application in MIFit8 http://code.g

Re: [ccp4bb] Computer hardware and OS "survey"

For MIFit downloads stats are 63% windows, 27% Linux (no fully functional Mac port yet). I have been doing crystallography on moderately high-end Windows laptops for a few years now - mostly MIFit with CCP4 but SHELX, MOSFLM, d*TREK etc are also fine. Performance is NOT a practical issue as far

[ccp4bb] 2nd Announcement:Fragment screening library for protein crystallography

Many people responded with questions following our first announcement of a ready-to-use small fragment screening library designed for protein crystallographic screening. Given suitable crystals, the methodology is of interest to anyone wishing to probe ligand binding interactions and motifs in

Re: [ccp4bb] coupling between occupancy and b-values in refinement

Simple test is to vary the occupancy (say increments of 0.1) and check for residual densities following quickie refinements on each. Then at least you know if you can make a conclusion or not. I suppose you could also try refining coupled occupancies on ligand-sized chunks of the protein to g

[ccp4bb] Announcement: Beta test of software for picking compounds for binding analysis

The SDsearch application is intended to allow crystallographers and other structure analysts quickly find analogs of known ligands or build small fragment/scaffold libraries without incurring the cost or requiring the technical resources needed to establish commercial database software. For exa