Re: [ccp4bb] changing names of many files

2008-03-12 Thread Frank von Delft
There's a dead-ordinary linux command 'rename': >> rename 1055 '' 1055*.osc Saved my butt numerous times. phx. James Stroud wrote: I don't know where this comes from, but its called rename-alot. Its a perl script. I'm guessing "Larry" is Larry Wall, but who knows. chmod a+x it and then put it

Re: [ccp4bb] changing names of many files

2008-03-12 Thread Rajesh Kumar Singh
for me following works (just an example): The objective was to remane all 336 images files to 760D6a0001(to 336).img to 760D6a0_001(to _336).img Just save the script below (like filename.com) and run as sh filename.com *** for i in 760D

[ccp4bb] Feature of CCP4i for 6.0.99 (SIGF/Weight label menu)

2008-03-12 Thread Serge Cohen
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello; While using the CCP4 version 6.0.99 during the Bangalore workshop, I realised that it is not any more possible to "freely" choose the weight/sigma labels from a mtz input file. In particular when trying to use phases coming from refmac

Re: [ccp4bb] changing names of many files

2008-03-12 Thread Tim Gruene
Just for the sake of completeness: mmv is also a package available for some linux distributions (SuSE at least), so you don't need the alias. If you like doing so using shell features, you could, with bash, issue for i in 1105\ A*; do mv "$i" "${i#1105\ }" ; done This might work in m

[ccp4bb] Procheck, MolProbity

2008-03-12 Thread Vellieux Frederic
Dear all, What is the currently accepted view on the percentage of residues in disallowed regions of the Ramachandran plot (for publication purposes) ? This is because I have a structure where there are several stretches of not so well defined density. As a consequence there are about 5% of t

[ccp4bb] Postdoctoral Researcher Crystallography/Biochemistry

2008-03-12 Thread Claire Russell
University of Oxford Weatherall Institute of Molecular Medicine Department of Molecular Oncology Cell Signalling Group Postdoctoral Researcher Crystallography/Biochemistry University Grade 7: £26,666 - £32,796 p.a A highly motivated postdoctoral researcher is sought for our team to work on a proj

[ccp4bb] Staff Position Available: Macromolecular Crystallography Laboratory Manager

2008-03-12 Thread Ann West
This is a re-post (the previous ad had an incorrect job requisition number - my apologies for any confusion this might have caused): Macromolecular Crystallography Laboratory Manager. The University of Oklahoma Department of Chemistry and Biochemistry seeks an individual with a doctorate in C

[ccp4bb] X6A @ NSLS: Beam time available

2008-03-12 Thread Stojanoff, Vivian
Beam time available @ X6A http://protein.nsls.bnl.gov The NIGMS beam line X6A at the National Synchrotron Light Source provides FAST access to beam time through out the year. To apply submit a short proposal to http://protein.nsls.bnl.gov at any time. Proposals are continuously reviewed and

Re: [ccp4bb] changing names of many files

2008-03-12 Thread Ian Tickle
Beware that 'rename' on Fedora/Redhat and the like works differently from 'rename' on Debian/Ubuntu etc. Both are in /usr/bin but the former is an executable and the latter is a Perl script (it's apparently installed with Perl), and is probably descended from your 'rename-alot' (the syntax appears

[ccp4bb] PostDoc / Research Engineer available at the University Kiel (Germany)

2008-03-12 Thread Scheidig, Axel
A Postdoctoral Research position / Senior Research Engineer is available from May, 1st 2008 in the Department of Structural Biology, University Kiel, Germany. The position is initially on a 3-year contract. The position involves research in structural biology of medical relevant proteins (www.

Re: [ccp4bb] changing names of many files

2008-03-12 Thread Dennis Arvidson
This is also easily done using midnight commander. http://en.wikipedia.org/wiki/Midnight_Commander http://linuxgazette.net/issue23/wkndmech_dec97/mc_article.html Here are the details on changing names. http://www.chm.tu-dresden.de/edv/mc/mc4.5/manual1.html#45

[ccp4bb] Missing reflections

2008-03-12 Thread Simon Kolstoe
Dear CCP4bb, I was looking through the REFMAC manual today and found the following advice: "Completing the data to include all possible hkls. Should do this after data reduction, and certainly before using REFMAC. This is now done with the uniqueify script. It is best done using CCP4i."

Re: [ccp4bb] Missing reflections

2008-03-12 Thread George M. Sheldrick
All these programs only refine against reflections that were actually measured. REFMAC, but not SHELXL, provides the 'Sigma-A' weight coefficients for Coot to use DFc instead of 2mFo-DFc for the reflections for which Fo is not known (or is reserved for the free R) to calculate a map. This will

Re: [ccp4bb] Feature of CCP4i for 6.0.99 (SIGF/Weight label menu)

2008-03-12 Thread Chavas Leo
Dear Serge -- While using the CCP4 version 6.0.99 during the Bangalore workshop, I realised that it is not any more possible to "freely" choose the weight/sigma labels from a mtz input file. In particular when trying to use phases coming from refmac (after MR + rigid body) with there FoM

Re: [ccp4bb] Missing reflections

2008-03-12 Thread Simon Kolstoe
Thanks for the reply, Does this mean REFMAC/Coot does need the missing number flags (and thus you will get improved maps ONLY if uniqueify is run) or does REFMAC/Coot recognise when a reflection is missing and use DFc regardless (in which case there is no point running uniqueify)? Simon

Re: [ccp4bb] Missing reflections

2008-03-12 Thread Kevin Cowtan
Refmac (and dm and pirate and probably some other programs like phaser too) will only restore missing reflections if there are entries (albeit bblank ones) for those reflections in the MTZ file. So it's not a matter of running uniquify before refmac, its a matter of running uniquify before you

[ccp4bb] ecoli outer membrane / yeast cell wall permeability

2008-03-12 Thread Jacob Keller
Dear Crystallographers, does anybody know the extent to which the outer membranes of e. coli and/or the cell walls of s. cerevisiae are permeable to various solutes? In particular, I was thinking of small, hydrophilic molecules. References would be great as well--I am not sure where to look...

[ccp4bb] Color of heme containing Xtals

2008-03-12 Thread Jan Schoepe
Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop) influence the intensity of the color? Many thanks!

Re: [ccp4bb] Color of heme containing Xtals

2008-03-12 Thread Ian Ollmann
On Mar 12, 2008, at 12:48 PM, Jan Schoepe wrote: Hello everybody, I wonder if anybody has experience with heme (or to be more precise: heme b) containing proteins which Xtals do not look red under the microscope. How might the technique for crystallization (e.g. sitting drop, hanging drop

Re: [ccp4bb] Color of heme containing Xtals

2008-03-12 Thread Sanishvili, Ruslan
Crystals are supposed to be red if you have oxidized iron in the heme and deep pink/scarlet if the iron is reduced. If you removed the iron (for example EDTA during purification) or substituted with something during purification or crystallization, you could loose the color. It is trivial to check

Re: [ccp4bb] Color of heme containing Xtals

2008-03-12 Thread R Michael Garavito
Jan Are you saying that the protein you are starting with is not colored (heme is gone or damaged) or that the native protein is only weakly colored (low extinction coefficient at the Soret wavelength)? The former is more disturbing than the latter. For some heme proteins, like peroxidases,

[ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

2008-03-12 Thread Dale Tronrud
Hi, I am looking over a number of models from the PDB but have been unable to reproduce the R-factors for any model that was refined with Refmac and contains TLS parameters. I usually can't get within 5% of the reported value. On the other hand, I usually do pretty well for models w/o TLS.

Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

2008-03-12 Thread Ramaswamy
Dale, You raise a very important point. The electron density server will not put out the data unless there is a reasonable agreement between the Author reported R-factor and the calculated R-factor. I guess for the same reasons (and more - Gerard?). The question I have is - if we are going to

Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

2008-03-12 Thread Winn, MD (Martyn)
Clearly a few interesting entries . 2) in the context of PX, only the total "B factor" contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is) 3) how do you calculate the "TLS origin" ? The PDB entries should contain the origi

Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

2008-03-12 Thread Pavel Afonine
Hi Martin, 2) in the context of PX, only the total "B factor" contribution to Fcalc needs to be positive definite, the TLS component might not be (though it is satisfying if it is) Please correct me if I'm wrong My understanding was that the T and L matrices must be positive definite,

[ccp4bb] Possible to make this movie?

2008-03-12 Thread Yanming Zhang
Hello, I want to make a movie to show the process of ligand switch. In the movie, the first ligand will gradually be replaced by the second ligand(Include the conformation change such as the bond rotation when the second is approaching). possible to make this movie? I will use Pymol+eMovie to

[ccp4bb] eCheminfo Hands-on Drug Discovery Workshop in Oxford

2008-03-12 Thread barry . hardy
The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; St