[ccp4bb] refmac rigid body module in ccp4i interface

hello, could i ask the developers to check for me that the rigid body refinement module in the latest update works correctly. when i open the rigid body menu i see no possibility to neither define my own domains nor select auto. rather i see all kinds of options for auto map sharpening etc. my

Re: [ccp4bb] New restraints, same name

... and why don't we move on from pdb format to something a bit more modern ? i think it would only require a handful of programmers to agree on this and the rest would (have to) follow. i.e. if coot and refmac could both read and write something more modern we'd have a huge part of ccp4 world co

[ccp4bb] batchwise completeness in multirecord .mtz

hello, my poor dementia ridden brain has gone on screensaver ... i need to calculate the completeness and redundancy of reflections in batches or ranges of batches in a multi-record .mtz file. sftools can do this, but the numbers are pretty much meaningless, i.e., my feeling is, if i measure 10%

[ccp4bb] CCPALC: not enough memory

hello, it seems i am recently getting the above error quite a lot in mapmask. i have searched for a solution, but only found the problem mentioned a few times with no precise solution indicated. would there be a way to find out HOW MUCH memory mapmask is hoping for ? i do have 2 Gb of memory and

Re: [ccp4bb] I/sigmaI of >3.0 rule

not sure whether this option has been mentioned before ... i think what we really would like to do is decide by the quality of the density. i see that this is difficult. so, short of that ... how about the figure of merit in refinement ? wouldn't the fom reflect how useful our data really are ?

[ccp4bb] scala and xds data

dear colleagues, i convert xds_ascii.hkl with pointless to .mtz. but recently (possibly since the latest xds release, not sure) scala then exits my attempts to reduce the data : Reflection rotation value outside range in Batch header Reflection2 1 6 Isym =3 Batch 73

[ccp4bb] AMORE: Fatal error in s/r TRAFT

dear fellow ccp4ers, while trying to run a translation function in amore, with a certain crystal form we get the above error. in a little more detail, what we get is this ... centred-overlap stop >> traft << no reflection selected AMORE: Fatal error in s/r TRAFT the required input files ar

[ccp4bb] ccp4-6.1.2 on intrepid and jaunty

hello, i have succesfully installed 6.1.2 on ubuntu 8.04 using the automatic installer. the one single correction i had to do was change references from phaser 2.1.6 to phaser 2.1.4 in the setup scripts. runs all fine. now i tried the same with ubuntu 9.04 and get the following error ***

[ccp4bb] SOLVED: about the most recent ccp4 installation

sorry ... user error ... input is case sensitive ... :-) ingo >it seems you have a version of coot in there, where the "get monomer" >via 3-letter code is broken. alternatively "search monomer" does work, >you can click on the molecule of choice and it gets nicely imported ... > >not sure whether

[ccp4bb] about the most recent ccp4 installation

it seems you have a version of coot in there, where the "get monomer" via 3-letter code is broken. alternatively "search monomer" does work, you can click on the molecule of choice and it gets nicely imported ... not sure whether there is a newer version that would work ... cheers ingo -- CREL

Re: [ccp4bb] Refmac5 on Windows

I can confirm this: I see the following running times for the exact same job under linux with no other work being done on the machine: ccp4.6.1.1 Refmac_5.5.0072: End of Refmac_5.5.0072 Times: User: 176.1s System: 78.2s Elapsed: 4:15 ccp4.6.0.2 Refmac_5.4.0062: End of Refmac_5.4.

[ccp4bb] pdbset surprise ?

dear colleagues, i just noticed a to me somewhat unexpected behaviour of pdbset. as it turns out, it seems to make a difference whether i do run pdbset all in one go, changing the cell and applying transformations at once: pdbset XYZIN ... << eof-pdbset cell spacegroup ... rotate euler shif

[ccp4bb] Post-Doctoral Position, CrystaX

submit your CV and a cover letter to [EMAIL PROTECTED] For further information, please visit us at www.crystax.com -- Ingo P. Korndoerfer CrystaX Pharmaceuticals, S.L. Parc Científic de Barcelona Josep Samitier 1-5 08028 Barcelona Tel.: +34 93 403 9093 Fax: +34 93 403 4788 e-mail: ipkcrystax.com

[ccp4bb] remediated pdb and coordinate formates ...

dear all ... beyond iupac nomenclature ... the remediated pdb sounds very nice, so i had a short look at the formats they provide and found this: mmcif, pdbxml, and pdb and http://biomol.dowling.edu/WPDB/ has a very nice discussion of advantages and disadvantages of the various formats ...

[ccp4bb] directly write .mol or .sdf files

dear colleagues, after working around the topic for a while now or avoiding it alltogether, it has now become time to ask: could some friendly soul point me to a program that would create a .mol or .sdf file from 1. a refmac dictionary file (to yield a .mol file randomly positioned and oriented)

Re: [ccp4bb] Filament lifetime on Rigaku Micromax007

Senior Experimental Officer >> Macromolecular Crystallography Core Facility >> Faculty of Life Sciences >> Michael Smith Building >> The University of Manchester >> Oxford Road >> Manchester M13 9PT, UK >> Phone: +44-161-275-5090/5658 >> Fax: +44-161