[ccp4bb] install crystallography software on mac
Hi all, I am trying to install ccp4, phenix, coot and other crystallography software on my mac. I am not familiar with mac, neither Linux system. Please give me some protocols to install these software and how to update them. I appreciate it. Lisa
Re: [ccp4bb] install crystallography software on mac
Best place to start: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OS_X -- A. Radu Aricescu, PhD University Research Lecturer University of Oxford Wellcome Trust Centre for Human Genetics Division of Structural Biology Roosevelt Drive, Oxford OX3 7BN United Kingdom Phone: +44-1865-287564 Fax: +44-1865-287547 Original message Date: Mon, 28 Jan 2013 17:09:30 +0800 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of LISA science...@gmail.com) Subject: [ccp4bb] install crystallography software on mac To: CCP4BB@JISCMAIL.AC.UK Hi all, I am trying to install ccp4, phenix, coot and other crystallography software on my mac. I am not familiar with mac, neither Linux system. Please give me some protocols to install these software and how to update them. I appreciate it. Lisa
[ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs 30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Dear Huw, It looks as though you have correctly diagnosed a problem with AMPLE. For expansion from borderline partial structures, I recommend the latest SHELXE (on my beta-test server since Jan. 20th) and experimenting with the -O and -F switches, e.g. -F0.9 -O100 -a30 However SHELXE is still a work in progress, so this may change in future versions. Best wishes, George Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi Huw, Well spotted! We originally gave structure factors to SHELXE in our testing as for most of our test cases we only had F/SIGF available. We were advised to change to intensities but somehow in the released version the -f flag remained. I'll make the change and put it in a CCP4 update. Ideally we should be using the original intensities rather than converting the structure factors so we'll look to adding that as an input option. Thanks again for spotting this. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Huw Jenkins Sent: 28 January 2013 10:14 To: ccp4bb Subject: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion Hi, I've been running Ample and I'm a bit confused about the input for the shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it appears that Ample converts the structure factor amplitudes to intensities using mtz2various with the FSQUARED keyword as the log file contains the following: Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag Data line--- OUTPUT SHELX Data line--- FSQUARED Fs are squared on output - better to use original Is from TRUNCATE output Data line--- END However then shelxe is run with the command: shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3 I thought that the -f flag tells shelxe that the input hkl file contains Fs not Is so this should not be present? When I run shelxe with the phaser/molrep solutions and a hkl file generated either from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I get much lower CCs for the autotracing which makes sense as all of the solutions so far are rubbish! The Ample logs contain CCs 30 for all solutions which doesn't seem correct. Any information would be greatly appreciated! Thanks, Huw -- Scanned by iCritical.
Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Correct, shelxe does not use the free -R flags, and works just as well with the original unmerged unctruncated intensities. George Hi Ronan, On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote: Well spotted! We originally gave structure factors to SHELXE in our testing as for most of our test cases we only had F/SIGF available. We were advised to change to intensities but somehow in the released version the -f flag remained. I'll make the change and put it in a CCP4 update. Ideally we should be using the original intensities rather than converting the structure factors so we'll look to adding that as an input option. Thanks for confirming that! Perhaps the option to add a hkl file for shelxe would be a useful? Since I use XDS to integrate and scale data it's as easy to generate the shelx format hkl file from the unmerged XDS_ASCII.HKL as it is to use the merged intensities in the mtz from the aimless/truncate/unique/freerflag pipeline. The only issue with this I can see is that there will be no freeR flags but I don't think that shelxe uses these anyway? Thanks, Huw -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] off topic: DSSP
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear -- rashmi, if you would kindly let us know what exactly you are thanking for, you may actually have a reason for doing so - a good start is a cut-and-paste copy of the error message(s) from the terminal where you typed 'make' and 'make install'. If you get this error only from 'make install' but not from 'make', chances are that the compilation worked fine but the Makefile attempts to install file to a location you do not have write access to. Cheers, Tim On 01/26/2013 10:11 AM, Rashmi Panigrahi wrote: Hi All Apologies for the off topic. Could some one help me in installing DSSP in Mac OSX 10.5.8 I tried downloading dssp-2.0.3.tbz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.3.tbz dssp-2.0.4-linux-amd64ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 dssp-2.1.0.tgz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz from http://swift.cmbi.ru.nl/gv/dssp/ I tried doing make followed by make install. I got error on compiling. Thanks in advance - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRBpI8UxlJ7aRr7hoRAu1bAJ9q3TWZbBMAlrOWchZnrPo4Iy42YQCg1K+c uo0hlOQ0oTPyTDHmXjM57Bw= =dBMv -END PGP SIGNATURE-
Re: [ccp4bb] off topic: DSSP
Dear Rashmi, you may want to try this web server instead of compiling installing it: http://www.cmbi.ru.nl/hsspsoap/ Otherwise, you'd better follow Tim's advice and give us more clues! Jon 2013/1/28 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear -- rashmi, if you would kindly let us know what exactly you are thanking for, you may actually have a reason for doing so - a good start is a cut-and-paste copy of the error message(s) from the terminal where you typed 'make' and 'make install'. If you get this error only from 'make install' but not from 'make', chances are that the compilation worked fine but the Makefile attempts to install file to a location you do not have write access to. Cheers, Tim On 01/26/2013 10:11 AM, Rashmi Panigrahi wrote: Hi All Apologies for the off topic. Could some one help me in installing DSSP in Mac OSX 10.5.8 I tried downloading dssp-2.0.3.tbz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.3.tbz dssp-2.0.4-linux-amd64 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 dssp-2.1.0.tgz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz from http://swift.cmbi.ru.nl/gv/dssp/ I tried doing make followed by make install. I got error on compiling. Thanks in advance - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRBpI8UxlJ7aRr7hoRAu1bAJ9q3TWZbBMAlrOWchZnrPo4Iy42YQCg1K+c uo0hlOQ0oTPyTDHmXjM57Bw= =dBMv -END PGP SIGNATURE- -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] off topic: DSSP
Sorry to cross-pollute… If you don't mind using the ksDSSP implementation, it is already installed with the phenix suite if you have it. phenix.ksdssp from the command line. With regards, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Jan 28, 2013, at 3:25 PM, Jon Agirre wrote: Dear Rashmi, you may want to try this web server instead of compiling installing it: http://www.cmbi.ru.nl/hsspsoap/ Otherwise, you'd better follow Tim's advice and give us more clues! Jon 2013/1/28 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear -- rashmi, if you would kindly let us know what exactly you are thanking for, you may actually have a reason for doing so - a good start is a cut-and-paste copy of the error message(s) from the terminal where you typed 'make' and 'make install'. If you get this error only from 'make install' but not from 'make', chances are that the compilation worked fine but the Makefile attempts to install file to a location you do not have write access to. Cheers, Tim On 01/26/2013 10:11 AM, Rashmi Panigrahi wrote: Hi All Apologies for the off topic. Could some one help me in installing DSSP in Mac OSX 10.5.8 I tried downloading dssp-2.0.3.tbz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.3.tbz dssp-2.0.4-linux-amd64ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 dssp-2.1.0.tgz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz from http://swift.cmbi.ru.nl/gv/dssp/ I tried doing make followed by make install. I got error on compiling. Thanks in advance - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRBpI8UxlJ7aRr7hoRAu1bAJ9q3TWZbBMAlrOWchZnrPo4Iy42YQCg1K+c uo0hlOQ0oTPyTDHmXjM57Bw= =dBMv -END PGP SIGNATURE- -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] off topic: DSSP
On Mon, Jan 28, 2013 at 8:04 AM, Antony Oliver antony.oli...@sussex.ac.uk wrote: If you don't mind using the ksDSSP implementation, it is already installed with the phenix suite if you have it. Correct, but although the method is supposed to be the same, the output is not, and there are bugs in how it presents helix annotations. So I'm not sure it's a reliable substitute for the original DSSP - we use it in Phenix to calculate secondary structure restraints, with some extra filtering to catch the buggy annotations. (Unfortunately it was the only open-source program I could find for this purpose.) -Nat
Re: [ccp4bb] off topic: DSSP
Hi Nat, DSSP recently went open source with a very liberal license. So you can consider using the real DSSP now. This may also be the moment to integrate DSSP in CCP4. Cheers, Robbie Sent from my Windows Phone From: Nat Echols Sent: 2013-01-28 17:32 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off topic: DSSP On Mon, Jan 28, 2013 at 8:04 AM, Antony Oliver antony.oli...@sussex.ac.uk wrote: If you don't mind using the ksDSSP implementation, it is already installed with the phenix suite if you have it. Correct, but although the method is supposed to be the same, the output is not, and there are bugs in how it presents helix annotations. So I'm not sure it's a reliable substitute for the original DSSP - we use it in Phenix to calculate secondary structure restraints, with some extra filtering to catch the buggy annotations. (Unfortunately it was the only open-source program I could find for this purpose.) -Nat
Re: [ccp4bb] off topic: DSSP
On Mon, Jan 28, 2013 at 8:39 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: DSSP recently went open source with a very liberal license. So you can consider using the real DSSP now. This may also be the moment to integrate DSSP in CCP4. Based on the info here: http://swift.cmbi.ru.nl/gv/dssp/ the license isn't very liberal - it looks more like the proprietary-with-source-code licenses used by CCP4 and Phenix (among others), which preclude redistribution or anything resembling commercial use without permission. I also saw this: The new DSSP, is distributed as executable only. You can get the new DSSP source code only if you can convince us that it is really needed for a worthy scientific cause. Or am I looking in the wrong place? -Nat
[ccp4bb] CCP4 Update 016
Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. * Qtrview: Now uses runwincoot.bat script to start Wincoot on Windows * MrBUMP: Assumes intensities rather than structure factor amplitudes when calling SHELXE * Pdb_merge: Execution permissions added to binary (Mac OSX and Linux) * Pdbcur: Execution permissions added to binary (Mac OSX and Linux) * Pisa: Execution permissions added to binary (Mac OSX and Linux) * INDEX.html: CCP4 documentation index updated to have link to Aimless program documentation If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have the CCP4 Update Manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Ronan Keegan -- Scanned by iCritical.
[ccp4bb] post-doctoral position in structural virology
Dear all, post-doctoral position is available in Pavel Plevka's group at Ceitec in the Czech Republic: http://www.ceitec.eu/programs/structural-biology/x-ray-crystallography-ii/ The projects involve x-ray crystallography and cryo-electron microscopy of human viruses. If you are interested, details of the jobs and how to apply can be found here: http://www.ceitec.cz/uploads/post_docs_Structural_virology2.pdf All the best, Pavel
