[ccp4bb] FW: [ccp4bb] off topic: DSSP
---BeginMessage--- Hi, I thought the latest version of dssp ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz contains the fixes to build a Mac version. However, it may be you have to remove the -static flag from the Makefile. If so, please let me know, I have no Mac capable of running 10.5 to test this. If it doesn't work, please send me the output so I can try to infer the required extra changes. best regards, -maarten Van: Robbie Joosten [robbie_joos...@hotmail.com] Verzonden: zaterdag 26 januari 2013 10:16 Aan: Maarten Hekkelman Onderwerp: FW: [ccp4bb] off topic: DSSP Hoi Maarten, Enig idee? Groetjes, Robbie Sent from my Windows Phone From: Rashmi Panigrahi Sent: 2013-01-26 10:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off topic: DSSP 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.tbzftp://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-lin ux-amd64 dssp-2.1.0.tgzftp://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 -- rashmi Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. ---End Message---
Re: [ccp4bb] CCP4 Update 015
Dear Boaz, If that was not done, it's an oversight. Surely this is possible, will have a look into. Thanks for reporting (but please use c...@stfc.ac.uk for future bug reports please), Eugene On 26 Jan 2013, at 14:00, Boaz Shaanan wrote: Dear Developers, As part of the wonderful work you're doing with development and upgrades, would it be possible to also update the INDEX.html in the $CCP4/html directory whenever a new program html is entered into this directory (e.g. the latest aimless.html)? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ville Uski [ville.u...@stfc.ac.uk] Sent: Saturday, January 26, 2013 1:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 Update 015 Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. * Ctruncate: Memory leak fixed. * Aimless, Pointless, Ctruncate: Documentation updated following previous changes. 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. Ville Uski -- Scanned by iCritical. -- Scanned by iCritical.
[ccp4bb] gedit on mac terminal
Hi all, I installed gedit on my mac applications. But i can not use it by terminal. Please help me figure it out. Thanks. lisa
Re: [ccp4bb] gedit on mac terminal
Try this http://www.mac-forums.com/forums/os-x-apps-games/239657-gedit-command-not-found-terminal.html Original message From: LISA science...@gmail.com Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] gedit on mac terminal Hi all, I installed gedit on my mac applications. But i can not use it by terminal. Please help me figure it out. Thanks. lisa
[ccp4bb] freerflag bug
FREERFLAG fails as part of the uniqueify script to complete a test set on a cif-file downloaded from the PDB. My observations: 1) The bug is version-dependent - freerflag 6.2 succeeds, freerflag 1.1 fails (comes with ccp4 6.3, apparently newer than version 6.2 from ccp4 6.2) 2) The input cif-file has 105382 working and 502 test reflections (deposited pdb file confirms that as a relatively small 0.5% test set size). 3) freerflag throws this error Error in LWREFL_NOEXIT: mindx 2 not open for write! FREERFLAG: LWREFL: failed to write reflection I have not done any updates since 6.3.0, but I do not see any mention of freerflag in updates summary. I can supply the input mtz file that produces the error if needed. Thanks, Ed. -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] freerflag bug
Hi Ed, I've had this problem as well. It's the result of the very small R-free set fraction. There is an error routine that catches really small R-free sets, but 0.5% gets through and triggers ar problem. My workaround is to just use a larger R-free set fraction (more than 1%). The version number is actually an improvement: 6.2 was just the version of CCP4. The program now has its own version number. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edwin Pozharski Sent: Saturday, January 26, 2013 22:06 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] freerflag bug FREERFLAG fails as part of the uniqueify script to complete a test set on a cif- file downloaded from the PDB. My observations: 1) The bug is version-dependent - freerflag 6.2 succeeds, freerflag 1.1 fails (comes with ccp4 6.3, apparently newer than version 6.2 from ccp4 6.2) 2) The input cif-file has 105382 working and 502 test reflections (deposited pdb file confirms that as a relatively small 0.5% test set size). 3) freerflag throws this error Error in LWREFL_NOEXIT: mindx 2 not open for write! FREERFLAG: LWREFL: failed to write reflection I have not done any updates since 6.3.0, but I do not see any mention of freerflag in updates summary. I can supply the input mtz file that produces the error if needed. Thanks, Ed. -- Edwin Pozharski, PhD University of Maryland, Baltimore
[ccp4bb]
Dear all I have solved one structure at resolution 2.6 Angstrom in the space group P212121. The R/ Rfree are 22 / 26 with FOM of .806, but when i am trying to upload on the online validation server its not working. Just to cross check there is no problem with my mtz i took altogether unrelated mtz file and saw it working. i am not able to figure out whats wrong with my mtz. its giving structure, refining well but not working with the submission procedure. -- Regards Faisal School of Life Sciences JNU
