Re: [COOT] Coot 0.5.2 and Molprobity problem
Hi Ben, Ben Eisenbraun wrote: I seem to be running into the same problem reported by other people with Coot showing a blank clashes window. I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with probe 2.12 and reduce 3.13. Probe/reduce seem to run correctly; I get a coot-molprobity output directory with files and their exit status is 0, but the dots are never drawn and the Molprobity Probe Clash Gaps window is blank with just a single OK button. I am using 2.12.071128 and that works fine on my Ubuntu machine. On my FC4 machine that causes an immediate crash. However, 2.12.070727 doesn't crash but behaves in the same manner as you describe. look at probe-dots.out. If you have (something like) :1->1:wc:A 6 VAL HG13 :A 92 ILE HA : that fails. If you have :1->1:wc: A 6 VAL HG13 : A 92 ILE HA : that works. Or so I think. If that is not the issue, then I don't know what it is. (The format change is to support hybrid_36 pdb files). An email in a similar thread from Bernhard Lohkamp on 11/18 suggested that if the window was blank, the version of probe was too old, but I don't see a more recent version. We encouraged them to make a new version for Windows. It would be nice if I could have a version that worked on FC4 too. Any clues on what I'm doing wrong would be much appreciated. HTH? See you soon, Paul.
Re: [COOT] Coot 0.5.2 and Molprobity problem
Hi, The Phenix Molprobity binaries work for me on Coot 0.5 pre1 rev 1563 and 0.5 rev 1444. I can't say for Coot 5.2. I should do an update I guess, but I'm having a pause after CCP4 6.1, and Phenix 1.4.3. Updating Phenix also updates molprobity binaries too, which is handy: (define *probe-command* "/usr/local/phenix/phenix-1.4- 3/build/intel-linux-2.6/bin/phenix.probe") (define *reduce-command* "/usr/local/phenix/phenix-1.4-3/build/intel-linux-2.6/bin/phenix.reduce") These are the phenix versions, which work for me. probe.2.12.071128 reduce.3.14.080821 ...whereas these don't work and just give the blank windows and no pink clashes. probe.2.12.070727 reduce.3.10.080107 so be careful with the minor, minor version numbers! HTH, Mark 2009/1/7 Paul Emsley > Hi Ben, > > Ben Eisenbraun wrote: > > I seem to be running into the same problem reported by other people with >> Coot showing a blank clashes window. >> >> I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with >> probe 2.12 and reduce 3.13. Probe/reduce seem to run correctly; I get a >> coot-molprobity output directory with files and their exit status is 0, >> but >> the dots are never drawn and the Molprobity Probe Clash Gaps window is >> blank with just a single OK button. >> > > I am using 2.12.071128 and that works fine on my Ubuntu machine. > > On my FC4 machine that causes an immediate crash. However, 2.12.070727 > doesn't crash but behaves in the same manner as you describe. > > look at probe-dots.out. If you have (something like) > :1->1:wc:A 6 VAL HG13 :A 92 ILE HA : > that fails. > > If you have > :1->1:wc: A 6 VAL HG13 : A 92 ILE HA : > that works. > > Or so I think. If that is not the issue, then I don't know what it is. > (The format change is to support hybrid_36 pdb files). > > An email in a similar thread from Bernhard Lohkamp on 11/18 suggested that >> if the window was blank, the version of probe was too old, but I don't see >> a more recent version. >> > > We encouraged them to make a new version for Windows. It would be nice if > I could have a version that worked on FC4 too. > > Any clues on what I'm doing wrong would be much appreciated. >> > > HTH? > > See you soon, > > Paul. > -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
[COOT] no way to calculate an E map
At present the only way to calculate an E map via "the input option to read an MTZ file" is to redefine the COLUMN type of E to that of F Could this be fixed please? Eleanor
Re: [COOT] no way to calculate an E map
In message <4964b4e6.4000...@ysbl.york.ac.uk> e.dod...@ysbl.york.ac.uk writes: > At present the only way to calculate an E map via "the input option to > read an MTZ file" is to redefine the COLUMN type of E to that of F Bleugh. > Could this be fixed please? Certainly. Paul.
Re: [COOT] Coot 0.5.2 and Molprobity problem
Hi Paul (and Mark), > I am using 2.12.071128 and that works fine on my Ubuntu machine. > > On my FC4 machine that causes an immediate crash. However, 2.12.070727 > doesn't crash but behaves in the same manner as you describe. Argh. It was the minor, minor version that got me. As you pointed out, it works fine with the latest version. > We encouraged them to make a new version for Windows. It would be nice > if I could have a version that worked on FC4 too. Hmm, I just tested this on my FC4 virtual machine, and it seems to work okay here. This is the Coot 0.5.2-CentOS 4-python-gtk2 binary download, probe.2.12.071128.linuxi386 and a hand-compiled reduce.3.13.080428, since the download version doesn't like the glibc on FC4. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu
