[COOT] Problem with Coot validation after Phenix twinned refinement
Hello all, I have just been experimenting with the refinement options for twinned data in phenix.refine (final 1.3 version), and I ran into a strange problem with the density fit validation function in Coot 0.4 and 0.5. When I "auto-open" the MTZ file with map coefficients produced by phenix.refine, I get a normal-looking map, but every single residue in the density fit plot is squarely in the red. When I open the 2Fo-Fc CNS format file also produced by phenix.refine, I get a map that looks identical to the first one, and when I validate the same model against the new map, I get the normal density fit pattern, with most residues in the green, and the occasional orange one. So it seems that the density fit calculation goes wrong for MTZ files from twinned refinement. Does anyone know what might be causing this? I can send the data files if required. Cheers, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel
Re: [COOT] Problem with Coot validation after Phenix twinned refinement
brr at the moment, the maps are indeed not on absolute scale, will change that. P 2008/10/10 Paul Emsley <[EMAIL PROTECTED]>: > Lieven Buts wrote: >> >> Hello all, >> >> I have just been experimenting with the refinement options for twinned >> data >> in phenix.refine (final 1.3 version), and I ran into a strange problem >> with >> the density fit validation function in Coot 0.4 and 0.5. When I >> "auto-open" >> the MTZ file with map coefficients produced by phenix.refine, I get a >> normal-looking map, but every single residue in the density fit plot is >> squarely in the red. When I open the 2Fo-Fc CNS format file also produced >> by phenix.refine, I get a map that looks identical to the first one, and >> when I validate the same model against the new map, I get the normal >> density fit pattern, with most residues in the green, and the occasional >> orange one. So it seems that the density fit calculation goes wrong for >> MTZ files from twinned refinement. Does anyone know what might be >> causing this? I can send the data files if required. > > > Randy Read told me about this issue the other day. > > The density fit graphs work assuming that the map is on the absolute scale - > I suspect that your maps have a different scale (test by looking at the > absolute level given the same number of sigma). It would be better if Coot > used correlation vs a calculated map, but today it does not. > > You can adjust the scale using Extensions -> Refine -> Set Density Fit Graph > Weight [1] > > [1] I may move this soon - Settings would seem a better submenu. > > Paul. > -- - P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -
Re: [COOT] Problem with Coot validation after Phenix twinned refinement
Lieven Buts wrote: Hello all, I have just been experimenting with the refinement options for twinned data in phenix.refine (final 1.3 version), and I ran into a strange problem with the density fit validation function in Coot 0.4 and 0.5. When I "auto-open" the MTZ file with map coefficients produced by phenix.refine, I get a normal-looking map, but every single residue in the density fit plot is squarely in the red. When I open the 2Fo-Fc CNS format file also produced by phenix.refine, I get a map that looks identical to the first one, and when I validate the same model against the new map, I get the normal density fit pattern, with most residues in the green, and the occasional orange one. So it seems that the density fit calculation goes wrong for MTZ files from twinned refinement. Does anyone know what might be causing this? I can send the data files if required. Randy Read told me about this issue the other day. The density fit graphs work assuming that the map is on the absolute scale - I suspect that your maps have a different scale (test by looking at the absolute level given the same number of sigma). It would be better if Coot used correlation vs a calculated map, but today it does not. You can adjust the scale using Extensions -> Refine -> Set Density Fit Graph Weight [1] [1] I may move this soon - Settings would seem a better submenu. Paul.
[COOT] Nucleotide Builder
I'm using the 'Ideal DNA/RNA...' function. When I try to build A-form RNA, I get what I want. When I ask for B-form RNA, I get DNA! Looks like something to fix... Many thanks
Re: [COOT] Nucleotide Builder
I agree, but why do you want to build B-form RNA? On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote: I'm using the 'Ideal DNA/RNA...' function. When I try to build A- form RNA, I get what I want. When I ask for B-form RNA, I get DNA! Looks like something to fix... Many thanks
[COOT] Centos5 64-bit install notes
I have finally gotten coot to compile on my Centos5 64-bit computer. Both the autobuild flavors (i.e. build-it and build-it-gtk2-simple) failed to compile coot so I compiled everything manually following the same order in the build-it script. My install and the dependencies are not in /usr/local (or /srv/local64 in my case) and I try to keep each program I install in its own directory so multiple versions are present in case you need to fall back to a previous version so this may have confused the autobuild script. Also, since I was installing manually, I decided to put all the coot dependencies in a separate "deps" directory within the coot directory so future builds wouldn't need to have the dependencies built each time (i.e. "/srv/local64/programs/coot/" contains "deps/" "0.4.1/" and "0.5/" directories within it). I was able to use the autobuild script for version 0.4.1 but I don't remember if I had Centos5 or RHEL4 installed then. Here are things I needed to do to get the manual install to work in case someone else wants to have a go at it. - setenv LD_LIBRARY_PATH /srv/local64/programs/coot/deps/lib:/srv/local64/lib:/usr/lib64 - setenv PKG_CONFIG_PATH /srv/local64/programs/coot/deps/lib/pkgconfig:/srv/local64/lib/pkgconfig:/us r/lib64/pkgconfig - set generic_prefix = /srv/local64/programs/coot/deps - set path = ( $generic_prefix/bin $path ) - cd into each dependency's directory and 1) "make clean" to remove the autobuilder stuff 2) configure as seen in the build-it script, including applying any patches/modifications that would have been changed when re-running configure. 3) make 4) make install *** For guile-gtk-0.41, there is a problem when it looks for one library file (/usr/lib/libgdk_pixbuf.so). It should be looking in /usr/lib64 instead. I temporally removed the link in /usr/lib and made it point to /usr/lib64. Once it was compiled and installed, I fixed the link - compile coot with the following: ./configure --prefix=/srv/local64/programs/coot/0.5 --with-gtkcanvas-prefix=$generic_prefix --with-mmdb-prefix=$generic_prefix --with-clipper-prefix=$generic_prefix --with-ssmlib-prefix=$generic_prefix --with-gtkgl-prefix=$generic_prefix --with-glut-prefix=$generic_prefix --with-guile --with-guile-gtk --with-guile-gtk-prefix=$generic_prefix --disable-shared CXXFLAGS="-g -O" make make install - Needed to link the guilegtk library files from /srv/local64/programs/coot/deps/lib/ to /srv/local64/lib (since this path is not in /etc/ld.so.conf??). ln -s /srv/local64/programs/coot/deps/lib/libguilegtk* /srv/local64/lib James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED]
Re: [COOT] Nucleotide Builder
I'm just interested in taking one residue (a 5'-AMP or 3',5'-ADP with the ribose in the C2'-endo conformation) and using it as the basis for a novel ligand. On Fri, 10 Oct 2008 09:13:57 -0700, William G. Scott <[EMAIL PROTECTED]> wrote: >I agree, but why do you want to build B-form RNA? > >On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote: > >> I'm using the 'Ideal DNA/RNA...' function. When I try to build A- >> form RNA, >> I get what I want. When I ask for B-form RNA, I get DNA! Looks like >> something to fix... >> >> Many thanks
Re: [COOT] Nucleotide Builder
Oh, I thought you had discovered a new form of RNA. You might want to use phenix's elbow builder module. Then you will have a cif file for the ligand too. On Oct 10, 2008, at 9:36 AM, Daniel Holloway wrote: I'm just interested in taking one residue (a 5'-AMP or 3',5'-ADP with the ribose in the C2'-endo conformation) and using it as the basis for a novel ligand. On Fri, 10 Oct 2008 09:13:57 -0700, William G. Scott <[EMAIL PROTECTED]> wrote: I agree, but why do you want to build B-form RNA? On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote: I'm using the 'Ideal DNA/RNA...' function. When I try to build A- form RNA, I get what I want. When I ask for B-form RNA, I get DNA! Looks like something to fix... Many thanks
