CCP4 wiki - User contributions [en]

Visualization: graphics cards and 3D

2009-02-25T15:29:44Z

Rock34: /* ATI */

== graphics cards and drivers (Linux) ==

For 3D applications like COOT and O, only recently (2007) cheap hardware has become fast enough to ''not'' require proprietary drivers for decent performance. Proprietary drivers (for NVidia, ATI and Intel chips) are usually not open-source and are thus not distributed with the [[Operating_systems_and_Linux_distributions#Linux_Distributions|Linux distros]].
Some distros make it easy to install them through their installation tools; for other distros you have to install and maintain them yourself.

If the open-source Xorg driver (i.e. no proprietary driver) is installed, the output of "glxinfo|head" is something like:
name of display: :0.0
display: :0 screen: 0
direct rendering: No
server glx vendor string: SGI
server glx version string: 1.2
server glx extensions:
GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating,
GLX_EXT_import_context, GLX_EXT_texture_from_pixmap, GLX_OML_swap_method,
GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_hyperpipe,
GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_MESA_copy_sub_buffer
client glx vendor string: SGI

== NVidia ==

NVidia cards are most popular for visualization in protein crystallography. The proprietary driver (called "nvidia" driver in xorg.conf) is stable, and even the cheapest cards are suitable for crystallographic work when it is used.
Some mid-range graphics cards (starting with GeForce x600) are fast enough for useful 3D work even with the drivers that are part of Xorg (called "nv" driver in xorg.conf).

* [http://www.nvidia.com NVidia] - proprietary driver download for Linux at [http://www.nvidia.com/object/unix.html]
* "Latest cards" list at [http://www.nvidia.com/object/IO_18897.html]
* "Legacy cards" list at [http://www.nvidia.com/object/IO_32667.html]
* RedHat/Fedora/Debian/[K]Ubuntu installation information can be found at [http://www.nvnews.net/vbulletin/showthread.php?t=72490]. In particular, for RedHat/Fedora one needs to install the kernel-devel RPM package. Other than this, the information in that posting seems a bit overkill - the NVidia driver usually works very well without any SElinux jiggling.

=== checking the integrity of the NVidia driver ===

If everything is ok with the driver, you get the following output from "glxinfo|head":

<code>
name of display: :0.0
display: :0 screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:
GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
GLX_EXT_texture_from_pixmap, GLX_ARB_multisample, GLX_NV_float_buffer
client glx vendor string: NVIDIA Corporation
</code>

=== maintaining the NVidia driver ===

The proprietary driver works well but it needs a bit of care. More to the point: parts of it need to be re-installed after kernel updates and updates of xorg-x11-* (both of which happen regularly).
On RedHat systems that are regularly booted, the following lines in /etc/rc.local result in the necessary parts of the driver being re-installed automagically after booting:

if [ ! -h /usr/lib/xorg/modules/extensions/libglx.so ]; then
# this should be /usr/lib64/xorg/modules/extensions/libglx.so on a 64bit machine !
echo "re-installing NVIDIA driver. This takes some time. Ignore any warnings."
/root/NVIDIA.run --no-network -s -n
fi

if [ ! -e /lib/modules/`uname -r`/kernel/drivers/video/nvidia.ko ]; then
echo "installing NVIDIA kernel module. This takes some time. Ignore any warnings."
/root/NVIDIA.run --no-network -s -K -n
fi

This requires that you first "chmod +x" the driver package (e.g. NVIDIA-Linux-x86-169.04-pkg1.run) downloaded from the NVidia site, and then establish a symbolic link from it, to /root/NVIDIA.run .

Newer distributions using SELinux may encounter problems with restrictions that prevent init scripts from executing certain commands related to kernel modules. Creating an SELinux rule exception is the correct solution, but may be difficult. A work-around is to insert "/usr/bin/setenforce 0" before running the NVIDIA installer, and "/usr/bin/setenforce 1" afterwards.

== ATI ==

ATI now belongs to AMD. Download the proprietary driver from http://ati.amd.com .
Recently the (open source) [http://www.free3d.org/ radeon driver] shipped with [http://www.x.org Xorg] has improved DRI capabilities that are often sufficient for crystallographic purposes, and the need to hastle with the installation of the propriety driver has become void.

If you are experiencing problems with Coot and ATI graphic cards with rv5xx chipset on FC10, you should switch from the 'radeon' driver to 'radeonhd', for example in the following way (as root):

* yum install system-config-display
* yum install radeonhd
* system-config-display

Now you can conveniently change the graphic card driver via a graphical interface, then restart X windows

Unfortunately, you have to disable 3D desktop effects, otherwise you get a blank screen and have to undo the settings via terminal. Furthermore, do not try to use the proprietary ATI 'fglrx' drivers, since they made things even worse, at least in my personal experience (with an ATI Radeon X1650).

== Intel ==

The X3100 graphics accelerator is known to be quite fast. FIXME: does it require special drivers?

== Table of Cards and drivers ==
{| border="1" cellpadding="0"
|-
|width="70pt"|Brand
|width="100pt"|Model number
|width="100pt"|Distro and/or OS
|width="70pt"|Working ?
|width="100pt"|Driver
|width="200pt"|Remarks
|-
|ATI || Radeon X1300 || Ubuntu 8.10 - Intrepid Ibex || Yes||fglrx|| automagically installed from Ubuntu
|-
|ATI || Radeon 9200 || Ubuntu 8.10 - Intrepid Ibex || Yes||open source radeon|| automagically installed from Ubuntu
|-
|Nvidia||Quadro FX 1400||SuSe 10.2||Yes|| Nvidia||installed from SuSE repos
|}

== See also ==
* [[Stereo]]

Twinning

2008-04-08T11:42:40Z

Rock34: /* Refinement */

== '''Definition''' ==

"Twins are regular aggregates consisting of crystals of the same species joined together in some definite mutual orientation" (Giacovazzo, 2002). So for the description of a twin two things are necessary: a description of the orientation of the different species relative to each other (the twin law) and the fractional contribution of each component. The twin law can be expressed as a matrix that transforms the hkl indices of one species into the other.

== '''Classification''' ==

Depending on the twin law four types of twins can be distinguished:

=== Twinning by Merohedry ===

In a merohedral twin, the twin law is a symmetry operator of the crystal system, but not of the point group of the crystal. This means that the reciprocal lattices of the different twin domains superimpose exactly and the twinning is not directly detectable from the reflection pattern. This type is possible in the trigonal, tetragonal, hexagonal and cubic crystal systems, which have more than one Laue group. The twin law corresponds to the two-fold operation that is present in the apparent Laue group, but not in the true space group. Only for trigonal crystals is there more than one possible twin law.

=== Twinning by Pseudo-Merohedry ===

In a pseudo-merohedral twin, the twin operator belongs to a higher crystal system than the structure. This may happen if the metric symmetry is higher than the symmetry of the structure. Depending on how well the higher metric symmetry is fulfilled, it may happen that the reciprocal lattices overlap exactly and the twinning is not detectable from the diffraction pattern. But, compared to merohedral twins,the number of possible twin laws is much higher.

=== Twinning by Reticular Merohedry ===

Part of the reflections overlaps exactly, while others are non-overlapped. A typical example is an obverse/reverse twin in case of a rhombohedral crystal.

=== Non-Merohedral Twins ===

For non-merohedral twins, the twin law does not belong to the crystal class of the structure nor to the metric symmetry of the cell. Therefore the different reciprocal lattices do not overlap exactly. There are three types of reflections, non-overlapped, partially overlapped and exactly overlapped reflections. Here the problems start in the data collection. If both twin domains are similar in size, there are often problems with the cell determination and usual automatic indexing programs fail. More than one orientation matrix is needed to index all reflections. In the integration process the information of all matrices should be used.

== Tests for Twinning ==

== Solution ==

== Refinement ==

Refinement of merohedral twinned data is possible using [[CNS]] (for input files, see CNS homepage - main menu - input files - x ray - twinning) . Pseudo-merohedrally twinned data can be refined with [[SHELXL]] ([http://shelx.uni-ac.gwdg.de/~rherbst/twin.html Twin-Refinement with SHELXL]) and [[PHENIX]] ([http://www.phenix-online.org/documentation/refinement.htm#anch144 Refinement using twinned data]).

== '''Warning Signs for Twinning''' ==
Experience shows that there are a number of characteristic warning signs of twinning, as given in the following list. Of course not all of them can be present in any particular example, but if one or several apply, the possibility of twinning should be given serious consideration.

a) The metric symmetry is higher than the Laue symmetry.

b) The Rint-value for the higher symmetry Laue group is only slightly higher than for the lower symmetry Laue group.

c) If different crystals of the same compound show significantly different Rint values for the higher symmetry Laue group, this clearly shows that the lower symmetry Laue group is correct and indicates different extents of twinning.

d) The mean value for |E^2-1| is much lower than the expected value of 0.736 for the non-centrosymmetric case (see also [[Intensity statistics]]). If we have two twin domains and every reflection has contributions from both, it is unlikely that both contributions will have very high or that both will have very low intensities, so the combined intensities are distributed to give fewer extreme values.

e) The space group appears to be trigonal or hexagonal.

f) The apparent systematic absences are not consistent with any known space group.

g) Although the data appear to be in order, the structure cannot be solved. This may of course also happen if the cell is wrong, for example with an halved axis

h) The Patterson function is physically impossible.

The following features are typical of non-merohedral twins, where the reciprocal lattices do not overlap exactly and only some of the reflections are affected by the twinning:

i) There appear to be one or more unusually long axes.

j) There are problems with the unit cell refinement.

k) Some reflections are sharp, others split.

l) K = mean(Fo^2)/mean(Fc^2) is systematically high for reflections with low intensity. This may also indicate a wrong choice of space group in the absence of twinning.

== References ==

Giacovazzo, C. ed. (2002). Fundamentals in Crystallography, I.U.Cr. & O.U.P.: Oxford, UK.

Twinning

2008-04-03T15:36:43Z

Rock34: /* Refinement */

== '''Definition''' ==

"Twins are regular aggregates consisting of crystals of the same species joined together in some definite mutual orientation" (Giacovazzo, 2002). So for the description of a twin two things are necessary: a description of the orientation of the different species relative to each other (the twin law) and the fractional contribution of each component. The twin law can be expressed as a matrix that transforms the hkl indices of one species into the other.

== '''Classification''' ==

Depending on the twin law four types of twins can be distinguished:

=== Twinning by Merohedry ===

In a merohedral twin, the twin law is a symmetry operator of the crystal system, but not of the point group of the crystal. This means that the reciprocal lattices of the different twin domains superimpose exactly and the twinning is not directly detectable from the reflection pattern. This type is possible in the trigonal, tetragonal, hexagonal and cubic crystal systems, which have more than one Laue group. The twin law corresponds to the two-fold operation that is present in the apparent Laue group, but not in the true space group. Only for trigonal crystals is there more than one possible twin law.

=== Twinning by Pseudo-Merohedry ===

In a pseudo-merohedral twin, the twin operator belongs to a higher crystal system than the structure. This may happen if the metric symmetry is higher than the symmetry of the structure. Depending on how well the higher metric symmetry is fulfilled, it may happen that the reciprocal lattices overlap exactly and the twinning is not detectable from the diffraction pattern. But, compared to merohedral twins,the number of possible twin laws is much higher.

=== Twinning by Reticular Merohedry ===

Part of the reflections overlaps exactly, while others are non-overlapped. A typical example is an obverse/reverse twin in case of a rhombohedral crystal.

=== Non-Merohedral Twins ===

For non-merohedral twins, the twin law does not belong to the crystal class of the structure nor to the metric symmetry of the cell. Therefore the different reciprocal lattices do not overlap exactly. There are three types of reflections, non-overlapped, partially overlapped and exactly overlapped reflections. Here the problems start in the data collection. If both twin domains are similar in size, there are often problems with the cell determination and usual automatic indexing programs fail. More than one orientation matrix is needed to index all reflections. In the integration process the information of all matrices should be used.

== Tests for Twinning ==

== Solution ==

== Refinement ==

Refinement of merohedral twinned data is possible using [[CNS]] (for input files, see CNS homepage - main menu - input files - x ray - twinning) . Pseudo-merohedrally twinned data can be refined with SHELXL ([http://shelx.uni-ac.gwdg.de/~rherbst/twin.html Twin-Refinement with SHELXL]) and [[PHENIX]] ([http://www.phenix-online.org/documentation/refinement.htm#anch144 Refinement using twinned data]).

== '''Warning Signs for Twinning''' ==
Experience shows that there are a number of characteristic warning signs of twinning, as given in the following list. Of course not all of them can be present in any particular example, but if one or several apply, the possibility of twinning should be given serious consideration.

a) The metric symmetry is higher than the Laue symmetry.

b) The Rint-value for the higher symmetry Laue group is only slightly higher than for the lower symmetry Laue group.

c) If different crystals of the same compound show significantly different Rint values for the higher symmetry Laue group, this clearly shows that the lower symmetry Laue group is correct and indicates different extents of twinning.

d) The mean value for |E^2-1| is much lower than the expected value of 0.736 for the non-centrosymmetric case (see also [[Intensity statistics]]). If we have two twin domains and every reflection has contributions from both, it is unlikely that both contributions will have very high or that both will have very low intensities, so the combined intensities are distributed to give fewer extreme values.

e) The space group appears to be trigonal or hexagonal.

f) The apparent systematic absences are not consistent with any known space group.

g) Although the data appear to be in order, the structure cannot be solved. This may of course also happen if the cell is wrong, for example with an halved axis

h) The Patterson function is physically impossible.

The following features are typical of non-merohedral twins, where the reciprocal lattices do not overlap exactly and only some of the reflections are affected by the twinning:

i) There appear to be one or more unusually long axes.

j) There are problems with the unit cell refinement.

k) Some reflections are sharp, others split.

l) K = mean(Fo^2)/mean(Fc^2) is systematically high for reflections with low intensity. This may also indicate a wrong choice of space group in the absence of twinning.

== References ==

Giacovazzo, C. ed. (2002). Fundamentals in Crystallography, I.U.Cr. & O.U.P.: Oxford, UK.

Twinning

2008-04-03T15:35:03Z

Rock34: /* Refinement */

== '''Definition''' ==

"Twins are regular aggregates consisting of crystals of the same species joined together in some definite mutual orientation" (Giacovazzo, 2002). So for the description of a twin two things are necessary: a description of the orientation of the different species relative to each other (the twin law) and the fractional contribution of each component. The twin law can be expressed as a matrix that transforms the hkl indices of one species into the other.

== '''Classification''' ==

Depending on the twin law four types of twins can be distinguished:

=== Twinning by Merohedry ===

In a merohedral twin, the twin law is a symmetry operator of the crystal system, but not of the point group of the crystal. This means that the reciprocal lattices of the different twin domains superimpose exactly and the twinning is not directly detectable from the reflection pattern. This type is possible in the trigonal, tetragonal, hexagonal and cubic crystal systems, which have more than one Laue group. The twin law corresponds to the two-fold operation that is present in the apparent Laue group, but not in the true space group. Only for trigonal crystals is there more than one possible twin law.

=== Twinning by Pseudo-Merohedry ===

In a pseudo-merohedral twin, the twin operator belongs to a higher crystal system than the structure. This may happen if the metric symmetry is higher than the symmetry of the structure. Depending on how well the higher metric symmetry is fulfilled, it may happen that the reciprocal lattices overlap exactly and the twinning is not detectable from the diffraction pattern. But, compared to merohedral twins,the number of possible twin laws is much higher.

=== Twinning by Reticular Merohedry ===

Part of the reflections overlaps exactly, while others are non-overlapped. A typical example is an obverse/reverse twin in case of a rhombohedral crystal.

=== Non-Merohedral Twins ===

For non-merohedral twins, the twin law does not belong to the crystal class of the structure nor to the metric symmetry of the cell. Therefore the different reciprocal lattices do not overlap exactly. There are three types of reflections, non-overlapped, partially overlapped and exactly overlapped reflections. Here the problems start in the data collection. If both twin domains are similar in size, there are often problems with the cell determination and usual automatic indexing programs fail. More than one orientation matrix is needed to index all reflections. In the integration process the information of all matrices should be used.

== Tests for Twinning ==

== Solution ==

== Refinement ==

Refinement of merohedral twinned data is possible using [[CNS]] (for input files, see CNS homepage - main menu - input files - x ray - twinning) . Pseudo-merohedrally twinned data can be refined with SHELXL ([http://shelx.uni-ac.gwdg.de/~rherbst/twin.html Twin-Refinement with SHELXL]) and [[PHENIX]] ([http://www.phenix-online.org/documentation/refinement.htm Structure refinement in PHENIX]).

== '''Warning Signs for Twinning''' ==
Experience shows that there are a number of characteristic warning signs of twinning, as given in the following list. Of course not all of them can be present in any particular example, but if one or several apply, the possibility of twinning should be given serious consideration.

a) The metric symmetry is higher than the Laue symmetry.

b) The Rint-value for the higher symmetry Laue group is only slightly higher than for the lower symmetry Laue group.

c) If different crystals of the same compound show significantly different Rint values for the higher symmetry Laue group, this clearly shows that the lower symmetry Laue group is correct and indicates different extents of twinning.

d) The mean value for |E^2-1| is much lower than the expected value of 0.736 for the non-centrosymmetric case (see also [[Intensity statistics]]). If we have two twin domains and every reflection has contributions from both, it is unlikely that both contributions will have very high or that both will have very low intensities, so the combined intensities are distributed to give fewer extreme values.

e) The space group appears to be trigonal or hexagonal.

f) The apparent systematic absences are not consistent with any known space group.

g) Although the data appear to be in order, the structure cannot be solved. This may of course also happen if the cell is wrong, for example with an halved axis

h) The Patterson function is physically impossible.

The following features are typical of non-merohedral twins, where the reciprocal lattices do not overlap exactly and only some of the reflections are affected by the twinning:

i) There appear to be one or more unusually long axes.

j) There are problems with the unit cell refinement.

k) Some reflections are sharp, others split.

l) K = mean(Fo^2)/mean(Fc^2) is systematically high for reflections with low intensity. This may also indicate a wrong choice of space group in the absence of twinning.

== References ==

Giacovazzo, C. ed. (2002). Fundamentals in Crystallography, I.U.Cr. & O.U.P.: Oxford, UK.