FAQ (Frequently Asked Questions)

What file can sv decode

"sv" can read shelx series output file and CIF or CSD(FDAT) format file. When optional filename is omitted in command line, "sv" searches "shelxl.res", "shelxl.ins", "shelxb.out" and "shelxs.res" as defaults, and the first file found is used. This sequence can be changed by $SVBINDIR/svx.ini or ~/.svx. Sample(defaults) svx.ini is in the source archive. You need some external program (quasar, perl,...) to use with CIF.

How to make specified atom centering

Use "view" command. "vw CO1" make the CO1 atom centering in the model window.

How to view along axes

Use "view" command with axis name. For example, use "view a" or "view x" to view along a axis. You can't use "view c" to view along c axis. Use "view z" instead of it.

How to rotate stereo diagrams

You can rotate stereo diagrams using right button drag or command. If you feel difficult to rotate with mouse, you can use cursor key to rotate around x and y axes.

How to find atoms in the specified distance from specified atom

Use "bond" command. "bond <atom> <distance>"

How to draw packing diagrams

You can use "pack" commands with some optional parameters. [xref] CmdList

How to hide atoms from model window.

Use "omit" command. For example, "omit h" means that remove all atoms that have name begin with "h".

How to recover hidden atoms.

Use "include" command.

How to select multiple atoms with mouse

You can select rectangular range using left button drag. You can select one 'molecule' using Ctrl Key + left button click.

How to generate atoms by symmetry expansion.

Sorry, not yet supported. Use combination of "pack","pack2" and "omit" command.

Cavity

What is the direction of axis

The direction of x,y,z axis are relative to the screen. x-axis is from left to right, y-axis is from bottom to top, z-axis is from other side to this side. Origin is the gravity center of displayed atoms if you select automatic range.

What is grid size

Grid size is the parameter of mesh density. Selection of smaller size causes longer calculation time and precise volume. You should select 0.3-0.5 to check the shape of cavity, 0.1 for volume calculation. Smaller than 0.1 value is usually meaningless, since the precision of coordinates of hydrogen atoms is not so good.

How to hide cavity drawing from model window.

Type "readmeta" at the command window. You can redisplay it again with "readmeta cav.ps".

How to calculate continuous cavity along symmetry expanded molecules.

Before calculation, use "pack" command and select atoms in the cavity. Usually you need to set calculation range manually.

How to draw cavity from disordered structure.

You can calculate in a usual way, but please reconsider if it is meaningful or not. Usually you should reconsider what value is meaningful for you.

Ortep

How to draw smaller size figure.

After generation of ortep input data, edit ortep.in at 301(paper size) command line. Or use 603(Manual Scaling) instead of 604 (Auto Scaling).

How to draw/hide atom label.

At once, quit ortep. Then type "include label" or "omit label" at the sv command window. Export ortep file again.