v0.25

Important Changes

・Supports files with multiple MODELs.

New Options

[-nomodelname]
Does not print the model name (id) in the texture.

[-first_model]
Uses only the first MODEL.

v0.24

Important Changes

・.svg file will not be generated without the option [-save_svg].

New Features

・gzip support for .pdb, .cif, or .sdf files.

New Options

*If the -plain_input or -gz_input option is not specified, the file format will be determined automatically from the file name.
[-plain_input]
Input .pdb, .cif, or .sdf files are treated as plain ascii files.

[-gz_input]
Input .pdb.gz, .cif.gz, or .sdf.gz files are treated as gzip-ed files.

[-save_svg]
Outputs .svg files for texture.

v0.23.5

Bug Fix

・Fixed bug that the program does not stop when duplicate option is found.
・Fixed bug that the program can not process two adjacent comment lines in mmcif.
・Fixed bug that the program can not process TER record without chain name.

New Options

・[-quiet (0:print all output, 1: print simple output, 2: print nothing)]
Changes the level of output messages.

v0.23.3

Bug Fix

・Fixed bug which causes infinite loops in unwrapping step

Changes

・Trianglate faces before unwrap

New option

・[-voronoi_image_size int_value (default:2000)]
Change size of the image used in slice.

v0.23.2

Bug fix

• Fixed bug that all residues become "gray" with "-useca" or "-usebackbone" options.
• Fixed bug that behavior of "-usebackbone" is the same with that of "-useca".

Changes

• DA, DT, DG, DC, DU, DI, DN, A, G, C, U, I, and N are now considered as DNA or RNA .
• Atoms with its alt code "A" are not removed by "-noalt" option.
• PYL is converted to "O" in -residue_oneletter mode.

0.23.1

Changes

• Updated readme.txt (SurfStamp_src.zip is the same with the one in 0.23).

0.23

New Options

[-asym_surface asym_ids]
Pass comma-separated asym_ids and they will be used for surface model.

[-asym_dnarna asym_ids]
Pass comma-separated asym_ids and they will be used for fancy nucleotide model.

[-asym_ballandstick asym_ids]
Pass SLASH-separated asym_ids and they will be used for surface model.
If the ids are comma-separated, the asym units will be auto-connected.
e.g. -asym_ballandstick A,B/C
makes bonds between atoms in A and atoms in B (and of-course atoms in the same asym units). Bonds between "atoms in A and atoms in C" and "atoms in B and atoms in C" are not created.

[-sep_block]
Separate faces much more frequently. This is recommended for cartoon models made by PyMOL.

[-ignore_occupancy]
Do not darken low occupancy regions.

[-color_missing]
Turn off the function to put gray color on residues which have missing atoms or next to the missing residues.

Changes

• Color for carbon atoms are set to 255,255,255

v 0.22.1

Bug fix

• I found several bugs in Color preset.
  I sincerely sorry for inconvenience.
• Cysteine -> Pink .
• Exchanged colors between Chain 73 and 74.
• Changed colors for DNA or RNA
  A->Red
  U,T->Green
  C->Blue
  G->Orange
• Changed color for atom S (Yellow).
• Added atom NA and FR.
• Removed atom KA and removed atom PE.
  (I think they are typos...)

Changes

• Added some texts in readme.txt.

v 0.22

Bug fix

・Fixed bug in applying PDBX_STRUCT_ASSEMBLY_GEN in mmcif.

Changes

・To fix above bug (+ other reasons), I had to modify fundamental portion of the codes. Please let me know if you find something unexpected.

New feature

・Added "-color_scheme 7" option which uses gradient of chain colors for background.

v 0.21.1

Bug fix

・Fixed bug that produces irregular outlines with very small faces.