2.06 ********************
* MAPVIEW WRITE-UP *
********************
MAPVIEW is an interactive program to contour and display electron
density map sections, display mask sections and to facilitate
construction of one or more "molecular masks", by allowing one to
interactively "trace out" envelope boundaries with a cursor tied to a
mouse. The selected map (and mask) regions may be output for use in
other programs, or simply displayed on a workstation monitor. The
program is extremely useful for examining ANY map, be it an electron
density, difference density or Patterson map, but it is essential for
creation of molecular masks for use in noncrystallographic symmetry
averaging. The program functions interactively, and must be run on a
workstation with a color monitor. Two program versions are available,
one specific for Silicon Graphics systems which uses the GL, and another
(called mapview_X) which uses X-window graphics. The X-window version
also functions on SGI hardware, but the original mapview runs only
on SGI systems. If running mapview on an SGI, be sure to initiate the
program from a WINTERM window (as opposed to from an XTERM window).
mapview_X can be initiated from either window type. Both programs use
only the left and middle mouse buttons to accept user input (and the
keyboard). When either program is started up, the following sequence
of events takes place.
***** MAP SELECTION *****
The program first prompts the user for the name of a "map" file, and
inquires whether or not it is a "FSFOUR" type file. Usually it will be
a FSFOUR file (which runs over the whole unit cell), but if not, one
can input a map as an "averaging" style file (e.g xz sections, as
generated by EXTRMAP,MAPORTH,MAPAVG,SKEW or the saved output from an
earlier run of this program).
***** MASK SELECTION *****
The program then prompts to find out whether a mask will be created or
used. If one simply wants to look at contoured maps it won't, but to
create/examine/edit masks for noncrystallographic symmetry averaging
purposes or to look at solvent boundary maps answer yes. If yes, the
program prompts as to whether a previously created mask file should be
used, and if so, for the file name.
***** MAP REGION SELECTION INFORMATION *****
If a "FSFOUR" style map was input, the program then prompts for the
minimum and maximum coordinates in each direction, to define the
region to be displayed. Any values are allowed (including multiple
cells, i.e. the range can span one or more cell edges, as any needed
unit cell translations will be done automatically). The program then
prompts for the desired section orientation, i.e xz, xy or yz
sections. Note that if a previously created mask file is recovered,
then only xz sections can be used, and the range selected MUST cover
EXACTLY that used when the mask was created. For looking at the
solvent masks created by BNDRY this means one must select the entire
cell, i.e x,y,z all ranging from 0. to 0.999, although program EXTRMSK
can be used first if a different region must be chosen. If an
"averaging" style map was input this section is bypassed as only xz
sections are possible, and the range will cover precisely that in the
input map.
***** SECTION SELECTION INFORMATION *****
The program will then inform the user as to how many map sections are
present, how they are numbered, and inquire which section should be
displayed initially.
***** CONTOUR LEVEL INFORMATION *****
The program then informs the user what the minimum, maximum and sigma
values for the entire input electon density map are. It then prompts
for minimum, maximum and increment values for contour levels. The
program then contours and displays the requested section, and enters
interactive mode.
*************** I N T E R A C T I V E M O D E ***************
When in interactive mode, a menu is displayed and all subsequent
actions are requesed by the user pressing the left mouse button while
the cursor is in the desired menu option area. The following actions
then take place, when the appropriate item is selected.
***** NEXT SECTION OPTION *****
Replaces the display with the contoured map corresponding to the next
(adjacent, higher) map section
***** PREV SECTION OPTION *****
Replaces the display with the contoured map corresponding to the
previous (adjacent, lower) map section
***** NEW SECTION OPTION *****
Prompts user for section to be displayed. It lets the user "jump
around" the map, rather than having to scroll up or down with
multiple "prev" or "next" requests.
***** C LEVEL OPTION *****
Prompts user for new contour level information, then recontours and
displays the currently selected section.
***** NEW DIRECTION OPTION *****
Allows user to reselect display region range and/or map orientation.
Allowed only when FSFOUR style maps are in use.
***** ADD NEXT SECTION OPTION *****
Contours and displays next (adjacent, higher) section, but doesn't
clear old one first, i.e can be used to create projections, since the
contoured sections accumulate one on top of another on the screen.
Note!! There is no "shifting" as sections are added, thus projections
are strictly true only when viewed down an axis orthogonal to the
section. (When only a small number of sections are accumulated it is
reasonably valid even for nonorthogonal systems, as long as the cell
angles are not extreme).
***** ADD PREV SECTION OPTION *****
Same as "ADD NEXT SECTION" option, but the previous (adjacent, lower)
section is contoured and added. Same considerations as above.
***** SET MASK NO. OPTION *****
Active only when masks are in use. Allows user to select which mask
number (from 1 to 12) is to be used during mask tracing via "TRACE
MASK" option. This allows one to create multiple molecular envelope
masks, usually one for each molecule within the asymmetric unit. The
currently active mask no. will be displayed at the bottom right of the
screen, along with a sample of the color assigned to that mask.
***** EXIT OPTION *****
If the orientation is not such that xz sections are in use, the program
simply terminates. If xz sections are in use, the program prompts as
to whether the map region selected should be saved, and if masks are
in use, whether the masks should be saved. If either maps or masks are
to be saved, the user is informed as to what region is currently
available. If masks are in use and the "MAKE ASU" option had
previously been selected, the user is also informed about the ranges
delineating the "molecule" as determined from the mask. The user is
then prompted as to what region should be saved. The saved region can
only be the entire region currently available, or a subset of it. The
user is then prompted for file names for each saved file. The "saved"
map file is in "AVERAGING" style format, and thus can be read back in
to the program later, or can be input to the averaging programs. The
mask file can also be read back and/or used with the averaging
programs.
***** CLEAR OPTION *****
Clears the screen and redraws the current section, with all parameters
unchanged. Useful if one wants to start over and recreate a mask for a
specific section, if not happy with the original choice. Also, if the
system is very busy, occasionally switching from an open textport back
to interactive mode can leave remnants of the textport on the screen.
This option can then be used to correct the display.
***** SAVE IMAGE OPTION *****
Pressing the left mouse button while in the "SAVE IMAGE" menu area
will save the entire screen contents as an "image" file, with the name
"MAPV_N.RGB", where N is a one or two digit number. Numbers start from
zero and are automatically incremented each time an image is saved. Up
to 100 images can be made in any job. Note!! This function is only
operational in the SGI version.
The following additional menu options are functional only when
masks are in use
***** SHOW MASK OPTION *****
Displays "masks" for current section (if available). Each masked grid
point is displayed as a colored dot superimposed on the contoured
section. Unassigned points (outside all molecular envelopes) are shown
in blue. Points inside molecular envelopes are shown with the color of
the particular envelope mask (with black, i.e no color for mask 1). If
the "MAKE ASU" option was run, points within molecular envelopes which
are redundant (by crystal symmetry) are shown in red. Points outside
molecular envelopes, but related to those within molecular envelopes
by crystal symmetry are shown in green.
***** MAKE ASU OPTION *****
Should be invoked after all needed mask sections are created. Will
prompt the user for the standard parameter file specifying the
symmetry information. The program will then examine each point within
all molecular envelopes, and check for redundant (by crystallographic
symmetry) entries. Mask values for redundant points will then be
changed. After using this option, the "SHOW MASK" option will flag
redundant points with the color red. If one is happy with the
particular asymmetric unit "retained" (not red), then one can exit as
the averaging programs will recognize the updated mask value as
redundant and ignore it. If however, one feels a symmetry related part
of the redundant area should have been retained instead, then the
masks should be recreated for the offending sections. After examining
all sections, the total number of redundant points, and unique points
within all envelopes is output. After identifying redundant points,
the user is prompted as to whether points related by symmetry to those
within the envelopes should also be identified. If so, the "SHOW MASK"
option will color all grid points related to those within the
envelopes green. This is useful to insure that all density is
accounted for, and to emphasize intermolecular borders. Note that the
"MAKE ASU" option SHOULD NOT be used with SKEWED maps. (If a mask
is created on a "skewed" map, program TRNMSK can convert it to
correspond to normal sections, so that this option can still be used,
provided the original extracted map used to create the skewed map
is input as well).
***** COPY PREV MASK OPTION *****
Copies mask for previous (adjacent, lower) section to current section,
and displays it. It is automatically saved, but one can recreate it
with the "TRACE MASK" option, if desired.
***** COPY NEXT MASK OPTION *****
Copies mask for next (adjacent, higher) section to current section,
and displays it. It is automatically saved, but one can recreate it
with the "TRACE MASK" option, if desired.
***** TRACE MASK OPTION *****
Invoking this option allows the cursor and mouse buttons to be used to
trace out the boundary for one or more electron density "islands" in
order to isolate individual molecular envelope or averaging
boundaries. Press the LEFT mouse button to invoke the option. Then
move cursor into map region, and press the LEFT mouse button once at a
point on the boundary. Move to new point on boundary and press again.
A blue line will be drawn connecting to the previous point. Continue
selecting points all along the boundary until you connect back to the
initial point. If other "islands" are needed, move the cursor to a
point on the boundary of the next "island", and press the MIDDLE mouse
button. As before, continue selecting points around the new boundary
with the LEFT mouse button until connected to the initial point for
this "island". Repeat as often as needed, starting each new island
with the MIDDLE mouse button. When the section is completed, move the
cursor back to the "TRACE MASK" menu area and press the LEFT button
again to let the program know you are done. The mask section will then
be "filled" such that a blue dot will be placed at each grid point
outside the envelope(s) to show you the mask you created. Note that
such a mask must be created for each section which contains part of
the envelopes. Note also that the mask creation is done for only one
section at a time, thus if multiple sections are displayed (e.g. "ADD
NEXT SEC" or "ADD PREV SEC" options were used), the created mask is
only for the last (most recent) section. This will always correspond
to the section indicated at the top of the plot area. Also be aware
that the mask created for each section is initialized (with respect to
the mask no. currently active) each time the option is invoked
(although the screen display will not be redrawn). Thus once invoked
you must complete the mask for that section. Once the process is
completed (area "filled"), the mask is saved for that section, and can
be displayed at a later time with the "SHOW MASK" option. You can then
use the "SET MASK NO." option to select a different mask, and use
"TRACE MASK" again on the same section. In this way multiple mask
envelopes (with each encompassing a different molecule) can be
created, which will be needed for averaging if the noncrystallographic
symmetry is not purely rotational or the rotational symmetry is not
N-fold where N is an integer.
HINTS!!! When pure rotational noncrystallographic symmetry is present,
the boundary is much easier to determine if the mask is constructed on
a "skewed" map such that sections are orthogonal to the NC symmetry
axis. Also, it is much clearer to see if three or four sections are
accumulated via "ADD NEXT" or "ADD PREV" commands. A useful procedure
therefore is to accumulate 4 sections and create an initial mask, then
select "PREV SECTION" twice, followed by "ADD SECTION" three times.
This will position you one section higher than the first mask, but
with a projection over 4 sections visable. The same thing can be done
in the reverse direction with the related commands. You can do this
repeatedly as you step through the map. Also, often the density
changes slowly, so you may be able to simply copy the previous or next
sections mask, and use it unchanged. If you do such a copy but then
decide to edit the mask (via TRACE MASK option), the new mask will
overwrite the old, but the visable display will reflect the
superposition of both old and new masks, and will be confusing. To
convince yourself that the new one is in fact used, just select
"CLEAR" followed by "SHOW MASK", to see the actual mask saved. Note
that when pure rotational symmetry (N-fold) is involved, only one mask
is needed which encompasses all related molecules. In that case the
mask itself should generally display the same symmetry as the contents
of the envelope, thus masks over noncrystallographic twofold symmetry
regions should also look like they have twofold symmetry, and only
density which at least approximately obeys the expected NC symmetry
should be encompassed by the mask.
************** FILE FORMATS ***************
FSFOUR style map files are described in the FSFOUR write-up
If a map and/or mask file is generated by the program (or a non-FSFOUR
style map is to be read in), the following formats apply.
***** "AVERAGED" style map file (binary) format *****
RECORD 1) A,B,C,AL,BE,GA,NX,NY,NZ,IXMN,IYMN,IZMN,IXMX,IYMX,IZMX
with first 6 values REAL*4, next 9 INTEGER*4, lengths in angstroms,
angles in degrees.
NX =
Number of grid points defining one "cell length" along
NY = respective axis. Implicitly defines grid spacing as
del x = A/NX, del y = B/NY and del z = C/NZ
NZ =
IXMN, IXMX =
Minimum, maximum grid index defining map region such
IYMN, IYMX = that x (fractional) = IX * (del x) / A etc.
There are no restrictions on magnitudes or signs.
IZMN, IZMX =
The map follows as (IYMX-IYMN+1)*(IZMX-IZMN+1) records, with
each containing one row (IXMX-IXMN+1 REAL*4 values) along x,
starting at IXMN. y is slowest varying, i.e. the file could have
been created with the following FORTRAN code:
DO 30 IY=IYMN,IYMX
DO 20 IZ=IZMN,IZMX
20 WRITE(LU)(RHO(IX,IY,IZ),IX=IXMN,IXMX)
30 CONTINUE
***** all mask files (binary) format *****
Header record identical to that in "AVERAGED" style map file.
Mask records similar to "AVERAGED" style map records except that
the mask values are written as FORTRAN type "BYTE" (INTEGER*1).
Mask values which are 0, 10, 20, 30, 40 etc idicate corresponding
grid point is part of the envelope for masks 1,2,3,4,5 etc,
respectively. All other values indicate the points do not belong
to any mask envelope, and should not be used for refinement or
averaging.