[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap
ABEL Stephane
Stephane.ABEL at cea.fr
Sat Nov 3 17:19:41 CET 2018
Hello,
I am using the below .m2p file as input for xpm2ps obtained from gmx densmap (v2018.2), but I am not able to get axis range label. The commands I use for densmap and xpm2ps
gmx_mpi densmap -f MYXTC.xtc -s MYTPR.tpr -n MYINDEX.ndx -b 150000 -e 210000 -bin 0.5 -aver z -unit nm-2 -o MYXPM.xpm
gmx_mpi xpm2ps -f MYXPM.xpm -di MYM2P.m2p -rainbow blue -gradient 0 0 0 -o MYEPS.eps
The range in the xpm for the x and y axis are 0 to 12.5097 (see below)
---- m2p -----
black&white = no
linewidth = 1
titlefont = Helvetica
titlefontsize = 20
legend = yes
legendfont = Helvetica
legendlabel =
legend2label =
legendfontsize = 14
xbox = 0
ybox = 0
matrixspacing = 20
xoffset = 0
yoffset = 0
boxlinewidth = 1
ticklinewidth = 1
zerolinewidth = 1
x-lineat0value = none
x-major = 15.0
x-minor = 0.1
x-firstmajor = 0.0
x-majorat0 = yes
x-majorticklen = 8
x-minorticklen = 4
x-label = X (nm)
x-fontsize = 16
x-font = Helvetica
x-tickfontsize = 12
x-tickfont = Helvetica
y-lineat0value = none
y-major = 15.0
y-minor = 0.5
y-firstmajor = 0.1
y-majorat0 = yes
y-majorticklen = 8
y-minorticklen = 4
y-label = Y (nm)
y-fontsize = 16
y-font = Helvetica
y-tickfontsize = 12
y-tickfont = Helvetica
------- beginning of the xpm file
/* legend: "(nm^-2)" */
/* x-label: "x (nm)" */
/* y-label: "y (nm)" */
/* type: "Continuous" */
static char *gromacs_xpm[] = {
"250 250 51 1",
"A c #FFFFFF " /* "0" */,
"B c #FAFAFA " /* "7.34" */,
"C c #F5F5F5 " /* "14.7" */,
"D c #F0F0F0 " /* "22" */,
"E c #EBEBEB " /* "29.4" */,
"F c #E6E6E6 " /* "36.7" */,
"G c #E0E0E0 " /* "44" */,
"H c #DBDBDB " /* "51.4" */,
"I c #D6D6D6 " /* "58.7" */,
"J c #D1D1D1 " /* "66.1" */,
"K c #CCCCCC " /* "73.4" */,
"L c #C7C7C7 " /* "80.7" */,
"M c #C2C2C2 " /* "88.1" */,
"N c #BDBDBD " /* "95.4" */,
"O c #B8B8B8 " /* "103" */,
"P c #B3B3B3 " /* "110" */,
"Q c #ADADAD " /* "117" */,
"R c #A8A8A8 " /* "125" */,
"S c #A3A3A3 " /* "132" */,
"T c #9E9E9E " /* "139" */,
"U c #999999 " /* "147" */,
"V c #949494 " /* "154" */,
"W c #8F8F8F " /* "161" */,
"X c #8A8A8A " /* "169" */,
"Y c #858585 " /* "176" */,
"Z c #808080 " /* "183" */,
"a c #7A7A7A " /* "191" */,
"b c #757575 " /* "198" */,
"c c #707070 " /* "206" */,
"d c #6B6B6B " /* "213" */,
"e c #666666 " /* "220" */,
"f c #616161 " /* "228" */,
"g c #5C5C5C " /* "235" */,
"h c #575757 " /* "242" */,
"i c #525252 " /* "250" */,
"j c #4D4D4D " /* "257" */,
"k c #474747 " /* "264" */,
"l c #424242 " /* "272" */,
"m c #3D3D3D " /* "279" */,
"n c #383838 " /* "286" */,
"o c #333333 " /* "294" */,
"p c #2E2E2E " /* "301" */,
"q c #292929 " /* "308" */,
"r c #242424 " /* "316" */,
"s c #1F1F1F " /* "323" */,
"t c #1A1A1A " /* "330" */,
"u c #141414 " /* "338" */,
"v c #0F0F0F " /* "345" */,
"w c #0A0A0A " /* "352" */,
"x c #050505 " /* "360" */,
"y c #000000 " /* "367" */,
/* x-axis: 0 0.0500388 0.100078 0.150116 0.200155 0.250194 0.300233 0.350271 0.40031 0.450349 0.500388 0.550426 0.600465 0.650504 0.700543 0.750581 0.80062 0.850659 0.900698 0.950736 1.00078 1.05081 1.10085 1.15089 1.20093 1.25097 1.30101 1.35105 1.40109 1.45112 1.50116 1.5512 1.60124 1.65128 1.70132 1.75136 1.8014 1.85143 1.90147 1.95151 2.00155 2.05159 2.10163 2.15167 2.20171 2.25174 2.30178 2.35182 2.40186 2.4519 2.50194 2.55198 2.60202 2.65205 2.70209 2.75213 2.80217 2.85221 2.90225 2.95229 3.00233 3.05236 3.1024 3.15244 3.20248 3.25252 3.30256 3.3526 3.40264 3.45267 3.50271 3.55275 3.60279 3.65283 3.70287 3.75291 3.80295 3.85298 3.90302 3.95306 */
/* x-axis: 4.0031 4.05314 4.10318 4.15322 4.20326 4.25329 4.30333 4.35337 4.40341 4.45345 4.50349 4.55353 4.60357 4.6536 4.70364 4.75368 4.80372 4.85376 4.9038 4.95384 5.00388 5.05391 5.10395 5.15399 5.20403 5.25407 5.30411 5.35415 5.40419 5.45422 5.50426 5.5543 5.60434 5.65438 5.70442 5.75446 5.8045 5.85453 5.90457 5.95461 6.00465 6.05469 6.10473 6.15477 6.20481 6.25484 6.30488 6.35492 6.40496 6.455 6.50504 6.55508 6.60512 6.65515 6.70519 6.75523 6.80527 6.85531 6.90535 6.95539 7.00543 7.05546 7.1055 7.15554 7.20558 7.25562 7.30566 7.3557 7.40574 7.45577 7.50581 7.55585 7.60589 7.65593 7.70597 7.75601 7.80605 7.85608 7.90612 7.95616 */
/* x-axis: 8.0062 8.05624 8.10628 8.15632 8.20636 8.25639 8.30643 8.35647 8.40651 8.45655 8.50659 8.55663 8.60667 8.6567 8.70674 8.75678 8.80682 8.85686 8.9069 8.95694 9.00698 9.05701 9.10705 9.15709 9.20713 9.25717 9.30721 9.35725 9.40729 9.45732 9.50736 9.5574 9.60744 9.65748 9.70752 9.75756 9.8076 9.85763 9.90767 9.95771 10.0078 10.0578 10.1078 10.1579 10.2079 10.2579 10.308 10.358 10.4081 10.4581 10.5081 10.5582 10.6082 10.6583 10.7083 10.7583 10.8084 10.8584 10.9084 10.9585 11.0085 11.0586 11.1086 11.1586 11.2087 11.2587 11.3088 11.3588 11.4088 11.4589 11.5089 11.559 11.609 11.659 11.7091 11.7591 11.8091 11.8592 11.9092 11.9593 */
/* x-axis: 12.0093 12.0593 12.1094 12.1594 12.2095 12.2595 12.3095 12.3596 12.4096 12.4597 12.5097 */
/* y-axis: 0 0.0500388 0.100078 0.150116 0.200155 0.250194 0.300233 0.350271 0.40031 0.450349 0.500388 0.550426 0.600465 0.650504 0.700543 0.750581 0.80062 0.850659 0.900698 0.950736 1.00078 1.05081 1.10085 1.15089 1.20093 1.25097 1.30101 1.35105 1.40109 1.45112 1.50116 1.5512 1.60124 1.65128 1.70132 1.75136 1.8014 1.85143 1.90147 1.95151 2.00155 2.05159 2.10163 2.15167 2.20171 2.25174 2.30178 2.35182 2.40186 2.4519 2.50194 2.55198 2.60202 2.65205 2.70209 2.75213 2.80217 2.85221 2.90225 2.95229 3.00233 3.05236 3.1024 3.15244 3.20248 3.25252 3.30256 3.3526 3.40264 3.45267 3.50271 3.55275 3.60279 3.65283 3.70287 3.75291 3.80295 3.85298 3.90302 3.95306 */
/* y-axis: 4.0031 4.05314 4.10318 4.15322 4.20326 4.25329 4.30333 4.35337 4.40341 4.45345 4.50349 4.55353 4.60357 4.6536 4.70364 4.75368 4.80372 4.85376 4.9038 4.95384 5.00388 5.05391 5.10395 5.15399 5.20403 5.25407 5.30411 5.35415 5.40419 5.45422 5.50426 5.5543 5.60434 5.65438 5.70442 5.75446 5.8045 5.85453 5.90457 5.95461 6.00465 6.05469 6.10473 6.15477 6.20481 6.25484 6.30488 6.35492 6.40496 6.455 6.50504 6.55508 6.60512 6.65515 6.70519 6.75523 6.80527 6.85531 6.90535 6.95539 7.00543 7.05546 7.1055 7.15554 7.20558 7.25562 7.30566 7.3557 7.40574 7.45577 7.50581 7.55585 7.60589 7.65593 7.70597 7.75601 7.80605 7.85608 7.90612 7.95616 */
/* y-axis: 8.0062 8.05624 8.10628 8.15632 8.20636 8.25639 8.30643 8.35647 8.40651 8.45655 8.50659 8.55663 8.60667 8.6567 8.70674 8.75678 8.80682 8.85686 8.9069 8.95694 9.00698 9.05701 9.10705 9.15709 9.20713 9.25717 9.30721 9.35725 9.40729 9.45732 9.50736 9.5574 9.60744 9.65748 9.70752 9.75756 9.8076 9.85763 9.90767 9.95771 10.0078 10.0578 10.1078 10.1579 10.2079 10.2579 10.308 10.358 10.4081 10.4581 10.5081 10.5582 10.6082 10.6583 10.7083 10.7583 10.8084 10.8584 10.9084 10.9585 11.0085 11.0586 11.1086 11.1586 11.2087 11.2587 11.3088 11.3588 11.4088 11.4589 11.5089 11.559 11.609 11.659 11.7091 11.7591 11.8091 11.8592 11.9092 11.9593 */
/* y-axis: 12.0093 12.0593 12.1094 12.1594 12.2095 12.2595 12.3095 12.3596 12.4096 12.4597 12.5097 */
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
.....
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
-------------------
Same problem occurs with 1) older versions of GROMACS 2) if I do not use a m2p file or 3) the rainbow option in the xpm2ps command
Thank you in advance for your help
Stéphane
More information about the gromacs.org_gmx-users
mailing list