[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap
ABEL Stephane
Stephane.ABEL at cea.fr
Sat Nov 3 18:45:57 CET 2018
Thanks you Justin for your help but I still have the smae problem . I have changed in my m2p file the floowing fields
x-major = 1.0 ; Major ticks on x axis every .. frames
x-minor = 0.05 ; Id. Minor ticks
x-firstmajor = 0.0 ; First frame for major tick
y-major = 1.0 ; Major ticks on y axis every .. frames
y-minor = 0.05 ; Id. Minor ticks
y-firstmajor = 0.0
and use the xpm, some (not all) sticks appeared in each axis but w/o the labels. I still do not understand why ...
Stéphane
------------------------------
On 11/3/18 12:19 PM, ABEL Stephane wrote:
> 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
Here's your problem. You're telling xpm2ps to place major tick marks
every 15 units, but:
> /* 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 */
...your axis only goes to 12.5, so you get no labeling of any sort.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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