[gmx-users] strange xpm output of g_rmsdist!
Hassan Shallal
hshallal at PACIFIC.EDU
Fri Dec 17 01:33:25 CET 2010
Thanks Tsjerk for the response. Just to follow on the thread for other users who may get interested in recoloring matrix files, GUI of GIMP (newest version) can allow recoloring any grayscale matrix file using several color gradient maps already available within GIMP.
I have got another issue indeed to discuss with groamcs users, here is the description:
Target: finding out the effect of a given mutation on the average distance between the alpha carbon atom pairs in a given protein
Approach: after 20 ns simulation, g_rmsdist was used to derive the 2-dimensional matrix xpm for each system (mutant and wildtype) for comparison...
Problem: The xpm output for the wildtype system is very weird whereas the output for the mutant one looks fine. In the weird xpm, there is just a white diagonal line whereas everything else is black which means that the distances between the alpha carbons exhibited massively big RMSD throughout the whole trajectory. This is impossible, I checked the trajectory of that specific system using VMD, it looks like any usual trajectory and the distances between the alpha carbons were changing all the simulation time but the protein kept its overall shape and secondary structure elements. Given this weird output xpm, I would imagine that the protein completely unfolds!! So there must be something wrong that happened while g_rmsdist was processing that specific trajectory!!!
I plotted the corresponding xvg files (also generated by g_rmsdist). In both, RMSD calculations looks fine and within acceptable range and upon plotting, the RMSD curve of the mutant and that of the wildtpye were very close to each others.
Here is the command I issued for checking:
g_rmsdist -s wildtype.tpr -f wildtype_noPBC_from_trr.xtc -o wildtype_Calpha_rmsdist.xvg -rms wildtype_Calpha_rmsdist.xpm -scl wildtype_Calpha_rmsscale.xpm -mean wildtype_Calpha_rmsmean.xpm
and exactly a similar one for the mutant system.
I am including a part of the content of both thw wildtype and the mutant xpm for checking at the end of the message.. The numbers for color assignment in the wildtype xpm are much much higher than those in the mutant one.
Question: has anyone encountered a similar problem with the g_rmsdist -rms xpm output? is there any suggestion of what might have been wrong and what needs to be corrected so that the g_rmsdist can give normal output for all the systems?
Any help would be greatly appreciated
Great regards
Hassan
A] wildtype_Calpha_rmsdist.xpm
/* XPM */
/* Generated by /home/hassan/bin/bin/g_rmsdist */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "RMS of distance" */
/* legend: "RMS (nm)" */
/* x-label: "Atom Index" */
/* y-label: "Atom Index" */
/* type: "Continuous" */
static char *gromacs_xpm[] = {
"295 295 40 1",
"A c #FFFFFF " /* "0" */,
"B c #F8F8F8 " /* "7.7" */,
"C c #F2F2F2 " /* "15.4" */,
"D c #EBEBEB " /* "23.1" */,
"E c #E5E5E5 " /* "30.8" */,
"F c #DEDEDE " /* "38.5" */,
"G c #D8D8D8 " /* "46.2" */,
"H c #D1D1D1 " /* "53.9" */,
"I c #CBCBCB " /* "61.6" */,
"J c #C4C4C4 " /* "69.3" */,
"K c #BEBEBE " /* "77" */,
"L c #B7B7B7 " /* "84.7" */,
"M c #B1B1B1 " /* "92.5" */,
"N c #AAAAAA " /* "100" */,
"O c #A3A3A3 " /* "108" */,
"P c #9D9D9D " /* "116" */,
"Q c #969696 " /* "123" */,
"R c #909090 " /* "131" */,
"S c #898989 " /* "139" */,
"T c #838383 " /* "146" */,
"U c #7C7C7C " /* "154" */,
"V c #767676 " /* "162" */,
"W c #6F6F6F " /* "169" */,
"X c #696969 " /* "177" */,
"Y c #626262 " /* "185" */,
"Z c #5C5C5C " /* "193" */,
"a c #555555 " /* "200" */,
"b c #4E4E4E " /* "208" */,
"c c #484848 " /* "216" */,
"d c #414141 " /* "223" */,
"e c #3B3B3B " /* "231" */,
"f c #343434 " /* "239" */,
"g c #2E2E2E " /* "247" */,
"h c #272727 " /* "254" */,
"i c #212121 " /* "262" */,
"j c #1A1A1A " /* "270" */,
"k c #141414 " /* "277" */,
"l c #0D0D0D " /* "285" */,
"m c #070707 " /* "293" */,
"n c #000000 " /* "300" */,
/* x-axis: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 */
/* x-axis: 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 */
/* x-axis: 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 */
/* x-axis: 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 */
/* y-axis: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 */
/* y-axis: 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 */
/* y-axis: 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 */
/* y-axis: 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 */
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllmmlllA",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAl",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAll",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAlll",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAlllm",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAllllm",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAllllll",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAlllllll",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAllllllll",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAlllllllll",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAllllllllll",
"lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAlllllllllll",
"llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllAllllllllllll",
"lllllllllllllllllllllllllllllllll
B] mutant_Calpha_rmsdist.xpm
/* XPM */
/* Generated by /home/hassan/bin/bin/g_rmsdist */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "RMS of distance" */
/* legend: "RMS (nm)" */
/* x-label: "Atom Index" */
/* y-label: "Atom Index" */
/* type: "Continuous" */
static char *gromacs_xpm[] = {
"295 295 40 1",
"A c #FFFFFF " /* "0" */,
"B c #F8F8F8 " /* "0.0096" */,
"C c #F2F2F2 " /* "0.0192" */,
"D c #EBEBEB " /* "0.0288" */,
"E c #E5E5E5 " /* "0.0384" */,
"F c #DEDEDE " /* "0.048" */,
"G c #D8D8D8 " /* "0.0576" */,
"H c #D1D1D1 " /* "0.0672" */,
"I c #CBCBCB " /* "0.0768" */,
"J c #C4C4C4 " /* "0.0864" */,
"K c #BEBEBE " /* "0.096" */,
"L c #B7B7B7 " /* "0.106" */,
"M c #B1B1B1 " /* "0.115" */,
"N c #AAAAAA " /* "0.125" */,
"O c #A3A3A3 " /* "0.134" */,
"P c #9D9D9D " /* "0.144" */,
"Q c #969696 " /* "0.154" */,
"R c #909090 " /* "0.163" */,
"S c #898989 " /* "0.173" */,
"T c #838383 " /* "0.182" */,
"U c #7C7C7C " /* "0.192" */,
"V c #767676 " /* "0.202" */,
"W c #6F6F6F " /* "0.211" */,
"X c #696969 " /* "0.221" */,
"Y c #626262 " /* "0.23" */,
"Z c #5C5C5C " /* "0.24" */,
"a c #555555 " /* "0.25" */,
"b c #4E4E4E " /* "0.259" */,
"c c #484848 " /* "0.269" */,
"d c #414141 " /* "0.278" */,
"e c #3B3B3B " /* "0.288" */,
"f c #343434 " /* "0.298" */,
"g c #2E2E2E " /* "0.307" */,
"h c #272727 " /* "0.317" */,
"i c #212121 " /* "0.326" */,
"j c #1A1A1A " /* "0.336" */,
"k c #141414 " /* "0.346" */,
"l c #0D0D0D " /* "0.355" */,
"m c #070707 " /* "0.365" */,
"n c #000000 " /* "0.374" */,
/* x-axis: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 */
/* x-axis: 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 */
/* x-axis: 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 */
/* x-axis: 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 */
/* y-axis: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 */
/* y-axis: 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 */
/* y-axis: 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 */
/* y-axis: 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 */
"KKIHHGHHGFFFFGHGFFFFFGGGGHHHIJKKJJIHIHHHGGGGFFFFFGGGGHHHIJJKLNNNPRYVPKKJLKKJJHIHHFGGHHIIJIHHGFFEDEFEDFGFIHFHGHILKIFEFFGGFGGFFHHGHJKIMQMMSPMKIHGFGEDDEFFGIKJHIGHGGIGFFEDDDDCDDDDDEGFFFEEEEEFFGGHGFFGGHHJKKIIJHGHHFFGFEEFEEEEEEFFEDDDDDEEFFGGGIHGFGGGGHHJKMKIKKIIKJHIIJKLLLOPOWUOPUPMNOKJIJIKNUPNXVWTPGAA",
"IIHGGGGGGFFFFGGFFGFEFFFGGHHHJJLMLKJIJIHHGFFEEEEEEEFFFFGGGGHHIJJKLOWSQJIIKIJIGGFFFEEFFGHHJIIIHFEDDDEDCFGFIHFHHIJNLJECCCCCCEDDGHFHMNLPaaSXeVSPNLKIIGEEFEFGJMLIJGGGGIGGFFEEDEEEEFFFGHGHHFHGHHIJLKLKJJJJKLORQNNPMKLKIHHGEEEDCEEFGGFFFEFFFGHHIJJKLKJIHHGFFGHILJJLMKLNNLMMNPQQQUYYhZTSUPKJJGFEHIHLZTJOcKKGAAA",
"JIHGGFGGFFEFFGGGIJIHHHGFFFGGGHHIIHGGGGGGHHHHHGGHHHIIIIJJJKMKLNMMPQPQLKMJLKJIIHIHGGGHHIIIHGFFEEEEEDDDCEFFIHFHGHHLKJFDCCDDDDDEGGHJMPQRXcWXeaVSQNMKJHGGHHFFFIIGGGIKKKIIHHGGFFFFGHGFGHHHJGIHHHIJKJLLJIJKLMOQOMNNLKKIHHGFFEDDDEEFFFEEEEFFFGHGHIIIKIHGFFFEDEEFGGGHIIIJKJJKLMNMNORSVQMMLIGFGFEGJIGLWLHUVHFAAAG",
"IHGFFEFEEEDDDEEEEFEEEEEEEEFFFGHIHGFFFFEEFEEEEDEEEEFFFFFFFGHGHIHIKKLIHFGFHHHGGFGFEEEFFFFFFEDEDCCCBCDDCEGGJIGIHHHLKKGEDEFEDEECBCDDEFGHKNKLPOLJIGFEECCCDCCDEGGFEDDEFFEEDDCDCCCBCCDCDGHFFDECDCDEEEFFEEFFFGHIHGGFEEEDCCCBBCCBCCBBCDCCBCCEDCDDDDEEFEDCCDDDEEFEFEDEEDDEEDEEFGHGGHIIKIFEGFEHJIHIKIHNTIEJJFAAAGP",
"FFEDDDEDDDCDCDEDCDCCCDCDDDEEEFGHHFFEEEDDDDCCCCCCCCDDDDDDDEEEEFFFGHJHGEEDFFFEEDEDDDDDDEDEEDDEDCCCCCEDDFGGKKHIHIILLKGEDEGFEFFECEDCCCEEGIGHJIGFEDCCCBBBBBCDEGFFFDDCDDCCCBABBBAAAAAACEFDDBBAAABBCCDCBCCCCCDEDCCDCBBBBBCCCDDCCCCBCCCCBBAAAABBBBCDECBBCCDDEEFEEEDDCCBCCBCCCDEDDEFFHFDDFEFJJIIJKIJQaJFIGAAAFKT",
"EDDCCCCCCCBCCDECBCBBBCCCCCDDDEEGGFEDDDCCCBBBABDCCCDCCDDCDEEDEFEDEEHGECCBCCDDCCCCCBBCBCCCCCCDCCCDCDEEDFGGKKHIGHHLLKFEDEFEEGGEEGEDEECCEFDEFEDCCCBCCCCBBCCDDEEEEDCCBCCBCBABBBBBBAABBEDCDCABBCCBBBBBBABBBBCCCBCCCCDDCDDDDEEDDDCCDDDDCCCBBBBBCBBCEDCCDDEEEFGFFFEDDDCDCCCBCCDCCDDEGFEGHFHMLJJIHFHKMGEEAAAFHKW",
"EDCCCCCCCCBCCDECCDCCCCCCBCCCDEEFFEDDDDCCCCBCBBCCCDDDDDEDDEEEFGFEFFJIEDDCDDDDDCDCCCBCCCCCCCCCBBBCBBCCBDEEIHEFEFFJJHDDCCDCDEDDDFDDFFEEHHEFGFEDDDCCCCCCCCBCCEDDDCCDCDCCCBBBBBBBBBBBCFEDDCBBBBBCCBCCBBBBCCDDDCDDCCCCCCCBBCCCCDCCCDCCCBBBABBBCCCDFDBBCDDDEEFEFEDDDCCDDCCCCDDDDEFFJGEFHEFIIFFFECDFICDAAAGJVcV",
"EEDCCCDCCCBCCDEDCDCCCCCCCDDDDEFGGFEDEDCCCCCCBBCCCCDDCDEDDFFEFHGFFHMMGEEDEDDDDCDCCCCCCDCDDDDDCCBBBBCCBDEEIHEFEFFJIHDCBBCBBCCCBDDDCEFEHIFFGFEDDDCCCBCBCCCCDFEEEDDDDDCCCCBCCBBAABBBCFEDECBBBBBCCBDCBBBBBCDDDCCDCCCBBBBABBBABCCBBCBCBBAAAABBCCCDEDBBCCDCDDEDEDCCCCBDCCCCCDDCDDFFIFDEEDDGGEEEECDGLEAAAEIJUOX",
"EDDCCCCCCCCDDEFDCCCCCCCDCDDDDEFGGFEDEECCCCBBBBBCCCDCCDDDDEEEFGGEFGJKGFDCDDDDCCCCCBBBBCCCDDDEDCDDCDEDCEGGKJGHGHHMLJEDCCDDCDDDCDFEDEECEEDDEDCDCDCCDDCBCCCDDFEEFEDCCCCCCBBBBBABBBBBCGFEDCBBBBCBBBCBBABCCCCDCCCCCCDCCDCCDDCCCDCCCDCDCCCBBBBBCBBCEDCBCCDDEDEEEDCCCCBCCCCBBCCCCDEEGEEFFDEHFEFFEDFIGAAADEFEHJN",
"EEEDDDDDDDDDDEFDCDCCCDDEDEEEEFGHIGFFFFEEDDCCCCCCCCDDCDDDDEEEFGHFGHJKKHFFFEEEDDDCDCCCDDDEFEEFEEEEDDFEDGHGKJHIHIINLJEDDCDDDDEEDDFFCDFDDEECDDDDDDCDDDDCDEEFFHHHIGFEDDDCDCCCCCBBCBBBCFDEEDBCBBCBBBBCBBBCCCCCCBCCBCCCCDCCDDDCDDCCCCCDCCCBBBBBCBBCDDCBCCDDEEEEEDCCCCBCCBBBBBCBBCDDFDDEECDFFEFGGGGDAAAECGJILTP",
"EEEDDDDDDDDDDDEDCCCCCCDDDEEEFFGHIGFFFFEDDCCCBBDCCCCCCDDDDEEEFGHFGHKJHFEEEEEEDDDCDCCCCDDDEEEEEDDDCDDDCFGGJJHHGHHLKJEEEDEEDEEDCDDCCDECDFEDEEDDDDCCDCCBCCDEEGGHFEDCCCCCCBBBCBBBBAAABEGDDCBBABBBAABBBABCCCCCCBCCBBCBBCBBBCDCCCCBCCCCCCBBBBBABBBCDDCBCDDEEEFEFEDDCCBCCBBBBBCCBCCDEDDEFDEGGFHILLHAAAGLIMaTWZU",
"DDDCCCDCCCCDCDECBCCBBCCDCDDDEEFGGFEEEEDCCCBBBCFCDCCCCDDDDEEEEFFEFFIHFEDDDDDDCCCCCBBCCCCCDDDEDCCDCDEDDFHHLMIKIJJNMLFDDDEEDGFEEGEDEEDDDDCDDDCCCCBBCCCCCCCDDEFFEDDCCCBBBBBBBBBBBAAABDECDCBBBBBBBBCBBAABBBCCCBCCCCCCCCCCCDDDDDCCCDDDCCBBBBBBCCCDEDCCDDEEFFGGGFEEDDCDDCCCCCDDDDEEGFFGGFGIIHJJKEAAADIGFKQNLLN",
"DDCCCCCCCCCDDDFDBCCBBCCDCDDDDEFGGFEEEEDCCBBBAACCBBCCCCDCDDDEEFFEEEGGFEDCDCDCCBCBCBBBBCCCDDDEDDDEDDFEEGIINMIKIKKPPMGEEDEFEFHGEGGEEDCCDCCCCCBCCCCCDDDCCDDEDEFGGEDCCCBBCBBBCCBCCBBBCEDDDCBCBCCCBBBBBABBBBBCCCCCCCDDDDEDDEEDEEDDDEEEDDCCCCCCDCCDEEDCDDEFGGHGGFEDDDCDCCCBBCCCCDDEFEEFGEFIGDFJFAAAHGFDDHJHGHK",
"DDDCCCDCDDDEDEFDCCCCCCDDDDDDEEFGHGFEEEDDCCBBBCFBEECCBCCCCDDDEFFEEEFFFEDDDDDDCCCBCBBBBCCCDDEFFEEFFFHGFIKKPPMOMNNSSQJHHGIKHGKIGGGFDDCCCCBBCBBBCCCDEEEDDEEFFFHIHGEDCCCCDCCCDDCDDCCCCDFDEDCCCDDCCCBBCBBCBBBCCCCDDDEEEFFFFGGFGFFEEFFFEEDDDDDCDDCDEEDDEEFGHHIHGFFEDDDDDCCCBCCCCCCDEDDEEDEGFCCFAAAELGDCCFIIIII",
"DCCCCDCCCCCDDDEDBCBBCCCDCDDDDEEGGFEEEECCCBBACIKHKKGCBBCCCDDDEEEDEEFFEDCCCCDCCBBFGGDBBBBCCDDEEDDEDEFFFGIKQRNPMMLOQQJHIGJJGGHFEEDCCCCBCCBCCBBBBCCCDDDCCDDDDEFGEDCCBCBBCBCBCCCDCCCBCFHEDCBCCDCCCCBBBBBBBBBBCCCCCDDEDEFEEGGFFFEEEFFFEEDCDDDDDDCDEEEDEFGHIIKIHGFFEEDDDDCCCCCCCDDDEDDFFEEGHEDAAAFKLGEEEHKKJHJ",
"DCCCCCCCCCCEDEEDBCBBCCCDCDDDDDEFGFEEEECCCBBAAGJFIIECBCDCCDDDEEEDDDFFEDCCCCCCBBBEGFBABBBCCDDEDDDDDDFFEGJKSTNPLMLNQQJHJJOLHJIEFFDCDDDCCCCCCCBBBCCCDDDCCDCDDEFFFDCCBCBBCBCBCCCDDCCCCDDDDCCCCDDCCCBBCBBCBBBCCCCDDDEEEFGGFHIGGFFEFGGFEEEDDDDDEDDEFFFEFGHIKLMKIIGFFEEEDDDCCCCCDDDEEDEFEDFFFCAAAFJJIGFEFIJIGEI",
"DCCBCECCCCCDDEEDCCBBCCDDCDDCDDEFFEEDDD
________________________________
From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Thu 12/16/2010 12:16 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using recolor.sh to color the xpm matrix filesproduced by r_rms and g_mdmat
Hi Hassan,
It seems the scripting language of the Gimp has changed a bit since
the version I used at the time of writing that script. The Gimp is
also only used for conversion of the xpm to png, which it did better
than convert. The important parts for recoloring are the lines using
convert, first generating a gradient, then applying that gradient on a
grayscale image. Try to find another way to convert xpm to png (or
another lossless format), and modify the script to your needs.
Cheers,
Tsjerk
On Thu, Dec 16, 2010 at 4:19 AM, Hassan Shallal <hshallal at pacific.edu> wrote:
> Dear Gromacs users,
>
> I have been trying to use the recolor.sh mentioned in this wbsite http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html <http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html> <http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html <http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html> >
> to reclor an xpm file called rmsd-matrix.xpm file, whenever I issue the command recolor.sh rmsd-matrix.xpm, I get the following error message:
>
> #$ hassan~ $./recolor.sh rmsd-matrix.xpm
> GIMP-Error: Opening '/home/hshallal/(gimp-file-save 1 1 2 "./rmsd-matrix.png" "./rmsd-matrix.png")' failed: No such file or directory
> GIMP-Error: Opening '/home/hshallal/(gimp-quit 0)' failed: No such file or directory
> batch command: executed successfully
>
> It seems like a problem with gimp not being able to process as stated in the script, especially with the argument of "(gimp-file-save 1 1 2 \"$png\" \"$png\")" (look below for the contents of the script).
>
> I have gimp confidured in my system. has anyone ran across the same problem or can know what the problem is and what th solution might be?
>
> Thanks in advance
>
> Hassan
>
> The contents of the recolor.sh file:
>
> #!/bin/sh
>
> xpm=$1
> png=`dirname $xpm`/`basename $xpm .xpm`.png
> convert xc:red xc:orange xc:yellow xc:green1 xc:cyan xc:blue xc:magenta \
> +append -filter Cubic -resize 600x30\! -rotate 90 gradient_rainbow.jpg
> #convert -size 1x600 xc:'#0C0' -colorspace HSB \
> # gradient: -compose CopyRed -composite \
> # -colorspace RGB gradient_rainbow.jpg
> gimp -d -f -i -b "(gimp-file-load 1 \"$xpm\" \"$xpm\")" "(gimp-file-save 1 1 2 \"$png\" \"$png\")" "(gimp-quit 0)"
> convert $png gradient_rainbow.jpg -virtual-pixel edge -fx 'v.p{0,u*v.h}' $png
>
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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