VMD-L Mailing List

From: Rebecca Taylor (rebeccat_at_stanford.edu)
Date: Mon Dec 29 2014 - 11:08:21 CST

Dear Josh,

Thank you for your detailed response. I am concerning myself with just
protein models right now (not prot-dna or dna), and right now I'm only
concerned with rendering the backbone.

A good example is PDB file 12AS (
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=12AS)
from the RSCB database. If I run the TCL script (pasted below), it throws
an error about the unusual structure, but as far as I can tell, the entire
backbone has been rendered. With other molecules like 2MYS the
uncrystalized flexible chains are not included in the PDB and thus the
non-sequential resids lead to rendering errors.

I want to know where there are gaps in the model and was hoping that I
would be able to programmatically determine this. Barring that, I'd like to
be able to run a check for completeness of the backbone when that error
occurs, so even if VMD can't give me the specifics, I can get information
about whether or not the backbone is a complete, one-piece mesh.

To get this sort of info, I should modify the "draw_protein_ribbons_old"
function and recompile VMD on my machine? Based on your helpful email with
the calls that lead to my error, it sounds like that is the only way to get
a list of rendered backbone segments.

I can look into doing this if that's the way to go.

many thanks and happy holidays.

best,
-bex

*** Sample TCL script****
### TCL file for generating meshes of ribbon models of proteins.
menu files off
menu files on
display resetview
mol addrep 0
display resetview
mol new {/Users/bex/PDBs/12AS.pdb} type {pdb} first 0 last -1 step 1
waitfor 1
animate style Loop
menu graphics off
menu graphics on
axes location Off
mol modstyle 0 0 NewRibbons 1.520000 10.000000 2.520000 0
mol color Name
mol representation NewRibbons 1.520000 10.000000 2.520000 0
mol selection chain
mol material Opaque
display resetview
mol modstyle 0 0 NewRibbons 0.300000 10.000000 3.000000 0
mol modstyle 0 0 NewRibbons 1.520000 10.000000 2.520000 0
mol color Name
mol representation NewRibbons 1.520000 10.000000 2.520000 0
mol modselect 0 0 chain is A
mol material Opaque
mol addrep 0
mol modstyle 1 0 Beads 0.700000 12.000000
mol modstyle 1 0 Beads 1.100000 12.000000
mol color Name
mol representation Beads 1.000000 12.000000
mol selection name CA and chain is A and resid 10 20 30 40 50 60 70 80 90
100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280
290 300 310 320 330
mol material Opaque
mol modrep 1 0
mol addrep 0
mol modstyle 2 0 Beads 0.700000 12.000000
mol modstyle 2 0 Beads 0.700000 12.000000
mol color Name
mol representation Beads 0.700000 12.000000
mol selection name CA and chain is A and resid 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 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
149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167
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
225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243
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
282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319
320 321 322 323 324 325 326 327 328 329 330 331
mol material Opaque
mol modrep 2 0
display resetview
menu render off
menu render on
render STL /Users/bex/12AS_A_Basic.stl

On Fri, Dec 26, 2014 at 5:20 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Rebecca,
>
> There isn't a way of getting more detailed information beyond looking into
> the source code.
>
> rc |= draw_protein_ribbons_old(framepos, bres, brad, ribbon_width,
> use_cyl);
> rc |= draw_nucleic_ribbons(framepos, bres, brad, ribbon_width, use_cyl,
> 0, 0);
> rc |= draw_base_sugar_rings(framepos, bres, brad, ribbon_width, use_cyl);
>
> // XXX put the more specific error messages back in here if we feel
> // that they are helpful to the user.
> if (rc != 0) {
> if (emitstructwarning())
> msgErr << "Warning: ribbons code encountered an unusual structure,
> geometry may not look as expected." << sendmsg;
> }
>
> What this means is that one of those three methods failed to draw things,
> and as written, there is no way to determine which one. What is in your
> system (ideally you could share a pdb code...)? Is it just protein, or is
> it some combination of protein, DNA, or sugars? I've seen many different
> reasons why these methods fail, so there isn't one specific problem that
> causes this. Generally, non-sequential resids cause problems, or if there
> are any negative resids (particularly in DNA).
>
> -Josh Vermaas
>
>
> On 12/25/14 11:15 PM, Rebecca Taylor wrote:
>
> Hello everyone, I'm converting multiple PDB files into ribbon models ('new
> ribbons') and thereafter generating triangular meshes. I've scoured the
> previous posts for this topic, but I can't find anything.
>
> I get the following error when a ribbon isn't completely rendered:
> "ERROR) Warning: ribbons code encountered an unusual structure, geometry
> may not look as expected."
>
> I'd love to know the residue ids for the residues NOT rendered.
> Basically I want to know where the gaps are, but this information isn't an
> output. Is there some command I can issue to get VMD to output more
> information about each error?
>
> Many thanks and happy holidays,
> -rebecca
>
> --
> Rebecca Taylor
> Post Doctoral Fellow
> Spudich Lab (spudlab.stanford.edu)
> Biochemistry
> Stanford University
> 650-319-5534
>
>
> 

-- 
Rebecca Taylor
Post Doctoral Fellow
Spudich Lab (spudlab.stanford.edu)
Biochemistry
Stanford University
650-319-5534