id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16682 Volume raycasting with orthoplanes: Shader compile failure chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: Linux-5.14.0-503.14.1.el9_5.x86_64-x86_64-with-glibc2.34 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description I update pyopengl to 3.1.9, because for default version (3.1.7), I just can not open chimerax. I'm not sure is it cause the problem. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /eml2/xyan/ERGIC/titan2_20230712/dataset/CH6_3_lam1_1_defocus5_bin5_rotx_corrected.mrc Opened CH6_3_lam1_1_defocus5_bin5_rotx_corrected.mrc as #1, grid size 818,1152,300, pixel 1, shown at step 1, values float32 > volume #1 region 0,0,0,817,1151,299 step 4 [Repeated 1 time(s)] > volume #1 change image level -0.8597,0 level 0.2141,0.8 level 0.9877,1 > volume #1 level -0.05283 > volume projectionMode rays > lighting soft > volume projectionMode rays [Repeated 1 time(s)] > volume #1 level 0.3833 > volume #1 style image region 0,0,148,817,1151,148 step 1 showOutlineBox true > volume #1 region 0,0,299,817,1151,299 > volume #1 region 0,0,149,817,1151,149 > volume #1 region 0,0,240,817,1151,240 > volume #1 region 0,0,154,817,1151,154 > volume #1 region 0,0,0,817,1151,0 [Repeated 1 time(s)] > volume #1 region 0,0,0,817,1151,299 step 4 > volume #1 region 0,0,0,817,1151,299 step 1 colorMode opaque8 orthoplanes xyz > positionPlanes 408,575,149 imageMode orthoplanes An OpenGL graphics error occurred. Most often this is caused by a graphics driver bug. The only way to fix such bugs is to update your graphics driver. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. ('Shader compile failure (0): b\'0(289) : error C1503: undefined variable ""tex_coord_3d""\\\n0(292) : error C1503: undefined variable ""tex3d""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(293) : error C1503: undefined variable ""colormap""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(300) : error C1503: undefined variable ""key_light_direction""\\\n0(301) : error C1503: undefined variable ""fill_light_direction""\\\n0(302) : error C1503: undefined variable ""key_light_direction""\\\n0(303) : error C1503: undefined variable ""key_light_specular_exponent""\\\n0(305) : error C1503: undefined variable ""key_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""fill_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""key_light_specular_color""\\\n0(306) : error C1503: undefined variable ""ambient_color""\\\n\'', [b'#version 330 core\n#define USE_VOLUME_RAYCASTING 1\n#define MAX_SHADOWS 1024\n// vim: set ft=glsl:\n\n/*\n * === UCSF ChimeraX Copyright ===\n# Copyright 2022 Regents of the University of California. All rights reserved.\n# The ChimeraX application is provided pursuant to the ChimeraX license\n# agreement, which covers academic and commercial uses. For more details, see\n# \n#\n# This particular file is part of the ChimeraX library. You can also\n# redistribute and/or modify it under the terms of the GNU Lesser General\n# Public License version 2.1 as published by the Free Software Foundation.\n# For more details, see\n# \n#\n# THIS SOFTWARE IS PROVIDED ""AS IS"" WITHOUT WARRANTY OF ANY KIND, EITHER\n# EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. ADDITIONAL LIABILITY\n# LIMITATIONS ARE DESCRIBED IN THE GNU LESSER GENERAL PUBLIC LICENSE\n# VERSION 2.1\n#\n# This notice must be embedded in or attached to all copies, including partial\n# copies, of the software or any revisions or derivations thereof.\n * === UCSF ChimeraX Copyright ===\n */\n\n/* ----------------------------------------------------------------------------\n* Various debugging shaders\n*/\n#ifdef USE_SHOW_DEPTH_BUFFER\nuniform sampler2D depth_texture;\nin vec2 tex_coord_2d;\nout vec4 frag_color;\n\nvoid main()\n{\n float c = texture(depth_texture, tex_coord_2d).x;\n frag_color = vec4(c, c, c, 1.0);\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing selection outlines.\n*/\n#elif defined(USE_TEXTURE_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 step;\nout vec4 frag_color;\n\nvoid main (void)\n{\n float m0 = texture(tex2d, tex_coord_2d).r;\n if (m0 != 0)\n discard;\n float mn = texture(tex2d, vec2(tex_coord_2d.s+step.s, tex_coord_2d.t)).r;\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s-step.s, tex_coord_2d.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t+step.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t-step.t)).r);\n if (mn == 0)\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing silhouette edges.\n*/\n#elif defined(USE_DEPTH_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 jump;\t// depth jump and near/far ratio.\nuniform vec3 step;\t// dx,dy,thickness\nout vec4 frag_color;\n\nvoid main (void)\n{\n float d0 = texture(tex2d, tex_coord_2d).r;\n float ds = d0;\n float thickness = step.p;\n int r = int(thickness);\n float r2 = thickness*thickness;\n for (int i = -r ; i <= r ; ++i)\n for (int j = -r ; j <= r ; ++j)\n if (i*i + j*j <= r2 && !(i == 0 && j == 0))\n ds = min(ds, texture(tex2d, vec2(tex_coord_2d.s+i*step.s, tex_coord_2d.t+j*step.t)).r);\n float nf = jump.t;\t// Correct depth compression based on perspective near/far ratio.\n float nf1 = 1-nf;\n if (nf*(d0-ds) < jump.s * (1-nf1*ds) * (1-nf1*d0))\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for blending textures for multichannel volume image rendering.\n*/\n#elif defined(USE_BLEND_TEXTURE_2D) || defined(USE_BLEND_TEXTURE_3D)\n\nin vec2 tex_coord_2d;\n#ifdef USE_BLEND_TEXTURE_2D\nuniform sampler2D tex2d;\n#else\nuniform sampler3D tex3d;\nuniform float tex_coord_z;\n#endif\n\nuniform vec4 color;\t\t\t// modulation color\n#ifdef USE_BLEND_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_BLEND_TEXTURE_2D\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex2d, tex_coord_2d) * color;\n#endif\n#endif\n#ifdef USE_BLEND_TEXTURE_3D\n vec3 tex_coord_3d = vec3(tex_coord_2d, tex_coord_z);\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex3d, tex_coord_3d) * color;\n#endif\n#endif\n}\n\n\n#else\n\n/* ----------------------------------------------------------------------------\n* Shader for rendering scene with lighting.\n*/\n\n#if defined(USE_LIGHTING) || defined(USE_DEPTH_CUE)\nin vec3 v;\n#endif\n\n#ifdef USE_LIGHTING\n\nlayout(std140) uniform lighting_block\n{\n vec3 key_light_direction;\n vec3 key_light_diffuse_color;\n vec3 key_light_specular_color;\n float key_light_specular_exponent;\n vec3 fill_light_direction;\n vec3 fill_light_diffuse_color;\n vec3 ambient_color;\n};\n\n#ifdef USE_LIGHTING_NORMALS\nin vec3 N;\n#endif\n\n#ifdef USE_STEREO_360\nin vec3 vshadow;\n#endif\n\n#ifdef USE_SHADOW\nin vec3 shadow_tex_coord;\nuniform sampler2DShadow shadow_map;\n#endif\n\n#ifdef USE_MULTISHADOW\n// in vec3 vscene;\n// in vec3 nscene;\nuniform sampler2DShadow multishadow_map;\nlayout(std140) uniform shadow_matrix_block\n{\n mat4 shadow_transforms[MAX_SHADOWS];\n};\nuniform\tint shadow_count;\nuniform float shadow_depth;\n#endif\n\n#endif // end USE_LIGHTING\n\n#ifdef USE_DEPTH_CUE\nuniform vec3 depth_cue_color;\nuniform vec2 depth_cue_range;\t// start and end camera z values\n#endif\n\n#ifdef USE_VERTEX_COLORS\nin vec4 color;\n#else\nuniform vec4 color;\n#endif\n\n#ifdef USE_TEXTURE_2D\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\n#endif\n\n#ifdef USE_TEXTURE_3D\nin vec3 tex_coord_3d;\nuniform sampler3D tex3d;\n#endif\n\n#ifdef USE_VOLUME_RAYCASTING\n uniform float step_size;\n uniform vec3 camera_pos;\n uniform float camera_fov;\n uniform vec2 window_size;\n uniform mat4 view_matrix;\n uniform vec4 background_color;\n uniform vec3 bbox_min;\n uniform vec3 bbox_max;\n uniform vec3 full_region_min;\n uniform vec3 full_region_max;\n float PHI = 1.61803398874989484820459;\n\n float gold_noise(in vec2 xy, in float seed){\n return fract(tan(distance(xy*PHI, xy)*seed)*xy.x);\n }\n#endif\n\n#ifdef USE_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\n\n#ifdef USE_DEPTH_TEXTURE\nuniform vec2 tex_depth_projection;\t// near, far/(far-near)\nuniform vec3 tex_depth_scale;\t\t// tex coord xscale, yscale and value zscale\nuniform sampler2D tex_depth_2d;\n#endif\n\n#ifdef USE_TEXTURE_CUBEMAP\nin vec3 tex_coord_cubemap;\nuniform samplerCube texcube;\n#endif\n\n#ifdef USE_TEXTURE_3D_AMBIENT\nin vec3 ambient_tex_coord;\nuniform sampler3D tex3d;\n#endif\n\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_VOLUME_RAYCASTING\n float aspect_ratio = window_size.x / window_size.y;\n float focal_length = 1.0 / tan(radians(camera_fov / 2.0));\n vec3 ray_origin = camera_pos;\n vec3 ray_direction;\n ray_direction.xy = 2.0 * gl_FragCoord.xy / window_size - 1.0;\n ray_direction.y /= aspect_ratio;\n ray_direction.z = -focal_length;\n ray_direction = (vec4(ray_direction, 0.0) * view_matrix).xyz;\n\n vec3 direction_inv = 1.0 / ray_direction;\n vec3 t_bottom = direction_inv * (bbox_min - ray_origin);\n vec3 t_top = direction_inv * (bbox_max - ray_origin);\n\n vec3 t_min = min(t_top, t_bottom);\n vec3 t_max = max(t_top, t_bottom);\n\n float t_0 = max(t_min.x, max(t_min.y, t_min.z));\n float t_1 = min(t_max.x, min(t_max.y, t_max.z));\n\n if (t_0 > t_1) {\n discard;\n }\n\n // Centers the volume in the box\n vec3 ray_start = (ray_origin + ray_direction * t_0 - full_region_min) / (full_region_max - full_region_min);\n vec3 ray_stop = (ray_origin + ray_direction * t_1 - full_region_min) / (full_region_max - full_region_min);\n\n vec3 ray = ray_stop - ray_start;\n float ray_length = length(ray);\n //float step_length = length(ssize);\n float step_length = step_size; //min(step_size.x, min(step_size.y, step_size.z));\n vec3 step_vector = step_length * ray / ray_length;\n float jitter = gold_noise(gl_FragCoord.xy, 0.9) * 0.5;\n vec3 position = tex_coord_3d + (step_vector * jitter);\n frag_color = vec4(0);\n while(ray_length > 0 && frag_color.a < 1) {\n float intensity = (texture(tex3d, position).r - colormap_range.x) * colormap_range.y;\n vec4 cmap_color = texture(colormap, intensity) * color;\n vec3 gradientVec = normalize(vec3(\n texture(tex3d, position + vec3(step_length, 0.0, 0.0)).r - texture(tex3d, position - vec3(step_length, 0.0, 0.0)).r,\n texture(tex3d, position + vec3(0.0, step_length, 0.0)).r - texture(tex3d, position - vec3(0.0, step_length, 0.0)).r,\n texture(tex3d, position + vec3(0.0, 0.0, step_length)).r - texture(tex3d, position - vec3(0.0, 0.0, step_length)).r\n ));\n\n float keyDiffuse = max(0.0, -dot(gradientVec, key_light_direction));\n float fillDiffuse = max(0.0, -dot(gradientVec, fill_light_direction));\n vec3 R = normalize(reflect(key_light_direction,gradientVec));\n float specular_factor = pow(max(-dot(R,normalize(ray_direction)),0.0), key_light_specular_exponent);\n\n vec3 lightColor = keyDiffuse * key_light_diffuse_color + fillDiffuse * fill_light_diffuse_color + key_light_specular_color * specular_factor;\n lightColor += cmap_color.rgb * ambient_color;\n cmap_color *= vec4(lightColor,1);\n\n\n // Accumulate color and opacity\n frag_color += (1.0 - frag_color.a) * cmap_color;\n\n // Alpha correction for step sizes other than 0.001\n frag_color.a = 1 - pow(1 - frag_color.a, step_length / 0.001);\n\n ray_length -= step_length;\n position += step_vector;\n if(\n (position.x < 0.0) || (position.x > 1.0) ||\n (position.y < 0.0) || (position.y > 1.0) ||\n (position.z < 0.0) || (position.z > 1.0)\n ) {\n break;\n }\n }\n frag_color += (1.0 - frag_color.a) * background_color;\n}\n#else\n #ifdef USE_DEPTH_TEXTURE\n // Adjust depth of each fragment in rendering a texture.\n float xscale = tex_depth_scale.x, yscale = tex_depth_scale.y, dscale = tex_depth_scale.z;\n float zt = texture(tex_depth_2d, vec2(0.5+xscale*(tex_coord_2d.x-0.5), 0.5+yscale*(tex_coord_2d.y-0.5))).x;\n zt = (zt == 0 ? 1 : zt); // Depth 0 means unknown depth, change to maximum depth\n float znear = tex_depth_projection.x, fdfmn = tex_depth_projection.y;\n float zs = max(znear, zt*dscale);\n gl_FragDepth = min(.99999, fdfmn * (zs - znear) / zs);\n #endif\n\n #ifdef USE_TEXTURE_2D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex2d, tex_coord_2d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_3D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex3d, tex_coord_3d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_CUBEMAP\n vec4 fcolor = texture(texcube, tex_coord_cubemap) * color;\n #else\n #ifdef USE_ALL_WHITE\n vec4 fcolor = vec4(1,1,1,1);\n #else\n vec4 fcolor = color;\n #endif\n #endif\n #endif\n #endif\n\n #ifdef USE_TRANSPARENT_ONLY\n if (fcolor.a >= 0.99)\n discard;\n #endif\n\n #ifdef USE_OPAQUE_ONLY\n if (fcolor.a < .99)\n discard;\n #endif\n\n #ifdef USE_ALPHA_DEPTH\n gl_FragDepth = 0.99999 * fcolor.a; // Depth 1 is clipped.\n #endif\n\n #ifdef USE_LIGHTING\n\n #ifdef USE_LIGHTING_NORMALS\n // Unit normal, with two-sided lighting.\n vec3 N1 = normalize(N) * (gl_FrontFacing ? 1.0 : -1.0);\n // vec3 N1 = normalize(N); // single-sided lighting\n\n // Unit vector from camera to surface point.\n vec3 v1 = normalize(v);\n\n float key_factor = max(-dot(N1,key_light_direction),0.0);\n float fill_factor = max(-dot(N1,fill_light_direction),0.0);\n vec3 R = normalize(reflect(key_light_direction,N1));\n float specular_factor = pow(max(-dot(R,v1),0.0), key_light_specular_exponent);\n #else\n float key_factor = 1;\n float fill_factor = 1;\n float specular_factor = 0;\n #endif\n\n #ifdef USE_SHADOW\n float shadow = texture(shadow_map, shadow_tex_coord);\n #else\n float shadow = 1;\n #endif\n\n // diffuse color, radiated equally in all directions,\n // strength based on incoming light direction and surface normal.\n vec3 Idiff = fcolor.rgb * (key_light_diffuse_color * key_factor * shadow\n + fill_light_diffuse_color * fill_factor);\n\n // specular color, reflection of incoming light towards the camera.\n vec3 Ispec = key_light_specular_color * specular_factor * shadow;\n\n #ifdef USE_MULTISHADOW\n\n float mshadow = 0;\n for (int i = 0 ; i < shadow_count ; ++i)\n {\n mat4 stf = shadow_transforms[i];\n #ifdef USE_STEREO_360\n vec3 shadow_tex_coord = (stf*vec4(vshadow,1)).stp;\n #else\n vec3 shadow_tex_coord = (stf*vec4(v,1)).stp;\n // vec3 shadow_tex_coord = (stf*vec4(vscene,1)).stp;\n #endif\n #ifdef USE_LIGHTING_NORMALS\n vec3 light_direction = shadow_depth * vec3(stf[0][2], stf[1][2], stf[2][2]);\n float diffuse = max(-dot(N1,light_direction),0.0);\n \t // float diffuse = max(-dot(nscene,light_direction),0.0);\n #else\n float diffuse = 0.25;\n #endif\n mshadow += diffuse * texture(multishadow_map, shadow_tex_coord);\n }\n mshadow /= 0.25*shadow_count;\n vec3 Iamb = fcolor.rgb * ambient_color * mshadow;\n\n #else\n\n // ambient color, uniform intensity light from all surfaces.\n vec3 Iamb = fcolor.rgb * ambient_color;\n\n #endif\n\n // total color\n vec3 Ifrag = Iamb + Idiff + Ispec;\n\n #ifdef USE_TEXTURE_3D_AMBIENT\n Ifrag *= texture(tex3d, ambient_tex_coord).r;\n #endif\n\n #else // not USE_LIGHTING\n\n vec3 Ifrag = fcolor.rgb;\n\n #endif // end USE_LIGHTING\n\n #ifdef USE_DEPTH_CUE\n float d = -v.z;\t// Distance from eye to fragment.\n float dim = (depth_cue_range.y - d) / (depth_cue_range.y - depth_cue_range.x);\n Ifrag = mix(depth_cue_color, Ifrag, clamp(dim,0.0,1.0));\n #endif\n\n // transparency\n float a = fcolor.a;\n #ifdef USE_LIGHTING\n #ifdef USE_LIGHTING_NORMALS\n a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));\n #endif\n #endif\n\n // final color\n frag_color = vec4(Ifrag, a);\n}\n#endif\n#endif\n'], GL_FRAGMENT_SHADER) Traceback (most recent call last): File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2946, in compile_shader fs = shaders.compileShader(fshader, GL.GL_FRAGMENT_SHADER) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/OpenGL/GL/shaders.py"", line 235, in compileShader raise ShaderCompilationError( OpenGL.GL.shaders.ShaderCompilationError: ('Shader compile failure (0): b\'0(289) : error C1503: undefined variable ""tex_coord_3d""\\\n0(292) : error C1503: undefined variable ""tex3d""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(293) : error C1503: undefined variable ""colormap""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(300) : error C1503: undefined variable ""key_light_direction""\\\n0(301) : error C1503: undefined variable ""fill_light_direction""\\\n0(302) : error C1503: undefined variable ""key_light_direction""\\\n0(303) : error C1503: undefined variable ""key_light_specular_exponent""\\\n0(305) : error C1503: undefined variable ""key_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""fill_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""key_light_specular_color""\\\n0(306) : error C1503: undefined variable ""ambient_color""\\\n\'', [b'#version 330 core\n#define USE_VOLUME_RAYCASTING 1\n#define MAX_SHADOWS 1024\n// vim: set ft=glsl:\n\n/*\n * === UCSF ChimeraX Copyright ===\n# Copyright 2022 Regents of the University of California. All rights reserved.\n# The ChimeraX application is provided pursuant to the ChimeraX license\n# agreement, which covers academic and commercial uses. For more details, see\n# \n#\n# This particular file is part of the ChimeraX library. You can also\n# redistribute and/or modify it under the terms of the GNU Lesser General\n# Public License version 2.1 as published by the Free Software Foundation.\n# For more details, see\n# \n#\n# THIS SOFTWARE IS PROVIDED ""AS IS"" WITHOUT WARRANTY OF ANY KIND, EITHER\n# EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. ADDITIONAL LIABILITY\n# LIMITATIONS ARE DESCRIBED IN THE GNU LESSER GENERAL PUBLIC LICENSE\n# VERSION 2.1\n#\n# This notice must be embedded in or attached to all copies, including partial\n# copies, of the software or any revisions or derivations thereof.\n * === UCSF ChimeraX Copyright ===\n */\n\n/* ----------------------------------------------------------------------------\n* Various debugging shaders\n*/\n#ifdef USE_SHOW_DEPTH_BUFFER\nuniform sampler2D depth_texture;\nin vec2 tex_coord_2d;\nout vec4 frag_color;\n\nvoid main()\n{\n float c = texture(depth_texture, tex_coord_2d).x;\n frag_color = vec4(c, c, c, 1.0);\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing selection outlines.\n*/\n#elif defined(USE_TEXTURE_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 step;\nout vec4 frag_color;\n\nvoid main (void)\n{\n float m0 = texture(tex2d, tex_coord_2d).r;\n if (m0 != 0)\n discard;\n float mn = texture(tex2d, vec2(tex_coord_2d.s+step.s, tex_coord_2d.t)).r;\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s-step.s, tex_coord_2d.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t+step.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t-step.t)).r);\n if (mn == 0)\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing silhouette edges.\n*/\n#elif defined(USE_DEPTH_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 jump;\t// depth jump and near/far ratio.\nuniform vec3 step;\t// dx,dy,thickness\nout vec4 frag_color;\n\nvoid main (void)\n{\n float d0 = texture(tex2d, tex_coord_2d).r;\n float ds = d0;\n float thickness = step.p;\n int r = int(thickness);\n float r2 = thickness*thickness;\n for (int i = -r ; i <= r ; ++i)\n for (int j = -r ; j <= r ; ++j)\n if (i*i + j*j <= r2 && !(i == 0 && j == 0))\n ds = min(ds, texture(tex2d, vec2(tex_coord_2d.s+i*step.s, tex_coord_2d.t+j*step.t)).r);\n float nf = jump.t;\t// Correct depth compression based on perspective near/far ratio.\n float nf1 = 1-nf;\n if (nf*(d0-ds) < jump.s * (1-nf1*ds) * (1-nf1*d0))\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for blending textures for multichannel volume image rendering.\n*/\n#elif defined(USE_BLEND_TEXTURE_2D) || defined(USE_BLEND_TEXTURE_3D)\n\nin vec2 tex_coord_2d;\n#ifdef USE_BLEND_TEXTURE_2D\nuniform sampler2D tex2d;\n#else\nuniform sampler3D tex3d;\nuniform float tex_coord_z;\n#endif\n\nuniform vec4 color;\t\t\t// modulation color\n#ifdef USE_BLEND_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_BLEND_TEXTURE_2D\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex2d, tex_coord_2d) * color;\n#endif\n#endif\n#ifdef USE_BLEND_TEXTURE_3D\n vec3 tex_coord_3d = vec3(tex_coord_2d, tex_coord_z);\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex3d, tex_coord_3d) * color;\n#endif\n#endif\n}\n\n\n#else\n\n/* ----------------------------------------------------------------------------\n* Shader for rendering scene with lighting.\n*/\n\n#if defined(USE_LIGHTING) || defined(USE_DEPTH_CUE)\nin vec3 v;\n#endif\n\n#ifdef USE_LIGHTING\n\nlayout(std140) uniform lighting_block\n{\n vec3 key_light_direction;\n vec3 key_light_diffuse_color;\n vec3 key_light_specular_color;\n float key_light_specular_exponent;\n vec3 fill_light_direction;\n vec3 fill_light_diffuse_color;\n vec3 ambient_color;\n};\n\n#ifdef USE_LIGHTING_NORMALS\nin vec3 N;\n#endif\n\n#ifdef USE_STEREO_360\nin vec3 vshadow;\n#endif\n\n#ifdef USE_SHADOW\nin vec3 shadow_tex_coord;\nuniform sampler2DShadow shadow_map;\n#endif\n\n#ifdef USE_MULTISHADOW\n// in vec3 vscene;\n// in vec3 nscene;\nuniform sampler2DShadow multishadow_map;\nlayout(std140) uniform shadow_matrix_block\n{\n mat4 shadow_transforms[MAX_SHADOWS];\n};\nuniform\tint shadow_count;\nuniform float shadow_depth;\n#endif\n\n#endif // end USE_LIGHTING\n\n#ifdef USE_DEPTH_CUE\nuniform vec3 depth_cue_color;\nuniform vec2 depth_cue_range;\t// start and end camera z values\n#endif\n\n#ifdef USE_VERTEX_COLORS\nin vec4 color;\n#else\nuniform vec4 color;\n#endif\n\n#ifdef USE_TEXTURE_2D\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\n#endif\n\n#ifdef USE_TEXTURE_3D\nin vec3 tex_coord_3d;\nuniform sampler3D tex3d;\n#endif\n\n#ifdef USE_VOLUME_RAYCASTING\n uniform float step_size;\n uniform vec3 camera_pos;\n uniform float camera_fov;\n uniform vec2 window_size;\n uniform mat4 view_matrix;\n uniform vec4 background_color;\n uniform vec3 bbox_min;\n uniform vec3 bbox_max;\n uniform vec3 full_region_min;\n uniform vec3 full_region_max;\n float PHI = 1.61803398874989484820459;\n\n float gold_noise(in vec2 xy, in float seed){\n return fract(tan(distance(xy*PHI, xy)*seed)*xy.x);\n }\n#endif\n\n#ifdef USE_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\n\n#ifdef USE_DEPTH_TEXTURE\nuniform vec2 tex_depth_projection;\t// near, far/(far-near)\nuniform vec3 tex_depth_scale;\t\t// tex coord xscale, yscale and value zscale\nuniform sampler2D tex_depth_2d;\n#endif\n\n#ifdef USE_TEXTURE_CUBEMAP\nin vec3 tex_coord_cubemap;\nuniform samplerCube texcube;\n#endif\n\n#ifdef USE_TEXTURE_3D_AMBIENT\nin vec3 ambient_tex_coord;\nuniform sampler3D tex3d;\n#endif\n\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_VOLUME_RAYCASTING\n float aspect_ratio = window_size.x / window_size.y;\n float focal_length = 1.0 / tan(radians(camera_fov / 2.0));\n vec3 ray_origin = camera_pos;\n vec3 ray_direction;\n ray_direction.xy = 2.0 * gl_FragCoord.xy / window_size - 1.0;\n ray_direction.y /= aspect_ratio;\n ray_direction.z = -focal_length;\n ray_direction = (vec4(ray_direction, 0.0) * view_matrix).xyz;\n\n vec3 direction_inv = 1.0 / ray_direction;\n vec3 t_bottom = direction_inv * (bbox_min - ray_origin);\n vec3 t_top = direction_inv * (bbox_max - ray_origin);\n\n vec3 t_min = min(t_top, t_bottom);\n vec3 t_max = max(t_top, t_bottom);\n\n float t_0 = max(t_min.x, max(t_min.y, t_min.z));\n float t_1 = min(t_max.x, min(t_max.y, t_max.z));\n\n if (t_0 > t_1) {\n discard;\n }\n\n // Centers the volume in the box\n vec3 ray_start = (ray_origin + ray_direction * t_0 - full_region_min) / (full_region_max - full_region_min);\n vec3 ray_stop = (ray_origin + ray_direction * t_1 - full_region_min) / (full_region_max - full_region_min);\n\n vec3 ray = ray_stop - ray_start;\n float ray_length = length(ray);\n //float step_length = length(ssize);\n float step_length = step_size; //min(step_size.x, min(step_size.y, step_size.z));\n vec3 step_vector = step_length * ray / ray_length;\n float jitter = gold_noise(gl_FragCoord.xy, 0.9) * 0.5;\n vec3 position = tex_coord_3d + (step_vector * jitter);\n frag_color = vec4(0);\n while(ray_length > 0 && frag_color.a < 1) {\n float intensity = (texture(tex3d, position).r - colormap_range.x) * colormap_range.y;\n vec4 cmap_color = texture(colormap, intensity) * color;\n vec3 gradientVec = normalize(vec3(\n texture(tex3d, position + vec3(step_length, 0.0, 0.0)).r - texture(tex3d, position - vec3(step_length, 0.0, 0.0)).r,\n texture(tex3d, position + vec3(0.0, step_length, 0.0)).r - texture(tex3d, position - vec3(0.0, step_length, 0.0)).r,\n texture(tex3d, position + vec3(0.0, 0.0, step_length)).r - texture(tex3d, position - vec3(0.0, 0.0, step_length)).r\n ));\n\n float keyDiffuse = max(0.0, -dot(gradientVec, key_light_direction));\n float fillDiffuse = max(0.0, -dot(gradientVec, fill_light_direction));\n vec3 R = normalize(reflect(key_light_direction,gradientVec));\n float specular_factor = pow(max(-dot(R,normalize(ray_direction)),0.0), key_light_specular_exponent);\n\n vec3 lightColor = keyDiffuse * key_light_diffuse_color + fillDiffuse * fill_light_diffuse_color + key_light_specular_color * specular_factor;\n lightColor += cmap_color.rgb * ambient_color;\n cmap_color *= vec4(lightColor,1);\n\n\n // Accumulate color and opacity\n frag_color += (1.0 - frag_color.a) * cmap_color;\n\n // Alpha correction for step sizes other than 0.001\n frag_color.a = 1 - pow(1 - frag_color.a, step_length / 0.001);\n\n ray_length -= step_length;\n position += step_vector;\n if(\n (position.x < 0.0) || (position.x > 1.0) ||\n (position.y < 0.0) || (position.y > 1.0) ||\n (position.z < 0.0) || (position.z > 1.0)\n ) {\n break;\n }\n }\n frag_color += (1.0 - frag_color.a) * background_color;\n}\n#else\n #ifdef USE_DEPTH_TEXTURE\n // Adjust depth of each fragment in rendering a texture.\n float xscale = tex_depth_scale.x, yscale = tex_depth_scale.y, dscale = tex_depth_scale.z;\n float zt = texture(tex_depth_2d, vec2(0.5+xscale*(tex_coord_2d.x-0.5), 0.5+yscale*(tex_coord_2d.y-0.5))).x;\n zt = (zt == 0 ? 1 : zt); // Depth 0 means unknown depth, change to maximum depth\n float znear = tex_depth_projection.x, fdfmn = tex_depth_projection.y;\n float zs = max(znear, zt*dscale);\n gl_FragDepth = min(.99999, fdfmn * (zs - znear) / zs);\n #endif\n\n #ifdef USE_TEXTURE_2D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex2d, tex_coord_2d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_3D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex3d, tex_coord_3d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_CUBEMAP\n vec4 fcolor = texture(texcube, tex_coord_cubemap) * color;\n #else\n #ifdef USE_ALL_WHITE\n vec4 fcolor = vec4(1,1,1,1);\n #else\n vec4 fcolor = color;\n #endif\n #endif\n #endif\n #endif\n\n #ifdef USE_TRANSPARENT_ONLY\n if (fcolor.a >= 0.99)\n discard;\n #endif\n\n #ifdef USE_OPAQUE_ONLY\n if (fcolor.a < .99)\n discard;\n #endif\n\n #ifdef USE_ALPHA_DEPTH\n gl_FragDepth = 0.99999 * fcolor.a; // Depth 1 is clipped.\n #endif\n\n #ifdef USE_LIGHTING\n\n #ifdef USE_LIGHTING_NORMALS\n // Unit normal, with two-sided lighting.\n vec3 N1 = normalize(N) * (gl_FrontFacing ? 1.0 : -1.0);\n // vec3 N1 = normalize(N); // single-sided lighting\n\n // Unit vector from camera to surface point.\n vec3 v1 = normalize(v);\n\n float key_factor = max(-dot(N1,key_light_direction),0.0);\n float fill_factor = max(-dot(N1,fill_light_direction),0.0);\n vec3 R = normalize(reflect(key_light_direction,N1));\n float specular_factor = pow(max(-dot(R,v1),0.0), key_light_specular_exponent);\n #else\n float key_factor = 1;\n float fill_factor = 1;\n float specular_factor = 0;\n #endif\n\n #ifdef USE_SHADOW\n float shadow = texture(shadow_map, shadow_tex_coord);\n #else\n float shadow = 1;\n #endif\n\n // diffuse color, radiated equally in all directions,\n // strength based on incoming light direction and surface normal.\n vec3 Idiff = fcolor.rgb * (key_light_diffuse_color * key_factor * shadow\n + fill_light_diffuse_color * fill_factor);\n\n // specular color, reflection of incoming light towards the camera.\n vec3 Ispec = key_light_specular_color * specular_factor * shadow;\n\n #ifdef USE_MULTISHADOW\n\n float mshadow = 0;\n for (int i = 0 ; i < shadow_count ; ++i)\n {\n mat4 stf = shadow_transforms[i];\n #ifdef USE_STEREO_360\n vec3 shadow_tex_coord = (stf*vec4(vshadow,1)).stp;\n #else\n vec3 shadow_tex_coord = (stf*vec4(v,1)).stp;\n // vec3 shadow_tex_coord = (stf*vec4(vscene,1)).stp;\n #endif\n #ifdef USE_LIGHTING_NORMALS\n vec3 light_direction = shadow_depth * vec3(stf[0][2], stf[1][2], stf[2][2]);\n float diffuse = max(-dot(N1,light_direction),0.0);\n \t // float diffuse = max(-dot(nscene,light_direction),0.0);\n #else\n float diffuse = 0.25;\n #endif\n mshadow += diffuse * texture(multishadow_map, shadow_tex_coord);\n }\n mshadow /= 0.25*shadow_count;\n vec3 Iamb = fcolor.rgb * ambient_color * mshadow;\n\n #else\n\n // ambient color, uniform intensity light from all surfaces.\n vec3 Iamb = fcolor.rgb * ambient_color;\n\n #endif\n\n // total color\n vec3 Ifrag = Iamb + Idiff + Ispec;\n\n #ifdef USE_TEXTURE_3D_AMBIENT\n Ifrag *= texture(tex3d, ambient_tex_coord).r;\n #endif\n\n #else // not USE_LIGHTING\n\n vec3 Ifrag = fcolor.rgb;\n\n #endif // end USE_LIGHTING\n\n #ifdef USE_DEPTH_CUE\n float d = -v.z;\t// Distance from eye to fragment.\n float dim = (depth_cue_range.y - d) / (depth_cue_range.y - depth_cue_range.x);\n Ifrag = mix(depth_cue_color, Ifrag, clamp(dim,0.0,1.0));\n #endif\n\n // transparency\n float a = fcolor.a;\n #ifdef USE_LIGHTING\n #ifdef USE_LIGHTING_NORMALS\n a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));\n #endif\n #endif\n\n // final color\n frag_color = vec4(Ifrag, a);\n}\n#endif\n#endif\n'], GL_FRAGMENT_SHADER) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 227, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 632, in _compute_shadowmaps multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1727, in use_multishadow_map draw_depth(r, sdrawings, opaque_only = not mat.transparent_cast_shadows) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1579, in draw_depth draw_opaque(r, drawings) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567, in _draw_multiple d.draw(renderer, draw_pass) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py"", line 941, in draw self._draw_planes(renderer, draw_pass, dtransp, drawing) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py"", line 960, in _draw_planes drawing.draw(r, draw_pass) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py"", line 1278, in draw Drawing.draw(self, renderer, draw_pass) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780, in draw self.draw_self(renderer, draw_pass) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 818, in _draw_geometry shader = r.shader(sopt) ^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 703, in shader p = self._opengl_shader(options) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 805, in _opengl_shader p = Shader(capabilities = capabilities, max_shadows = self.multishadow.max_multishadows()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2886, in __init__ self.program_id = self.compile_shader(vertex_shader_path, fragment_shader_path, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/eml0/UserHome/xyan/my_rpm/usr/libexec/UCSF- ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2948, in compile_shader raise OpenGLError(str(e)) chimerax.graphics.opengl.OpenGLError: ('Shader compile failure (0): b\'0(289) : error C1503: undefined variable ""tex_coord_3d""\\\n0(292) : error C1503: undefined variable ""tex3d""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(292) : error C1503: undefined variable ""colormap_range""\\\n0(293) : error C1503: undefined variable ""colormap""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(295) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(296) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(297) : error C1503: undefined variable ""tex3d""\\\n0(300) : error C1503: undefined variable ""key_light_direction""\\\n0(301) : error C1503: undefined variable ""fill_light_direction""\\\n0(302) : error C1503: undefined variable ""key_light_direction""\\\n0(303) : error C1503: undefined variable ""key_light_specular_exponent""\\\n0(305) : error C1503: undefined variable ""key_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""fill_light_diffuse_color""\\\n0(305) : error C1503: undefined variable ""key_light_specular_color""\\\n0(306) : error C1503: undefined variable ""ambient_color""\\\n\'', [b'#version 330 core\n#define USE_VOLUME_RAYCASTING 1\n#define MAX_SHADOWS 1024\n// vim: set ft=glsl:\n\n/*\n * === UCSF ChimeraX Copyright ===\n# Copyright 2022 Regents of the University of California. All rights reserved.\n# The ChimeraX application is provided pursuant to the ChimeraX license\n# agreement, which covers academic and commercial uses. For more details, see\n# \n#\n# This particular file is part of the ChimeraX library. You can also\n# redistribute and/or modify it under the terms of the GNU Lesser General\n# Public License version 2.1 as published by the Free Software Foundation.\n# For more details, see\n# \n#\n# THIS SOFTWARE IS PROVIDED ""AS IS"" WITHOUT WARRANTY OF ANY KIND, EITHER\n# EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. ADDITIONAL LIABILITY\n# LIMITATIONS ARE DESCRIBED IN THE GNU LESSER GENERAL PUBLIC LICENSE\n# VERSION 2.1\n#\n# This notice must be embedded in or attached to all copies, including partial\n# copies, of the software or any revisions or derivations thereof.\n * === UCSF ChimeraX Copyright ===\n */\n\n/* ----------------------------------------------------------------------------\n* Various debugging shaders\n*/\n#ifdef USE_SHOW_DEPTH_BUFFER\nuniform sampler2D depth_texture;\nin vec2 tex_coord_2d;\nout vec4 frag_color;\n\nvoid main()\n{\n float c = texture(depth_texture, tex_coord_2d).x;\n frag_color = vec4(c, c, c, 1.0);\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing selection outlines.\n*/\n#elif defined(USE_TEXTURE_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 step;\nout vec4 frag_color;\n\nvoid main (void)\n{\n float m0 = texture(tex2d, tex_coord_2d).r;\n if (m0 != 0)\n discard;\n float mn = texture(tex2d, vec2(tex_coord_2d.s+step.s, tex_coord_2d.t)).r;\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s-step.s, tex_coord_2d.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t+step.t)).r);\n mn = max(mn, texture(tex2d, vec2(tex_coord_2d.s, tex_coord_2d.t-step.t)).r);\n if (mn == 0)\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for drawing silhouette edges.\n*/\n#elif defined(USE_DEPTH_OUTLINE)\n\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\nuniform vec4 color;\nuniform vec2 jump;\t// depth jump and near/far ratio.\nuniform vec3 step;\t// dx,dy,thickness\nout vec4 frag_color;\n\nvoid main (void)\n{\n float d0 = texture(tex2d, tex_coord_2d).r;\n float ds = d0;\n float thickness = step.p;\n int r = int(thickness);\n float r2 = thickness*thickness;\n for (int i = -r ; i <= r ; ++i)\n for (int j = -r ; j <= r ; ++j)\n if (i*i + j*j <= r2 && !(i == 0 && j == 0))\n ds = min(ds, texture(tex2d, vec2(tex_coord_2d.s+i*step.s, tex_coord_2d.t+j*step.t)).r);\n float nf = jump.t;\t// Correct depth compression based on perspective near/far ratio.\n float nf1 = 1-nf;\n if (nf*(d0-ds) < jump.s * (1-nf1*ds) * (1-nf1*d0))\n discard;\n frag_color = color;\n}\n\n/* ----------------------------------------------------------------------------\n* Shader for blending textures for multichannel volume image rendering.\n*/\n#elif defined(USE_BLEND_TEXTURE_2D) || defined(USE_BLEND_TEXTURE_3D)\n\nin vec2 tex_coord_2d;\n#ifdef USE_BLEND_TEXTURE_2D\nuniform sampler2D tex2d;\n#else\nuniform sampler3D tex3d;\nuniform float tex_coord_z;\n#endif\n\nuniform vec4 color;\t\t\t// modulation color\n#ifdef USE_BLEND_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_BLEND_TEXTURE_2D\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex2d, tex_coord_2d) * color;\n#endif\n#endif\n#ifdef USE_BLEND_TEXTURE_3D\n vec3 tex_coord_3d = vec3(tex_coord_2d, tex_coord_z);\n#ifdef USE_BLEND_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n frag_color = texture(colormap, tvalue) * color;\n#else\n frag_color = texture(tex3d, tex_coord_3d) * color;\n#endif\n#endif\n}\n\n\n#else\n\n/* ----------------------------------------------------------------------------\n* Shader for rendering scene with lighting.\n*/\n\n#if defined(USE_LIGHTING) || defined(USE_DEPTH_CUE)\nin vec3 v;\n#endif\n\n#ifdef USE_LIGHTING\n\nlayout(std140) uniform lighting_block\n{\n vec3 key_light_direction;\n vec3 key_light_diffuse_color;\n vec3 key_light_specular_color;\n float key_light_specular_exponent;\n vec3 fill_light_direction;\n vec3 fill_light_diffuse_color;\n vec3 ambient_color;\n};\n\n#ifdef USE_LIGHTING_NORMALS\nin vec3 N;\n#endif\n\n#ifdef USE_STEREO_360\nin vec3 vshadow;\n#endif\n\n#ifdef USE_SHADOW\nin vec3 shadow_tex_coord;\nuniform sampler2DShadow shadow_map;\n#endif\n\n#ifdef USE_MULTISHADOW\n// in vec3 vscene;\n// in vec3 nscene;\nuniform sampler2DShadow multishadow_map;\nlayout(std140) uniform shadow_matrix_block\n{\n mat4 shadow_transforms[MAX_SHADOWS];\n};\nuniform\tint shadow_count;\nuniform float shadow_depth;\n#endif\n\n#endif // end USE_LIGHTING\n\n#ifdef USE_DEPTH_CUE\nuniform vec3 depth_cue_color;\nuniform vec2 depth_cue_range;\t// start and end camera z values\n#endif\n\n#ifdef USE_VERTEX_COLORS\nin vec4 color;\n#else\nuniform vec4 color;\n#endif\n\n#ifdef USE_TEXTURE_2D\nin vec2 tex_coord_2d;\nuniform sampler2D tex2d;\n#endif\n\n#ifdef USE_TEXTURE_3D\nin vec3 tex_coord_3d;\nuniform sampler3D tex3d;\n#endif\n\n#ifdef USE_VOLUME_RAYCASTING\n uniform float step_size;\n uniform vec3 camera_pos;\n uniform float camera_fov;\n uniform vec2 window_size;\n uniform mat4 view_matrix;\n uniform vec4 background_color;\n uniform vec3 bbox_min;\n uniform vec3 bbox_max;\n uniform vec3 full_region_min;\n uniform vec3 full_region_max;\n float PHI = 1.61803398874989484820459;\n\n float gold_noise(in vec2 xy, in float seed){\n return fract(tan(distance(xy*PHI, xy)*seed)*xy.x);\n }\n#endif\n\n#ifdef USE_COLORMAP\nuniform vec2 colormap_range;\t\t// offset and scale\nuniform sampler1D colormap;\n#endif\n\n#ifdef USE_DEPTH_TEXTURE\nuniform vec2 tex_depth_projection;\t// near, far/(far-near)\nuniform vec3 tex_depth_scale;\t\t// tex coord xscale, yscale and value zscale\nuniform sampler2D tex_depth_2d;\n#endif\n\n#ifdef USE_TEXTURE_CUBEMAP\nin vec3 tex_coord_cubemap;\nuniform samplerCube texcube;\n#endif\n\n#ifdef USE_TEXTURE_3D_AMBIENT\nin vec3 ambient_tex_coord;\nuniform sampler3D tex3d;\n#endif\n\nout vec4 frag_color;\n\nvoid main (void)\n{\n#ifdef USE_VOLUME_RAYCASTING\n float aspect_ratio = window_size.x / window_size.y;\n float focal_length = 1.0 / tan(radians(camera_fov / 2.0));\n vec3 ray_origin = camera_pos;\n vec3 ray_direction;\n ray_direction.xy = 2.0 * gl_FragCoord.xy / window_size - 1.0;\n ray_direction.y /= aspect_ratio;\n ray_direction.z = -focal_length;\n ray_direction = (vec4(ray_direction, 0.0) * view_matrix).xyz;\n\n vec3 direction_inv = 1.0 / ray_direction;\n vec3 t_bottom = direction_inv * (bbox_min - ray_origin);\n vec3 t_top = direction_inv * (bbox_max - ray_origin);\n\n vec3 t_min = min(t_top, t_bottom);\n vec3 t_max = max(t_top, t_bottom);\n\n float t_0 = max(t_min.x, max(t_min.y, t_min.z));\n float t_1 = min(t_max.x, min(t_max.y, t_max.z));\n\n if (t_0 > t_1) {\n discard;\n }\n\n // Centers the volume in the box\n vec3 ray_start = (ray_origin + ray_direction * t_0 - full_region_min) / (full_region_max - full_region_min);\n vec3 ray_stop = (ray_origin + ray_direction * t_1 - full_region_min) / (full_region_max - full_region_min);\n\n vec3 ray = ray_stop - ray_start;\n float ray_length = length(ray);\n //float step_length = length(ssize);\n float step_length = step_size; //min(step_size.x, min(step_size.y, step_size.z));\n vec3 step_vector = step_length * ray / ray_length;\n float jitter = gold_noise(gl_FragCoord.xy, 0.9) * 0.5;\n vec3 position = tex_coord_3d + (step_vector * jitter);\n frag_color = vec4(0);\n while(ray_length > 0 && frag_color.a < 1) {\n float intensity = (texture(tex3d, position).r - colormap_range.x) * colormap_range.y;\n vec4 cmap_color = texture(colormap, intensity) * color;\n vec3 gradientVec = normalize(vec3(\n texture(tex3d, position + vec3(step_length, 0.0, 0.0)).r - texture(tex3d, position - vec3(step_length, 0.0, 0.0)).r,\n texture(tex3d, position + vec3(0.0, step_length, 0.0)).r - texture(tex3d, position - vec3(0.0, step_length, 0.0)).r,\n texture(tex3d, position + vec3(0.0, 0.0, step_length)).r - texture(tex3d, position - vec3(0.0, 0.0, step_length)).r\n ));\n\n float keyDiffuse = max(0.0, -dot(gradientVec, key_light_direction));\n float fillDiffuse = max(0.0, -dot(gradientVec, fill_light_direction));\n vec3 R = normalize(reflect(key_light_direction,gradientVec));\n float specular_factor = pow(max(-dot(R,normalize(ray_direction)),0.0), key_light_specular_exponent);\n\n vec3 lightColor = keyDiffuse * key_light_diffuse_color + fillDiffuse * fill_light_diffuse_color + key_light_specular_color * specular_factor;\n lightColor += cmap_color.rgb * ambient_color;\n cmap_color *= vec4(lightColor,1);\n\n\n // Accumulate color and opacity\n frag_color += (1.0 - frag_color.a) * cmap_color;\n\n // Alpha correction for step sizes other than 0.001\n frag_color.a = 1 - pow(1 - frag_color.a, step_length / 0.001);\n\n ray_length -= step_length;\n position += step_vector;\n if(\n (position.x < 0.0) || (position.x > 1.0) ||\n (position.y < 0.0) || (position.y > 1.0) ||\n (position.z < 0.0) || (position.z > 1.0)\n ) {\n break;\n }\n }\n frag_color += (1.0 - frag_color.a) * background_color;\n}\n#else\n #ifdef USE_DEPTH_TEXTURE\n // Adjust depth of each fragment in rendering a texture.\n float xscale = tex_depth_scale.x, yscale = tex_depth_scale.y, dscale = tex_depth_scale.z;\n float zt = texture(tex_depth_2d, vec2(0.5+xscale*(tex_coord_2d.x-0.5), 0.5+yscale*(tex_coord_2d.y-0.5))).x;\n zt = (zt == 0 ? 1 : zt); // Depth 0 means unknown depth, change to maximum depth\n float znear = tex_depth_projection.x, fdfmn = tex_depth_projection.y;\n float zs = max(znear, zt*dscale);\n gl_FragDepth = min(.99999, fdfmn * (zs - znear) / zs);\n #endif\n\n #ifdef USE_TEXTURE_2D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex2d, tex_coord_2d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex2d, tex_coord_2d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_3D\n #ifdef USE_COLORMAP\n float tvalue = (texture(tex3d, tex_coord_3d).r - colormap_range.x) * colormap_range.y;\n vec4 fcolor = texture(colormap, tvalue) * color;\n #else\n vec4 fcolor = texture(tex3d, tex_coord_3d) * color;\n #endif\n #else\n #ifdef USE_TEXTURE_CUBEMAP\n vec4 fcolor = texture(texcube, tex_coord_cubemap) * color;\n #else\n #ifdef USE_ALL_WHITE\n vec4 fcolor = vec4(1,1,1,1);\n #else\n vec4 fcolor = color;\n #endif\n #endif\n #endif\n #endif\n\n #ifdef USE_TRANSPARENT_ONLY\n if (fcolor.a >= 0.99)\n discard;\n #endif\n\n #ifdef USE_OPAQUE_ONLY\n if (fcolor.a < .99)\n discard;\n #endif\n\n #ifdef USE_ALPHA_DEPTH\n gl_FragDepth = 0.99999 * fcolor.a; // Depth 1 is clipped.\n #endif\n\n #ifdef USE_LIGHTING\n\n #ifdef USE_LIGHTING_NORMALS\n // Unit normal, with two-sided lighting.\n vec3 N1 = normalize(N) * (gl_FrontFacing ? 1.0 : -1.0);\n // vec3 N1 = normalize(N); // single-sided lighting\n\n // Unit vector from camera to surface point.\n vec3 v1 = normalize(v);\n\n float key_factor = max(-dot(N1,key_light_direction),0.0);\n float fill_factor = max(-dot(N1,fill_light_direction),0.0);\n vec3 R = normalize(reflect(key_light_direction,N1));\n float specular_factor = pow(max(-dot(R,v1),0.0), key_light_specular_exponent);\n #else\n float key_factor = 1;\n float fill_factor = 1;\n float specular_factor = 0;\n #endif\n\n #ifdef USE_SHADOW\n float shadow = texture(shadow_map, shadow_tex_coord);\n #else\n float shadow = 1;\n #endif\n\n // diffuse color, radiated equally in all directions,\n // strength based on incoming light direction and surface normal.\n vec3 Idiff = fcolor.rgb * (key_light_diffuse_color * key_factor * shadow\n + fill_light_diffuse_color * fill_factor);\n\n // specular color, reflection of incoming light towards the camera.\n vec3 Ispec = key_light_specular_color * specular_factor * shadow;\n\n #ifdef USE_MULTISHADOW\n\n float mshadow = 0;\n for (int i = 0 ; i < shadow_count ; ++i)\n {\n mat4 stf = shadow_transforms[i];\n #ifdef USE_STEREO_360\n vec3 shadow_tex_coord = (stf*vec4(vshadow,1)).stp;\n #else\n vec3 shadow_tex_coord = (stf*vec4(v,1)).stp;\n // vec3 shadow_tex_coord = (stf*vec4(vscene,1)).stp;\n #endif\n #ifdef USE_LIGHTING_NORMALS\n vec3 light_direction = shadow_depth * vec3(stf[0][2], stf[1][2], stf[2][2]);\n float diffuse = max(-dot(N1,light_direction),0.0);\n \t // float diffuse = max(-dot(nscene,light_direction),0.0);\n #else\n float diffuse = 0.25;\n #endif\n mshadow += diffuse * texture(multishadow_map, shadow_tex_coord);\n }\n mshadow /= 0.25*shadow_count;\n vec3 Iamb = fcolor.rgb * ambient_color * mshadow;\n\n #else\n\n // ambient color, uniform intensity light from all surfaces.\n vec3 Iamb = fcolor.rgb * ambient_color;\n\n #endif\n\n // total color\n vec3 Ifrag = Iamb + Idiff + Ispec;\n\n #ifdef USE_TEXTURE_3D_AMBIENT\n Ifrag *= texture(tex3d, ambient_tex_coord).r;\n #endif\n\n #else // not USE_LIGHTING\n\n vec3 Ifrag = fcolor.rgb;\n\n #endif // end USE_LIGHTING\n\n #ifdef USE_DEPTH_CUE\n float d = -v.z;\t// Distance from eye to fragment.\n float dim = (depth_cue_range.y - d) / (depth_cue_range.y - depth_cue_range.x);\n Ifrag = mix(depth_cue_color, Ifrag, clamp(dim,0.0,1.0));\n #endif\n\n // transparency\n float a = fcolor.a;\n #ifdef USE_LIGHTING\n #ifdef USE_LIGHTING_NORMALS\n a = (a >= 1 ? 1.0 : 1.0 - pow(max(1.0-a,0.0), 1.0/max(abs(dot(v1,N1)),0.01)));\n #endif\n #endif\n\n // final color\n frag_color = vec4(Ifrag, a);\n}\n#endif\n#endif\n'], GL_FRAGMENT_SHADER) OpenGL version: 3.3.0 NVIDIA 560.35.05 OpenGL renderer: Quadro P620/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=gnome XDG_SESSION_DESKTOP=gnome XDG_CURRENT_DESKTOP=GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: Precision 7920 Tower OS: Rocky Linux 9.5 Architecture: 64bit ELF Virtual Machine: none CPU: 56 Intel(R) Xeon(R) Gold 6132 CPU @ 2.60GHz Cache Size: 19712 KB Memory: total used free shared buff/cache available Mem: 125Gi 7.3Gi 98Gi 547Mi 20Gi 118Gi Swap: 63Gi 0B 63Gi Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107GL [Quadro P620] [10de:1cb6] (rev a1) Subsystem: Dell Device [1028:1264] Kernel driver in use: nvidia Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Graphics fixed Tom Goddard all ChimeraX