User Manual
Contents
1. pen Secondary Save DAP Save POV Ray input Save WRAL input Save paak fick position of paks in CRYSTALS compatible format 15 file output EDIT ATOMQ 1 X 0 921841 Y 0 254516 Z 0 873093 ATOMQ 1 X 0 941712 Y 0 185850 Z 0 830249 1 X 1 044382 Y 0 186113 Z 0 790634 END 16 Write use newatoms dat to the CRYSTALS command line to import this file into the CRYSTALS 16 Page 4 4 Use previous maps iso levels and maps settings 1 Use example 4 2 to set maps 1so levels and settings as shows the picture Level Control Primary Map M uran AOT Map mode b oa r Pde Capi brea un ics lace seing Revers norma Scroll Bar s mode e CFT Sudan corto Harare 1 650779 ves Suan Lontour ined Mara Lori il Honor krasu i w Revene ncm Sceol Ears mede ig es wv Les Corbis conical rl gih control AEST mede Lower vnde tables 1 a 15471 Lape i a B 15 62m m De v Lael 142708 Laer i p i CL man 20 map contend 0 al map Heg Cancel Agel m Level Control Secondary Map ganar Sure Mona Espora Lia value 8753 k IST n Ju k 0 2 Menu gt Preferences gt Display style Check Use previ2. J map conici 2D map 0 20 rap Hee 10 z DK i gpl Cancel 2 I would like to present this picture from this position but several atoms are in the way Co mmm me File Edit Preferences Tools View Help 5 amp a 19 Page 3 Check if you are in info mode Select atom you want to delete atom get yellow and press d Continue with selecting and delete all needed objects atoms or bonds Press b to go back step by step or press r to restore all deleted objects Untitled MCE File Edit Preferences Tools View Help A A 20 Page 4 6 How to erase the yellow dummy atom 1 If you place an incorrect or dummy yellow atom into the view as shown on the screenshot you have to firstly add this atom Edit gt Add new peak and then erase it Edit gt Clear peak list Delete all peaks From peak list NUM O oa
3. added Eso dte aea uta 10 USE PREVIOUS MAPS ISO LEVELS AND MAPS SETTINGS ccceccecceccccccecceccceccestecccescesteeeestecucestesteensestesueestesteestesees 17 ERASE ATOMS ANDBBONDS3 5 dede E added das salsu Out esca tend dodanou Vea rud odes ou n aale ala os 19 HOW TO ERASE THE YELLOW DUMMY ATOM iis tea ora eu aka SERE tea Cy XY Vu E Rye kon deda Fa Fe vus e Re pasa Ey Varese CEPR EE Y vo Va ae 21 1lPage 1 Introduction MCE 15 an experimental program for 3D and 2D voxel map visualization and for placing atoms into the loaded voxel map The software is mainly focused on visualization of ELD maps calculated from the X ray diffraction data of small unit cells but it also works for small proteins It is compiled for Microsoft Windows systems Windows 95 98 NT 4 Win 2000 Win XP Win 7 The code is written in Microsoft Visual C MFC library and OpenGL library was used MCE runs on PC with at least a Pentium class or equivalent processor This code does not need special device or special PC configuration For most of the work suffice the 1000MHz CPU 256MB RAM and 3D graphic card with OpenGL HW accelerator 2 File format support 2 1 Voxel maps input file formats MCE can read files from different crystallographic or other software e Oxford CRYSTALS e SHELX WinGX e GSAS e XD e JANA2006 e the general 3d ASCII file 2 2 Atom positions input file fo
4. User Manual MCE 2005 For version 3 2 xx Jan Rohl ek amp Michal Hu k Institute of Chemical Technology in Prague Technicka 5 Praha 6 Dejvice Czech Republic 12 7 2012 1 2 2 1 2 2 2 3 3 1 3 2 313 3 4 3 5 4 1 4 2 4 3 4 4 4 5 4 6 INTRODUCTION M te v 2 FILE FORMAT SUPPOR zezadu Ka dasad aaa aol 2 VOXEL MAPS INPUT FIFE FORA TS sos tita cos cea dus erba nan eder ecrit e eee ue a eo cedere ven esa oku a 2 ATOM POSITIONS INPUT FORMATS dee quce ta rua dete Eta edidere OE a 2 OUTPUT FILE FORMA TRE TI 2 MENU v aa sonatas a s dn 3 mii 3 PI PORTET RTT 3 p CER 3 TOOLS ca 4 MIEW Po Pr rcr TTE 4 EXAMPLES ee as en NO ee ao MO L la ao Cato USA A IN Dres 5 LOAD PRIMARY MAP AND CHANGE MAP SETTING CSE cccsccecceccceccecceccecccectectestecccestestecnsestecucestecteessestecusestenss 5 LOADING PRIMARY AND SECONDARY MAP CHANGE MAP PROPERTIES AND COLOR 7 PLACING ATOMS INTO THE MAP case
5. mode 2D or 3D Note If you draw 2D map how to draw 2D map see 3 5 and if you want to place the gold atom you should change picking mode to 2D There is also 3 Page option for changing the default max distance for showing the distances of nearest atoms during placing the new atom see 3 2 Add new peak Display style In this window it is possible to change how to show atoms bonds maps unit cell etc Be careful if you want to change ball or cylinder size or resolution o In ELD map display style it is possible to check use previous map settings If you want to load several similar maps one after another you can check this setting It means that if you load some map and you press Save map settings it saves maps iso levels After this 1f you load another map it starts this map with the saved iso levels o Data type If you check organic it will not calculate inter molecules bonds Color settings In this window it is possible to change background color and primary and secondary map color Periodic table It shows periodic table o Left mouse click change atoms colors o Right mouse click change atoms properties Add atom mode In this mode it is possible to use right mouse click for placing an atom to the map Info mode In this mode it is possible to use right click to select some molecule Note if you select some molecule you can delete it Press d for deleting 3 4 Tools SG setup If you load file with crystall
6. gt View gt Level control secondary map or use icon on toolbar a Uncheck Layerl in primary map green map is dumb b Check Contour amp Surface in Secondary it shows the first layer Layer 1 as a surface and Layerl Layer2 and Layer3 as a contour maps c Check Reverse normals it paints surface inside d UnCheck Layer2 and Layer3 it is now more synoptical This picture shows solvent butan 2 ol in void space in the crystal structure of CsE Level Control Primary Map Level Control Secondary Map Mranum Mamm M arar 22 12278 V 73 5 000900 Map mode Lona ires Canto SS ua ace uu LontoutS ud ace Surface Ki Revene nomi Sulara ran Bs mode Sars mads Lrew Lies E Tod i orim bee orbou line conieal Suslace control Soul ace conia vole Lry akla Laar value 1 80918 v Laert 18758 ied a a ad imn AEF map contol 2Dmap Het U zDmap He 0 Apply Di ppl Cancel 4 3 Placing atoms into the map 1 load primary and secondary map use prim_4_3 fou primary and sec 4 3 fou secondary files red green blue eld map yellow cyan and violet void map pem A I MCE Em Qe prei wwe pem ub uk od WAT AM pa i 131 555612 Map mode Corian bes Cortourh Surfaces Scroll B a
7. and 7 to place all gold atoms to the map pirm 4 3 MCE File Et Preference Tons View Hein I3lPage 9 If you think that these positions are incorrect select menu gt Edit gt Clear peak list It erases all gold atoms pirm A 3 MCE EE Preferences Took View Car peak Delete al peak from pe hst 10 If you have problem with placing atoms to the map or if you would like to place atoms to the minimum you should use 2D picking Set in menu gt preferences gt General setup 2D picking pirm A 3 M General setip 11 Open Level control primary Set 2D map and set the correct height of 2D map Level Control Primary Map 131858512 734098308 Contour ines Suri sce Cornou Suri sce Hone Surface Reverse noma Ln mae liners Scroll Bus mode v Lear Exponencial Lorca ine conmol Sudace conirol Lape M B Lm 753711 Mv leet 211524 Levers DL 20 map Haat 17 7 3 pe Apply Or 13 Now you can place atoms to the 2D map This setting allows you to place atoms anywhere in the 2D map pirm 4 4 Fie Edit Preferences Took View Help uH am 14 If you think you placed atoms correctly you can export theirs coordinates File gt Save peak list I5 Page pirm 4 3 MLE Edt Preference Took Whew Help Open Primary Model
8. ne in external software Save Peaks It saves inserted atoms as a ASCII file which is compatible with CRYSTALS software Save Fragment It saves selected part of the scene as a ASCII file the same file formats as Save Peaks Save restraints for JANA2006 It generates distance and angle restraints file according the actual scene useful for organic compounds 3 2 Edit Add new peak If MCE is in add atom mode you can place a gold atom by clicking right mouse button somewhere to the map If there is more than one unitcell visible only the area of the original unitcell unitcell with zero translation vector 1s working properly It is possible to change its position use right mouse button again If there are atoms in the scene the distances to the nearest atoms are shown up to 3 A by default The actual value can be changed in the menu gt Preferences gt General Setup If you place it to the correct position you can add this atom by using new peak menu item it makes gold atoms After this you can place another one Clear peak list It deletes all already added gold atoms Save map settings This item saves map iso levels If you load another map in the future it will start the map with the saved iso levels See 3 3 Display style how to enable this functionality 3 3 Preference Amination Drag and move scene will rotate General setup It changes projection mode perspective or orthographic and picking
9. ographic information you can select the correct space group It is possible to draw several unit cells together use from and edit boxes 3 5 View Level control primary map If you load some map you can change its properties and isolevel in this window It is possible to visualize map as contour lines surface or its combination Use scroll bars to set the 1solevel which you want to display or set the correct number to the layer value edit box mostly faster If you want to show 2D map tick the 2D map check box and select height If you want to place atom to the 2D map see 3 3 General Setup and 3 2 how to do it Note You can place atom to the red map only If you want to change maps colors see 3 3 Color Settings Level control secondary map If you load secondary map you can change map properties see level control primary 4 Page 4 Examples 4 1 Load primary map and change map setting CsE Example file is in Program files ICT MCE Examples Crystals CsE fou by default 1 uus CsE fou file fc Edit Prefsrences Took View zs seen Model True Save PO Ray input Save input Open primary map data fie 3 E ott CsE file tiled MOE X nc Tools Help ss dd i aft P 5 Page 4 If you want to change map settings use menu gt View gt Level control primary ma
10. ous map settings Ew adl Hla Line Cres B ad and Dimphy Hy Line 5g Dad 02 Cinder E al 05 Cy rider resolution and Scad bal Dic ales factor ball Bands she hwo col Bonds have one eokw ELD map dipl ELD map a ELD mag a1 ee Lre pner Cole bise man selben Setup vaty s Lini cele debit Le nce 13 BILIM lI7 Page 3 Menu gt Edit gt Save map settings 4 Load another map or close MCE and load another map Map s will be loaded with saved settings Umma nia Edit Tesis Yaw dw Hm 18 Page 4 5 Erase atoms and bonds 1 Do example 4 2 Level Control Primary Map m Level Control Secondary mM hiara Haran aiar E T Ti TET 3 3 mode mode ordi culi Ires ETE Contos ire 5 uten ene oce 5 url ics Hora Perant normal Tiera irag Revene nom Scroll Bar s mode Zool lans mode ae ee w b e Conde Corau imne corii Sustece control Soul control Lam vole 0918 i v Laai Mars B lige am Deo 2 29 i a T man
11. p or use icon on toolbar and change map isolevel Untitled File Edit Preferences Tools View Help zu E el Control Primary Ma Minimum Maximum 7 581247 75 089813 Map mode Contour lines Surface Contour amp Surface None Surface settings Reverse normals Surface like lines Scroll Bar s mode Linear Exponencial Contour line control Surface control er value 6 4728 Layers 49 4618 4 2D map control 2D map Height 0 Apply OK 6 Page 4 2 Loading Primary and secondary map change map properties and color settings Example file is in Program files ICT MCE Examples Crystals Primary_model fou ili 8 Open Secondary Model Tawa BMP Save PO Ray input Save VRAL input Open primary map data fie 2 Primary map loaded Untitled MCE _ Fie Ed4 Frefarerces Took Vw Hep I ig ir t Lee iH sk MA 2 7 Page 3 Load Secondary map Untitled MCE Untilird E a TE 3 Pacha Dokumenty 4 3 1 ila Ju Mita v ris Senora Saeed 3 0ubfy Molecule fou gd Iob deli prr olPage 5 Primary and secondary maps are loaded Primary map is electron density and secondary map 15 void map Ele Eda Preferences 6 Use menu gt View gt Level control primary map or use icon on toolbar and menu
12. rmats e Crystallographic file format cif 2 3 output file formats e pov e bitmap bmp e VRML wrl e Peak list ASCII file with atoms coordinates e Fragment position e Restraints for Jana2006 2 Page 3 Menu 3 1 File Open Primary Model See 2 1 for supported file formats Open Secondary Model MCE can read second voxel map which is overlapped with the first one The first and second map must have the same number of lines columns and sections Note if you load primary and secondary map only atoms included in the primary map if any are used You can load for example difference map with void map etc Load Atoms Load Atoms from cif file Voxel map has to be loaded before using this option Note that the unitcell in the cif file and voxel map should be the same Import Fragment Insert fragment from cif file The content of the asymmetric part is inserted to the scene The centre of mass of all inserted atoms 15 calculated and the model is placed to the 0 0 position Load Cavities Import cavities as a balls see the details about the file format on the MCE pages http www vscht cz min mce versions html Save BMP It is possible to save screen as bitmap picture better than CTRL Print Screen Save POV ray input Pov ray is a special file format which enables scene rendering For more details visit http www povray org Save VRML input VRML is a general file format which enables to visualize sce
13. s mode w rem Lontour ie Sue cir control La A 10 Page 3 Open secondary map control and set properties Sur ace d Scroll Bars mode v Linea Contour ine contol Sutface comin Lanes slut w Lai w Lapsi v ise 0888 20 map conira W map Mei Apply 4 Find green peaks in the void space as shows the picture pirm 4 3 dt Preferences Took View d zd 2 111 5 Set the red map primary map Layer3 _ If you want to place atoms to the map primary Layer3 has to be visible Level Control Priman Map m Revera normal uiros ka inet Scroll Bar s mode wv E ponercial Corton iro contol Surface contol Layer Lapar abun v Law 1759711 114524 6 Check if you are in Add atom mode Preferences gt Add atom mode Click on some red peak in the map use right mouse button and place gold atom Repeat right click until the gold atom is in the correct position Right click places atoms only to the maximum Not to the minimum For placing atoms to the other places use 2D map picking see 4 3 10 EEE Eis Edit Preferences Tools View SS zm 12 Page If you find the position correct select menu gt Edit gt Add new peak Eo pirm 4 3 MCE Fie Ei Preferences Took View Hep Sanne resa peak in the Bet at the current cursor position 8 Repeat step 6
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