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HELP This help library gives a brief guide to the programs. Help information is also available within the QUEST program. To access the help in QUEST run the program interactively. Example(s) $ CSD $ QUEST JUNK TT: > HELP CONNSER Additional information available: CITATION CSDCONVERT Getting_started GSTAT HELP LICENCE NEW_FEATURES PLUTO Problems QUEST RETFIL Topic?
GSTAT The old on-line help is so out of date as to be misleading and has therfore been removed from the current release. A new on-line help will be prepared if users think this would be useful. If you would like an on-line help feature for GSTAT please write to CCDC. For the address see CSDHELP PROBLEMS. Please refer to the printed manual. Topic?
--> HELP The HELP command accesses a carefully selected subset of the main QUEST documentation, enabling most users to construct search queries at an interactive session without recourse to the printed manuals. HELP is NOT recommended for rank novices: when attempting to use this program for the first time, all beginners are advised to read the introductory documentation thoroughly. At the outset, a proper understanding of how a search question is phrased using individual tests and the operators AND/OR/NOT is absolutely essential for proper and confident use of this software. Having read the above type "HELP GETTING STARTED" if required.
--> GETTING STARTED The "HELP" command should be followed immediately by one or more text strings, each string separated by at least one blank. The difference between upper and lower case characters is ignored. Searched lines containing the string(s) are flagged '-->' in the left hand margin. Consult HELP on the following items for basic information : GRAPHICS - starting the graphical software COMMANDS - main QUEST commands *(keywd) - search keys in QUEST ( "HELP *" for list ) TOPICS - other things known to HELP The HELP documentation is divided into several sections (or pages): the page which is accessed by a particular HELP command depends upon where you are in the program. For example "HELP ALLBOND" will print information on the ALLBOND keyword only when within a *CONNser or SIMIlarity command.
--> TOPICS HELP contains information on the following : Aser Aspect Symbol Bibliography Bravais Lattice CCDC Chemical Class Citation Coden Colours/Colors Commands Configuration Files Contents Crystal System Example Getting Started Initialisation Files Latest News Licence Logical Operator Mask Item Reduced Cell Refcode Searching CSD Topics 3D Screens
--> BIBLIOGRAPHY - June 1992 Bibliographic References to the Scientific Utilisation of the Cambridge Structural Database System have been categorized as follows and grouped under the following HELP keyword : Keyword DATABASE - Database descriptions REVIEW - Review articles NUMSTAT - Numerical and Statistical methods DIMENSION - Mean molecular dimensions INTRAMOL - Intramolecular geometry, substituent effects, bonding CONFORMATION - Conformational analysis and stereochemistry HBONDING - Hydrogen bonding INTERMOL - Intermolecular interactions, reaction pathways, molecular dynamics APPLICATION - Crystallographic applications MODEL - Drug design and modelling CHEMINF - Applications in chemical information science RELEVANT - Papers that are relevant but do not use CSD
This very useful bibliography contains ca. 350 entries. Within each category entries are ordered by decreasing year of publication. It is planned to incorporate these bibliographic entries into the database at a later date.
--> CONFORMATIONAL ANALYSIS AND STEREOCHEMISTRY On the Solid-State Conformations of 18-crown-6 Complexes T.M.Fyles,R.D.Gandour J.Inclusion Phenomena 12,313,1992 Structural Systematics. Part 4. Conformations of the Diphosphine Ligands in M2(mu-Ph2PCH2PPh2) and M(Ph2PCH2CH2PPh2) Complexes D.A.V.Morton,A.G.Orpen J.Chem.Soc.,Dalton Trans. 641,1992 Computation of N-C-N Systems: Theory vs. Experiment. H.Senderowitz,P.Aped,B.Fuchs Tetrahedron 48,1131,1992 etc. etc.
--> CCDC Cambridge Crystallographic Data Centre Union Road, Cambridge CB2 1EZ, United Kingdom Telephone (01223) 336408 Telephone (International) UK (+44) 1223 336408 FAX (01223) 336033 FAX (International) UK (+44) 1223 336033 --> CCDC e-mail email@example.com --> CCDC Fax: Cambridge (01223) 336033 [International +44 1223 336033]
--> LICENCE ======= (LICENCE OF ACCESS TO THE CAMBRIDGE STRUCTURAL DATABASE) The conditions governing all Organisations which have a Licence of Access Agreement to the Cambridge Structural Database are described below. These conditions apply to all users. Specific clauses and modifications, which depend on the nature of the Organisation, e.g. a National Affiliated Centre, an Industrial Company with a number of sites, etc., are included in the actual contract signed by your Organisation, or by the Network Organisation in the case of users who access the Database through a network. For further details please contact either the person responsible for the Licence of Access in your Organisation, or Dr Olga Kennard, Director, Cambridge Crystallographic Data Centre, Union Road, Cambridge CB2 1EZ, U.K. : Telephone from within UK (0223) 336408 International +44 223 336408 FAX from within UK (0223) 336033 >More(Y/N)? y International +44 223 336033 The CCDC, which is a non-profit making Organisation, acts on behalf of the academic community making the results of X-ray structure determinations available in a readily usable form worldwide. In this role the CCDC has a responsibility to ensure that any commercial exploitation of the data is properly regulated for the benefit of the academic community.
--> CITATION To cite the CSDS, use the following reference Allen,F.H., Davies,J.E., Galloy,J.J., Johnson,O., Kennard,O., Macrae,C.F., Mitchell,E.M., Mitchell,G.F., Smith,J.M., & Watson,D.G. (1991) J.Chem.Inf.Comp.Sci. 31, 187-204.
--> CONTENTS -------- Database Version 5.04 Number of entries 102589 Number of compounds 91325 Number of entries with 3D-coordinates 90315 Number of error-free 3D coordinate sets 88565 Number of entries corrected by the CCDC 11520 Number of X-ray Studies 101803 Number of neutron Studies 786 Absolute configuration by X-ray methods 2635 Number of low temperature studies 10795 Number of atoms with 3D coordinates 4737722 Number of different literature sources 634 Total number of Codens Defined 875 >More(Y/N)? y Distribution of Entries in the Different Chemical Classes Class Type of Compound Number of Entries % 1 - 12 Simple aliphatics 5471 5.3 13 - 23 Monocyclic hydrocarbons 5223 5.1 24 - 31 Polycyclic hydrocarbons 4337 4.2 32 - 42 Hetrocyclic compounds 16543 16.1 43 - 59 Natural products 12356 12.0 60 - 61 Molecular complexes, clathrates 2811 2.7 62 - 70 Main group compounds 11837 11.5 71 - 75 Transition Metal complexes (sigma,pi) 17603 17.2 76 - 86 Transition metal complexes (coordination) 26408 25.7 Precision of Structural Results Reliable Factor, R Precision Number of Entries % 1 - 3 Exceptional 6778 6.6 3 - 4 Very high 16976 16.5 4 - 5 High 21225 20.7 5 - 7 Good 29400 28.7 >More(Y/N)? y 7 - 9 Average 13422 13.1 9 - 10 Fair 3564 3.5 10 - 15 Poor 6482 6.3 15 and over Bad 1656 1.6 Not reported ? 3086 3.0
Please type a single-line instruction for QUEST (Press <RETURN> if you don't want to type a line)
--> GLIST `options' The GLIST command will output an entry Geometry LISTing to a separate external file for those hits which are kept during the search. Options can be any combination of BONDs, ANGLes, TORSions with the option NONE being used to cancel previous settings. Please press <RETURN> to continue. Thank you.
Please select a subject for HELP (re-select "HELP" for introductory blurb) (Either use the cursor to select, or type the subject and press <RETURN>)
--> FUSE "FUSE" joins two residues together, eliminating 2 atoms and 1 bond. The position, size, elements and bond-types in the resultant structure are determined by the FIRST residue selected.
Click a button to find out more about it
--> RESET Redraw 3D diagram in default minimum overlap view. Press RETURN to continue.
T1 *CONN <R>
AT1 C 2 <R>
--> *CONNser/SIMIlar HELP info exists for items in CAPITALS below ... *CONN The *CONNser Test initiation line ABANDON (=EXIT/QUIT) Deletes current *CONN/SIMIL command. ALLBOND CYCLIC/ACYCLIC setting of all specified bonds AT Atom definition : NODE NUMBER, ELEMENTS, MCA, NHYD, CHARGE, EXACT, TOTAL COORDN, ACYCLIC, CYCLIC BO Bond definition: NODE NUMBER, bondtype (BT), CYCLIC, ACYCLIC COMMENT Comment line(s) may be inserted anywhere in document DEFB n Reset default bondtype (BT) from 1 (default) to n ELDEF Variable element definition END END of *CONNser instruction packet NFRAG Number of fragment occurrences required NOCR No cyclic routes via unspecified substituents NOLN No links other than those specified NOSCREENS Deactivate connectivity and 3D SCREENS for this Test Q Optional TITLE SAMERES All atoms to be located in same chemical residue TYPE [On-line use only] Types complete current document
--> NOCR ---- Syntax: NOCR or: NOCR [i j k l ...... ] or: NOCR [i-j k l-o p ...... ] NOCR (NO Cyclic Routes) means that no atom in the coded fragment may be connected by a cyclic bond to any atom outside the fragment. It can avoid fusion or bridging of a cyclic fragment, or cyclic substitution of an acyclic fragment. NOCR is normally used without subkeywords, but may be followed by a list of ATom numbers. NOCR then applies only to those specified AToms, rather than all atoms in the fragment. NOCR may be used once only in the *CONNser instruction packet.
Sorry, no information available for this item.
This illustrates the HELP response when you mis-type the name of a topic or if indeed there is no information on the specified topic.
---------+---------+---------+---------+---------+---------+---------+---------+ ALDCAR 2-Methyl-2-methylthio-propionaldehyde O-(methylcarbamoyl) oxime Aldicarb orthorhombic form, insecticidal activity C7 H14 N2 O2 S1 F.Takusagawa,R.A.Jacobson J.Agric.Food Chem., 25, 333,1977 *FSKY=C 7H 14N 2O 2S 1 .. // *PROP="Mp. 98-100deg.C // *PREF=ALDCAR // *ADAT=771 118 // *MDAT=910926 // *MSDB=911014 // *CASN=0 // *NBSI=501145 // *CDRE=5 // *BA TC=8 // *BCLA=11 // *TOLE=.40 // *COOR=12 // *SPGN=61 // *SPAC=Pcab // *RFAC=.09 30 // *TEMP=295 // *MAXA=16 // *ZVAL=8.00 // *DENM=0 // *DENX=1.170 // *DENC=1.1 70 // *RCP1=10.00299 // *RCP2=10.20399 // *RCP3=21.15498 // *RCP4=90.0000 // *RC P5=90.0000 // *RCP6=90.0000 // *SIGF=3 // *MATF=3 // *INTF=3 // *CATF=3 // *METR =32 // *BRV2=10 // *BRV1=10 // *RCVO=2159 // *SCOR=0 // *ZPRI=1.00 // *NRES=1 // *NW01=248 // *NW02=48 // *NW03=140 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
--> Help syntax: "H <text>" e.g. type "H *ADATe" or "H acc da" for info on *ADATe .... etc. Type "K"(Keep), "R"(Reject) or "O"(for list of options)
--> *ZPRIme Number of molecules per asymmetric unit, defined as: cryst. Z-value / no. general equivalent positions for space group Z' may be less than or greater than unity. It can have some very strange values for disordered structures. If Z is not available or the space group is not properly determined, then Z' is set to zero. Type "K"(Keep), "R"(Reject) or "O"(for list of options)
Volume 1 Chapter 13 Customising your QUEST/QUEST3D Implimentation.