Volume 2 Chapter 10 Search Menu PEPTIDE-SEQ
PRINT is used to specify the content and format of text information displayed for a hit.
Graphics QUEST3D Procedure
Equivalent commands in Graphics QUEST3D are discussed under PRINT EXTRA, PRINT NO-HIT, PRINT REFC, PRINT STAND
Basic QUEST Syntax
PRINT n abcd efgh .....
n is the print option number
abcd, efgh etc. are optional search keywords
Remarks
The information which can be displayed for a hit is of 3 types:
(b) If the search question contains tests involving items other than those in (a) then these items will be displayed as part of the hit information.
For example, if a search test involves *BCLA then the basic class information will be displayed in the hit.
(c) Specified items are indicated by the appropriate search keywords.
For example, if you specify SPAC then the space group symbol will be displayed as part of the hit information.
The complete list of items which can be displayed is:
ADAT CCOM ERRO METR PREF RCP6 SYNO AUTH CODE EVER MSDB PROP RCVO TEMP BCLA COMP FORM NBSI QUAL REFC TOLE BATC COOR FSKY NRES RCP1 REMA VOLU BRV1 DENC INTF NW01 RCP2 RFAC YEAR BRV2 DENM MATF NW02 RCP3 SIGF ZPRI CASN DENX MAXA NW03 RCP4 SPAC ZVAL CATF DISO MDAT PAGE RCP5 SPGNThe value of n in PRINT n controls both the content and format of the hit display.
Allowed values of n are: 1-5 and 7-10.
For n=7-10 there are two possible formats - standard and compact.
In standard format each standard reference item starts on a new line whereas in compact format all items are concatenated and separated from each other by //
The standard format is undoubtedly much easier to read.
The various print options are now summarised with an indication of the examples which illustrate their use:
Ex. 12
Ex. 13
Ex. 14
Ex. 15
Ex. 16
Compact format
Ex. 11
Compact format
Ex. 9
Standard format
Ex. 10
Standard format
Exs. 1-8
In the above list option number 6 is missing - this value could be used for a special user-defined display.
N.B. If no PRINT instruction is used and no INIT declared then QUEST sets n=8.
If no PRINT instruction is used and INIT is declared then QUEST sets n=10.
Basic QUEST Procedure
Most of these examples will be illustrated using the entry with reference code ALDCAR.
Ex.1
PRIN 10 T1 *SURN JACOBSON QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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 ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
All standard reference items are present in this entry and are displayed with each starting on a new line.
Note that the four components of the journal reference are linked together on the same line and that the journal coden is replaced by the abbreviated journal name.
Ex.2
PRIN 10 SPAC ZVAL ZPRI NRES T1 *SURN JACOBSON QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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 *SPAC=Pcab // *ZVAL=8.00 // *ZPRI=1.00 // *NRES=1 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
In this example four items have been specified in terms of their search keywords. The values of these items are displayed starting on the line after the journal reference.
Each item is separated from the next by // .
Ex.3
PRIN 10 SPAC ZVAL ZPRI NRES T1 *BCLA .EQ. 11 QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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 *BCLA=11 // *SPAC=Pcab // *ZVAL=8.00 // *ZPRI=1.00 // *NRES=1 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
In this display the standard reference items are followed by the search test item (BCLA) and then by the specified items.
Ex.4
PRIN 10 -REFC SPAC ZVAL ZPRI NRES -SPAC T1 *BCLA .EQ. 11 QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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 *BCLA=11 // *ZVAL=8.00 // *ZPRI=1.00 // *NRES=1 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates that the display of a particular item can be suppressed by prefacing the search keyword with a minus sign. Thus -REFC suppresses the display of the reference code.
Also, SPAC was specified in the PRINT instruction and then later cancelled with -SPAC so that the space group symbol is not displayed.
Ex.5
PRIN 10 EVER T1 *SURN JACOBSON QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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)
In this example the PRINT instruction contains the keyword EVER (everything).
This indicates to QUEST that all items of information should be displayed. Thus the standard reference items (one per line) are then followed by all other items in compact form.
Ex.6
PRIN 10 -EVER REFC COMP T1 *COMP OXIME QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ ALDCAR 2-Methyl-2-methylthio-propionaldehyde O-(methylcarbamoyl) oxime ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
In this example -EVER in the PRINT instruction suppresses all items . Then REFC and COMP are specified with the net result that only the reference code and compound name are displayed.
Ex.7
PRIN 10 -EVER REFC COMP T1 *NAME OXIME QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ ALDCAR 2-Methyl-2-methylthio-propionaldehyde O-(methylcarbamoyl) oxime Aldicarb ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example differs from Ex.6 only in that the search test is based on *NAME rather than *COMP. Since *NAME involves a search of both COMP and SYNO both these records are displayed in the hit output even though only COMP was specified in the PRINT instruction.
Ex.8
PRIN 10 T1 *SURN PERO QUES T1
A hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ ALTENU (+-)-Altenuene C15 H16 O6 A.T.McPhail,R.W.Miller,D.Harvan,R.W.Pero J.Chem.Soc.,Chem.Comm., , 682,1973 ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example simply illustrates the hit information for an entry in which the following standard reference items are missing - SYNO, QUAL and VOLU.
Ex.9
PRIN 8 T1 *SURN PERO QUES T1
A hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ *REFC=ALTENU // *COMP=(+-)-Altenuene // *FORM=C15 H16 O6 // *AUTH=A.T.McPhail,R. W.Miller,D.Harvan,R.W.Pero // *CODE=182(J.Chem.Soc.,Chem.Comm.) // *VOLU= // *PA GE= 682 // *YEAR=1973 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 8.
Comparison with Ex.8 shows that the only difference between option 10 and option 8 is that the latter display is in compact format for all items (including standard reference items).
Ex.10
PRIN 9 SPAC ZVAL ZPRI NRES T1 *BCLA .EQ. 11 QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ 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 *SPAC=Pcab // *ZVAL=8.00 // *ZPRI=1.00 // *NRES=1 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 9.
This option results in the display of the standard reference items and specified items but not search test items. Thus *BCLA is not shown in the display. By contrast option 10 would display *BCLA - see Ex.3.
Ex.11
PRIN 7 SPAC ZVAL ZPRI NRES T1 *BCLA .EQ. 11 QUES T1
The hit display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ *REFC=ALDCAR // *COMP=2-Methyl-2-methylthio-propionaldehyde O-(methylcarbamoyl) oxime // *SYNO=Aldicarb // *QUAL=orthorhombic form, insecticidal activity // *FO RM=C7 H14 N2 O2 S1 // *AUTH=F.Takusagawa,R.A.Jacobson // *CODE=96(J.Agric.Food C hem.) // *VOLU= 25 // *PAGE= 333 // *YEAR=1977 // *SPAC=Pcab // *ZVAL=8.00 // *Z PRI=1.00 // *NRES=1 // ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 7.
Comparison with Ex.10 shows that the only difference between option 9 and option 7 is that the latter display is in compact format for all items (including standard reference items).
Ex.12
PRIN 1 T1 *SURN JACOBSON QUES T1
The display is as follows:
3 hits after 1000 entries, 97% screenout at ADIPAM10 9 hits after 2000 entries, 97% screenout at AMTHZL 9 hits after 3000 entries, 97% screenout at AZFAPD10 ...................................... ......................................This example illustrates the use of print option 1.
Print option 1 corresponds to a fast continue search mode with display only of the number of hits after every 1000 entries and an indication of the percentage screenout at every 1000th entry.
If print option 1 is used then no information is output to the journal file.
Note also that this option results in the default STOP-LIMIT of 1000 hits being ignored and the search continues to the end of the database.
Ex.13
PRIN 2 T1 *SURN JACOBSON QUES T1
The display is as follows:
>Hit = ACXBCD >Hit = ADCDNO >Hit = ADCDNO10 3 hits after 1000 entries, 97% screenout at ADIPAM10 >Hit = AGCNIA >Hit = AGCNIB >Hit = AHMPCU >Hit = ALDCAR >Hit = ALTOCO >Hit = AMIDTH 9 hits after 2000 entries, 97% screenout at AMTHZL 9 hits after 3000 entries, 97% screenout at AZFAPD10 >Hit = AZINPM ...................... ......................This example illustrates the use of print option 2. For hits only the reference codes are displayed.
As for print option 1 (see Ex.12) hit statistics are displayed after every 1000 entries.
Ex.14
PRIN 3 T1 *SURN AYERST QUES T1
The display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+
&&SCREEN:
711231 711231 101025 0 520667 0 0 1
1954 1 40 6 2 1800 295 8
100 1667 1667 1667 36253 51883 56583 8371
11411 11511 3003003 1001001 362499 490922 532950 899800
757189 731349 2 3 1 3 31 1
1 88 189214666 0 0 0 62714860 56513232
50 1 57 112 27 48 15 1
1610661888 33554443 4264008 1316252124470311 69281792 10241192235600
51155139 541065216 15607821 20971728 5369036801358954514 6712279121879048195
1812070712 3 134217728 0 0 0 12461 0
0 4 33 9 4 516 72 0
0 0 4096 20 256 0 148 0
0 0 0 0 17425 0 17 0
0 0 0 0
---------+---------+---------+---------+---------+---------+---------+---------+
Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 3.
This is a debug option which displays the contents of the SCREEN record for each hit.
Ex.15
PRIN 4 T1 *SURN AYERST QUES T1
The display is as follows:
---------+---------+---------+---------+---------+---------+---------+---------+ &&TEXT: ( 1, 7, 588,1954) Acta Crystallogr. Directory= 68 80 88 88 88 112 112 112 112 112 112 OXAMID OXAMID 7 588P-1 C 2H 4N 2O 2 ...C2 H4 N2 O2 Oxamide E.M.Ayerst,J.R.C.Duke ---------+---------+---------+---------+---------+---------+---------+---------+ Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 4.
This is a debug option which displays the contents of the TEXT record for each hit.
Ex.16
PRIN 5 T1 *SURN AYERST QUES T1
The display shows the SCREEN record as in Ex.14, then the TEXT record as in Ex.15, then:
&&CONN:
Directory= 2 6 6 11 17 17 17 17 17 17 23 23 27
>>Field 12
1 1
>>Field 13
100 0 1 6
>>Field 15
51001002 52001003 51001004 52002005 51002006
>>Field 16
103050 103050 6401050 5601250 6401050 5601250
>>Field 22
80 90 100
20000300 30000300 20000200 10000300 30000200 40000300
>>Field 24
2000001 4000002 2000056 2000064
&&DATA
Directory= 0 12 18 24 33 36 42 48
>>Field 2
2 1 1 0 1 2 1 0
1 1 2 0
>>Field 3
64 68 56 68 1 68
>>Field 4
3 3 4 5 0 4
>>Field 5
-610005 27920005 28320005 320005 72300005 23710005 -250005 49400005
36380005
>>Field 6
2566003 2566001 2566002
>>Field 7
3001 4001 1001 2001 5001 6001
>>Field 8
64 1 56 1 1 1
---------+---------+---------+---------+---------+---------+---------+---------+
Type "K"(Keep), "R"(Reject) or "O"(for list of options)
This example illustrates the use of print option 5.
This is a debug option which displays the contents of all records for each hit.