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FINDNCS (CCP4: Supported Program)NAMEfindncs - detect NCS operations automatically from heavy atom sitesSYNOPSISfindncs DESCRIPTION================================================ F I N D N C S Looking for NCS relations from heavy atoms sites Version 1.1 Sep-30-1997 ================================================
REFERENCES
IntroductionFINDNCS is a program which automatically find out Non-Crystallographic Symmetry (NCS) operations from heavy atom sites, in order to facilitate applying averaging technique in the MIR/MAD procedure. The program outputs NCS operations (a rotation matrix and translation vector), RMS, polar angles and screw distance, matching sites and other useful information for users. Optionally, the program can also generate some files so that NCS operations can be displayed by the O program automatically.The program requires at least 6 heavy atom sites for each NCS one operations unit i.e. at least 3 sites for each NCS assymetric unit (which can be a protein monomer, dimer, trimer or even higher oligomer). Once the coordinates of the sites were input, they were extended by crystallographic symmetry and lattic repetation. Then the program systematically searches whether a group of sites can match an other group of sites by a NCS operations. There are a number of criteria to choose one NCS operation among crystallographic symmetric related ones:
In some cases, for example, when the number of sites are not too many (less
than 20), the space group is simple (such as triclinic, monoclinic, R3, P3),
and/or the NCS relations are regular (like 222 tetramer 2-fold dimer and
so on) users can run the program fully automatic and accept the suggestions
from the output. However, if users have high symmetry, many HA sites or
many protein molculars with unregular NCS relations, they have to
follow the instruction in this manual to find the NCS step by step.
Alternatively, users can also define the seaching range (which includes
the entire oligomer of the protein) themselves using the knowledge from
solvent flattening map. Otherwise, it might take long CPU time and or
the results are too complicated to understand. For details, please read
through Key Word Command and Frequently Asked Questions of this document.
UNIX example script found in $CEXAM/unix/runnable/Key Word CommandsGeneral: Each line which starts with "!" or "#" will be ignored. The possible keywords are:CELL, COMPOUND, DISP, ERROR, FRCLIM, FSITE, LIST, MAXNCS, MINMATCH, SITE, SPACEGROUP, SPHERE, XYZLIM CELL <a> <b> <c> <alpha> <beta> <gamma>It is neccecary to have cell dimension when coordinates of HA sites are in fraction system or the HA sites have not been put into a correct asymmetric unit. This command must be given before SPACEGROUP, SITE and FSITE command.SPAcegroup <NAME>Space group name or number, e.g. P212121 or 19 If this command is not present, the program will not operate crystalloghpic symmetry and so it only works properly when you already put the HA sites in a correct assymetric unit.ERRor <error>Estimated error of heavy atom site. If the distance of two sites after a NCS operationis less than this value, the program will think these two site join the NCS. I recommend to start with 1/2 of the resultion used by difference PATTERSON/FOURIER which solved the HA sites.MAXNCS <maxncs>Example MAXNCS 20 [default: all the solutiuons] Maximium number of NCSs output in the final output files. If the command is not present, the program will output all the rankned solutions. Usually (I think in more than 99% cases), the solution(s) with highest rank are the correct one.COMPound <compound>Default compound name. The compound name of given sites followed this by comand will be asummed come fromt his compound unless otherwise specified. The name to let the program distinguish HA sites from different compound. If two heavy atom (even from different compound) can binds same site of different NCS related protein molecules but are given different compound name, the program will not use them to calculate NCS operations In this case, oportunity to find the correct NCS might be missed. But in the other hand, if two sites come from different compound by are not given the same, it might give a lot of false "noise" and so it will take longer CPU time to find the correct solution.FSITE <fx> <fy> <fz> [<compound>]Fraction coordinates and compound nameexample: fsite 0.755 0.282 0.146 or fsite 0.689 0.467 0.299 PCMBif the compound name is not give, the program will assume the name is same with the default name from COMPOUND. CELL command must be give before this command. SITE <x> <y> <z> [<compound>]Orthogonal coordinates and compound nameexamples site -13.752 16.271 27.267if the compound name is not give, the program will assume the name is same with the default name from COMPOUND. See convention of the orthogonal system. If the coordinates are already put into the correct asssymetric unit, user does not have to give cell dimension and space group. FRCLIM <xfrclow> <xfrchigh> <yfrclow> <yfrchigh> <zfrclow> <zfrchigh>Fractional xyz limit for searching rangesexample -1. 1. -1. 1. -1. 1.By default, the program extends HA sites to 8 unit cells (XYZ from -1. to 1.), to make sure the the searching range includes the entire protein molecule. However, if the users have many crystallographic operations, (like cubic, hexagonal or tetregonal), it is extramely time consuming to find out in such a range and there are a lot of chances to have "noise" (false NCS). So, users have to find out a smaller searching ranges themselves (see FAQ 4.a). This command can be repeated. see also XYZLIM and SPHEre XYZLIM <xlow> <xhigh> <ylow> <yhigh> <zlow> <zhigh>Orthogonal xyz limit for searching rangesexample -10 50 -100 40 -20 60This command can be repeated; see FRCLIM SPHEre <cenx> <ceny> <cenz> <radii>Searching sphere. Sites which are located inside a sphere with give center position and radii will be used for NCS searching . This command can be repeated. See FRCLIM.DISP <maxdisp> <axislength><MAXDISP> maximum number of sites for graphics displaying, <axislengh> lenghth of the axis displmed by the O program. This command is for generating PDB files and some files which can be used by the O program (Jones et al 1990) to automatically display the results on graphics. For details see FAQ 3.MINMATCH <minmatch>Miniumin site match number. If you have many sites or crystallographic symmetry operations, program will find many false NCS. This command will make the output much cleaner and can also speed up the caculation.LIST <yes> | <no>If yes, some detailed information will be output before the final solution found out.Conventions and example outputThe program uses following convention for orthogonal system X is in A direction Y is in AB plane Z is perpendicular to AB plane Each NCS operation can be described as that an object rotate kappa degree about a certain axis, then move a screwing distance along the direction of this axis In the following for each possible NCS, the program provides: Matching paris: number of matching pairs by the possible NCS solutions is ranked by this number Matching members: the ID number of each site (from input order before crystallographic operation) RMS: root mean square deviation of the superimposed sites Screw: the screwing distance Radii: average distance between center and all joining site Polar angles: they describes the NCS axis as follow psi is the angle between Z and NCS axis phi is the angle between X and image of NCS axis XY plane kappa is the rotation angle. 180=2fold, 90=4-old ... so on the polar angle definition is same as in the POLARRFN program Center: center position of all the joining sites, this can help to find out if two axis interact each otherExample Maximium number of NCS operations to be output 10 Space Group >>> P21 4 Symmetric operation ---- Total: 2 Rotation: 2 8 sites were read in 16 sites after symmetry operations 116 sites are extended to maximium cells Building a distance matrix...... Looking for NCS matches...... Total 285 NCS operations have been found Maxinium atom number 6 generating unit cell frame for O... ---------------------------------------------------------------------- NCS1 with matching pairs 6 1 2 3 4 5 7 4 3 2 1 7 5 NCS matrix: -0.99584 0.08831 0.02261 0.08831 0.87302 0.47961 0.02261 0.47961 -0.87719 65.24355 -19.55399 64.35049 RMS: 0.929 Screw: 0.00 Radii: 41.20 Polar angle: 75.65 87.30 180.00 & 104.35 -92.70 -180.00 Center: 32.07 -21.44 29.19 ---------------------------------------------------------------------- NCS2 with matching pairs 6 2 3 4 5 7 8 3 2 8 7 5 4 NCS matrix: -0.98548 -0.15782 -0.06262 -0.15782 0.71543 0.68063 -0.06262 0.68063 -0.72995 -39.70554 -30.00050 66.40594 RMS: 0.993 Screw: 0.00 Radii: 54.58 Polar angle: 111.56 -84.74 180.00 & 68.44 95.26 -180.00 Center: -21.63 4.36 40.89 ---------------------------------------------------------------------- NCS3 with matching pairs 6 2 3 4 5 6 7 3 2 6 7 4 5 NCS matrix: -0.99408 0.10813 0.01057 0.10813 0.97522 0.19301 0.01057 0.19301 -0.98114 67.17181 -9.37817 58.34059 RMS: 1.197 Screw: 0.00 Radii: 40.59 Polar angle: 84.43 86.87 180.00 & 95.57 -93.13 -180.00 Center: 32.69 -21.11 27.57 ---------------------------------------------------------------------- NCS4 with matching pairs 5 2 4 6 7 8 4 2 7 6 3 NCS matrix: 0.88325 0.04691 0.46656 -0.05447 -0.97798 0.20146 0.46574 -0.20335 -0.86124 -38.24167 57.20192 92.85443 RMS: 0.948 Screw: -14.65 Radii: 36.55 Polar angle: 75.94 -0.12 167.96 & 104.06 179.88 -167.96 Center: -22.16 21.90 50.91 ---------------------------------------------------------------------- NCS5 with matching pairs 5 1 2 4 6 8 8 4 2 7 1 NCS matrix: -0.99553 0.01697 -0.09289 0.01986 -0.92409 -0.38165 -0.09232 -0.38179 0.91963 51.18448 -21.65644 -2.32794 RMS: 1.292 Screw: 0.48 Radii: 56.42 Polar angle: 168.44 76.36 179.92 & 11.56 -103.64 -179.92 Center: 25.93 -9.40 -8.48 ..... CPU time: 1 min 20.5 sec Frequentely Asked Questions1) If I can find NCS real operation from heavy atom sites manually, is it sure the program can find it too?Yes!
2) Can I directly use the NCS matrix from FINDNCS in averaging programs? Sometimes the program does not output the NCS which you want, for example biologically, ABCD is the tetramer biologically, the program can give NCS A_to_B and A'_to_F' where A' and F' are crystallographically equivalent to A and F. You can find it when you try to make the mask before averaging. You can use SPHERE and XYZLIM or FRCLIM. Although FINDNCS does not always give you the exact NCS operation required by averaging programs, it is still much much faster to find out the correct NCS using the program as a tool than find NCS by hand.
2.a) How should I analyse the output of FINDNCS? ---------------------------------------------------------------------- NCS1 with matching pairs 12 1 2 3 4 5 6 7 8 9 10 11 12 4 3 2 1 8 7 6 5 12 11 10 9 NCS matrix: -1.00000 -0.00061 0.00025 -0.00061 0.70840 -0.70581 0.00025 -0.70581 -0.70840 0.74407 -0.21214 -0.51413 RMS: 0.091 Screw: 0.00 Radii: 30.48 Polar angle: 67.55 -89.98 180.00 & 112.45 90.02 -180.00 Center: 0.37 -0.01 -0.30 If you find the following NCS in the same time, ---------------------------------------------------------------------- NCS2 with matching pairs 12 1 2 3 4 5 6 7 8 9 10 11 12 2 1 4 3 6 5 8 7 10 9 12 11 NCS matrix: .... RMS: 0.210 Screw: 0.00 Radii: 30.48 Polar angle: 157.55 -89.46 180.00 & 22.45 90.54 -180.00 Center: 0.37 -0.01 -0.30 ---------------------------------------------------------------------- NCS3 with matching pairs 12 1 2 3 4 5 6 7 8 9 10 11 12 3 4 1 2 7 8 5 6 11 12 9 10 NCS matrix: .... RMS: 0.210 Screw: 0.00 Radii: 30.48 Polar angle: 89.82 0.10 180.00 & 90.18 -179.90 -180.00 Center: 0.37 -0.01 -0.30>From the matching site number, you can find this is a perfect 222 NCS symmetry only from the output. Of course it will be much easier to understand if you look at graphics using the PDB files (and O files if you use O).
3) How to display the results by graphics? If the DISPLAY command is present, the program will generate some files for graphics display. First, it generates a PDB file ncsall.pdb which include all the sites within the searching range. After NCSs have been find out, the program will generate ncs1.pdb ncs2.pdb ..... which includes sites joning operations of NCS1, NCS2 ... and so on. You can use any graphics program to display them.
In the case you use O and/or RAVE:
4) What should I do in the case the program takes an untolerable CPU time?
In this case users have to use smaller searching range defined by commands
FRCLIM, XYZLIM or SPHERE. (The sites number inside selected range can be
found in the line:
148 sites are inside the selection ranges )
4.a) How should I define the searching range? It does not matter if the searching range include more than one entire protein oligomers. (The program should be able to recogonize the crystallographic symmetric equivalent NCSs by finding the joining sites of these NCSs are crystallographic equivalent too.) However, too big searching range might make many sites to be searched and slow down the searching. It is not very practical if the sites inside the range are more than 300. There are several way you can decide the searching range.
AcknowledgementThe author appreciates Professors Gunter Schneider and Ylva Lindqvist for pointing out the possible impact and encouraging me to make the program, Drs. Cristofer Enroth and Ylva Lindqvist for providing test examples. |