findncs
[Keyworded input]
================================================ F I N D N C S Looking for NCS relations from heavy atoms sites Version 1.1 Sep-30-1997 ================================================
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.
Examples
CELL, COMPOUND, DISP, ERROR, FRCLIM, FSITE, LIST, MAXNCS, MINMATCH, SITE, SPACEGROUP, SPHERE, XYZLIM
example: 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.
examples 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.
example -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
example -10 50 -100 40 -20 60This command can be repeated; see FRCLIM
The 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
2) Can I directly use the NCS matrix from FINDNCS in averaging programs?
It depends on the circumstance of protein oligomers. For example,
if you only have a dimer AB in crystallography assymetric unit (asu), the
program can easily find the NCS from A to B (or B to A). However, if you have
tetramer ABCD, the program will give you the NCS matrix A_to_B, A_to_C,
A_to_D, B_to_C, B_to_D and C_to_D, with total 6 matrices while in
most averaging programs you probably only need first 3 matrix. However, your
tetramer is in 222 symmetry, A_to_B/D_to_C should be the same matrix, so
is A_to_C/B_to_D, A_to_D/B_to_C. The program in this case will only
ouput 3 matrix which you can use in the averaging program.
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?
Look at the graphics using the outpdb files and O files.
>From the log output.
For example, you find the following output shows a dimer of 2-fold
symmetry. The joining sites 1-fit-4 and 2-fit-3.... after the 180 deg NCS
operation. (only in two fold symmetry, ste 1 fit 4 and while 4 also fit 1
in the same NCS)
---------------------------------------------------------------------- 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:
The program also generates a file called ncs.ofm which include NCS
operaters, and vectors which can be used by the O program. Then program
will make an O macro file called oncs.mac (together with ncs1.mac, ncs2.mac...).
If users run O under the same directory and type @oncs.mac, there will be
a group of commands appearing in menu bar (@ncs1.mac, @ncs2.mac). If
user want to display first NCS operations found by FINDNCS, click
@ncs1.mac the O program will display a axis and the sites which join the
NCS in yellow and sites superimposed by this NCS.
After runing @oncs.mac The NCS matrix is stored as
.lsq_rt_ncs1
.lsq_rt_ncs2
....
If you have a bones, you can display as two objects (e.g. SKEL and SKEL1)
If you want to see how the 1st NCS works type:
lsq_obj ncs1 SKEL to see how it is superimpose to SKEL1
If you have a electron density call map1, you can use command:
lsq_rt_obj .lsq_rt_ncs1 map1 to superimpose this map.
If you edit the file oncs.mac to take out .lsq_rt_ncs1... to a new file,
it can be directly used by the RAVE packages.
4) What should I do in the case the program takes an untolerable CPU time?
The time of the program is proportional to N*N*N*N*(N-1), where N
is the total number of searhing sites after crystallographic operations. If
this number is more than 300, the calculation will become very slow (10 hours
in a DEC-alpha for 310 atoms, so about 300 hours for 620 atoms). If users
use an automatic mode for XYZ limit (8 unit cells XYZ from -1 to 1), this
number can be found in the follolwing line
736 sites are extended to maximium cells
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 )
Increase MINMATCH is also way to descrease a lot of the CPU time when
there are two many possible solutions are found. If the program
output something like this
Solution: 1000 Max match: 16
i1,i2,i3,j1,j2,j3 1 83 91 57 115 67 CPU time: 103.0 s
Solution: 2000 Max match: 16
i1,i2,i3,j1,j2,j3 4 47 76 58 36 85 CPU time: 379.2 s
You find out maximium matching number is 16 so put minmatch to 6 should
not hurt anything.
4.a) How should I define the searching range?
The idea of defining a searching range is to include at least one entire
protein oligomer so the program would not miss the correct NCS. If a searching
range includes 8 crystallographic ASU homogeneously in XYZ directions, I think
(not proved) an entire protein oligomer won't be missed
in more than 95% cases.
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.
MATCH # 3 with matching pairs 5 MATCH # 4 with matching pairs 5 MATCH # 15 with matching pairs 5 ........ MATCH # 1585 with matching pairs 12 MATCH # 1569 with matching pairs 13 MATCH # 681 with matching pairs 14 MATCH # 1070 with matching pairs 14Now you know the best matching is MATCH 681 so far. You open the file findncs.log and find the MATCH 681 and you can find NCS there. The atom file ncsall.pdb has been generate and you can use graphic to see what this NCS looks like and choose the searching range round the joining sites.