[Dock-fans] about critical points

Terry Lang terry at cgl.ucsf.edu
Mon Jul 11 17:13:08 PDT 2005


Dear Gaokeng,

Any number of points may be identified as critical, and any number of
groupings of these points may be identified.

1)I want to set sphere #598 to be a critical point. How can I do?

In order to identify sphere 598 as critical, you must change the
second-to-last column number to 1 (or whatever critical cluster you
want it to be associated with).  You have already done so with sphere
number 627. 

2) to set sphere #598, #606 as critical points interacting with one ligand atom?

An identified critical point will be checked to see if it is included in matches to any atom.  As far as I know, there is no way to indicate which of the ligand atoms needs to interact with the critical sphere.  

3) to set sphere #598, #606 as two critical points interacting with more than one ligand atom?

If a particular cluster of critical points is big enough to interact
with more than one ligand atom, then us the "multiple_points" parameter.
In this case, more than one ligand atom will interact with the same
cluster.


Good luck,
Terry


Gaokeng Xiao wrote:

>dear docker,
>   How can I do if I want to assign some sphere as critical point?
>   Here is an example:
>------------------>Begin <---------------------------
>DOCK spheres within 2 ang of ligands
>cluster     1   number of spheres in cluster    39
>  598  46.94954 -42.49070  18.93531   2.339  621 0  0
>  606  52.33147 -37.31442  22.79546   1.463  628 0  0
>  608  52.60658 -36.56995  22.70729   1.840  628 0  0
>  625  47.33886 -40.00112  16.85630   2.350 1072 0  0
>  627  50.23594 -35.06025  17.14066   2.157  958 1  0
>  628  52.47302 -34.45544  20.66748   2.482  971 0  0
>  629  46.66431 -41.89014  18.62379   2.495 1124 0  0
>  635  53.23707 -35.02160  20.93554   2.482 1941 0  0
>  638  55.71145 -35.24515  22.47689   1.804 1942 0  0
>  655  46.83896 -37.44500  16.77731   2.590  993 0  0
>  662  50.94354 -34.90051  16.44710   1.825  958 0  0
>  665  53.16925 -34.52553  20.77136   2.486 1941 0  0
>  666  55.63734 -34.17434  19.82780   1.536  934 0  0
>  932  53.86313 -34.02932  21.03213   2.194 1942 0  0
>  934  55.47961 -34.41681  20.28464   1.844  665 0  0
>  968  52.20306 -34.19293  20.00591   2.381  665 0  0
>  970  52.61612 -32.20029  19.25636   1.418  958 0  0
>  971  52.43204 -34.41806  20.56170   2.487  628 0  0
>  993  46.81341 -37.43943  16.72900   2.578  655 0  0
>  994  49.61068 -34.45226  18.81600   2.279  628 0  0
> 1056  45.53352 -37.18292  18.69988   2.172  629 0  0
> 1057  45.08740 -37.13724  17.53469   1.712 1072 0  0
> 1061  46.31559 -37.13200  15.09777   2.196  655 0  0
> 1067  46.36755 -37.54730  15.29951   2.208  655 0  0
> 1070  47.73100 -42.79192  15.27600   2.915  622 0  0
> 1072  46.73235 -41.84812  18.36446   2.567  629 0  0
> 1123  44.84096 -38.80882  20.12120   2.074  629 0  0
> 1124  46.73950 -44.59031  18.11124   2.897  621 0  0
> 1170  44.95774 -38.60456  20.37759   1.929  629 0  0
> 1251  50.31614 -33.92997  22.36945   1.874  968 0  0
> 1253  50.82179 -34.40342  21.70292   2.161  968 0  0
> 1261  49.62295 -34.38614  20.88740   2.089  968 0  0
> 1262  45.95641 -36.63227  18.79329   2.047  629 0  0
> 1286  50.02219 -33.73341  22.62469   1.721 1251 0  0
> 1941  53.25921 -34.79555  20.84837   2.485  665 0  0
> 1942  53.99007 -34.68626  20.97187   2.439  665 0  0
> 2101  56.24128 -35.36148  21.02347   1.688 2138 0  0
> 2138  55.63465 -35.15976  21.87438   1.863  635 0  0
> 2140  54.31294 -34.64251  20.97530   2.401  665 0  0
> ----------------->End<------------------------------
>For example,1)I want to set sphere #598 to be a critical point. How can I do?
>2) to set sphere #598, #606 as critical points interacting with one ligand atom?
>3) to set sphere #598, #606 as two critical points interacting with more than one ligand atom?
>
>     Best regards,
>     solomon
>
> 				
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Gaokeng Xiao
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡gkxiao at people.com.cn
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-07-09
>_______________________________________________
>Dock-fans mailing list
>Dock-fans at docking.org
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>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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