[Dock-fans] WriteDMS problem

Eric Pettersen pett at cgl.ucsf.edu
Wed May 20 11:46:26 PDT 2009


Hi Seungwon,
	I think this is a problem with sphgen, which I have no expertise  
with. The fact that one SC0 records are generated is an artifact of  
MSMS not distinguishing the vertices by type and really should have no  
relevance to the sphere generation AFAIK.  The fact that some of the  
residue atoms are at the start of the DMS file and some are much later  
(if you check, you will see that the atoms are different in the two  
sections) should again not affect sphgen AFAIK.
	It seems that sphgen cannot read the DMS file (which looks fine to  
me).  Not only does sphgen think it has zero atoms but it thinks the  
normal of the first surface point is zero, which it clearly isn't.   
I'm going to forward the file you sent to John Irwin and let him look  
at it and see if he thinks there's any reason sphgen would have  
trouble reading it.

--Eric

On May 19, 2009, at 12:35 AM, 한승원 wrote:

> Dear. Eric Pettersen
>
> I'm Seungwon Han, graduate student at Hanyang Univ. in South Korea
> To tell the truth, I today joined Dock-fans mailing list, but I  
> could'nt link my message
> And I could'nt find any solution for my problem about "dms" file  
> generation, so that suddenly decided to send a email to you. so  
> sorry!!
>
>
> I'm having trouble generating the "dms" file using the chimera's  
> WriteDMS program, which was today newly downloaded as last updated  
> ver1.4
> My dms generating process was like below
> 1. File > open pdb file --> Select > Residue : all nonstandard -->  
> Actions > delete
> 2. Tools > Structure Editing > Dock Prep --> add hydrogen --> save  
> mol2 file
> 3. Actions > suface > show
> 4. Favorites > Model panel > MSMS surface attributes  
> (representaion : dot, vertex density : 5.0)
> 5. Tools > structure analysis > Define Attribute > dmsrad.txt : open
> 6. Tools > Structure Editing > Write DMS : save
>
> From that saved dms file, I knew that "SR0" and "SS0" were not  
> generated(only "SC0"), and the informations of front part residues  
> were repeted at last.
> How can I correctly generate DMS file?
> And when I calculated "sphgen" with that dms file, OUTSPH file  
> could'nt recognize "# of atom"
> I think that my dms generating process was wrong. What's problem of  
> that?
> I'm looking forward to answer to my message...
>
>
>
> Sincerely yours,
>
> Seungwon Han
>
>
> Input pdb file : ../deemo/1_strucu/rec_fixed.pdb
> rec.ms file header of my result
> ---------------------------------------------------------------------------
> GLY 2 N 18.359 26.869 52.955 A
> GLY 2 N 17.053 27.378 52.421 SC0 0.160 -0.871 0.340 -0.356
> GLY 2 N 17.100 27.465 52.399 SC0 0.202 -0.840 0.397 -0.370
> GLY 2 N 17.327 27.044 51.881 SC0 0.287 -0.688 0.117 -0.716
> GLY 2 N 16.946 26.758 52.465 SC0 0.261 -0.942 -0.074 -0.327
> GLY 2 N 16.322 28.009 53.226 SC0 0.044 -0.348 -0.111 -0.931
> GLY 2 N 16.652 27.785 53.057 SC0 0.051 -0.584 0.049 -0.810
> GLY 2 N 16.903 27.568 52.780 SC0 0.040 -0.764 0.204 -0.613
>
> rec.ms file header of demo result
> ----------------------------------------------------------------
> GLY 2 N 18.359 26.869 52.955 A
> GLY 2 N 16.822 28.047 53.058 SR0 0.185 -0.437 0.318 -0.841
> GLY 2 N 16.967 28.492 53.058 SR0 0.185 -0.541 -0.000 -0.841
> GLY 2 N 17.176 28.062 52.797 SR0 0.185 -0.690 0.307 -0.655
> GLY 2 N 17.206! 27.820 54.986 SR0 0.185 -0.781 -0.608 -0.142
> GLY 2 N 17.331 27.628 54.587 SR0 0.185 -0.871 -0.471 0.142
> GLY 2 N 17.051 27.988 54.587 SR0 0.185 -0.670 -0.728 0.142
>
> OUTSPH file
> ----------------------------------------------------------------
> density type = X
> reading rec.ms type R
> #of atoms = 0 # of surf pts = 65867
> findingspheres for rec.ms
> dotlim= 0.000
> radmax= 4.000
> Minimumradius of acceptable spheres?
> 1.39999998
> outputto rec.sph
> SPHGEN:zero normal for surface point 1
> programstops
> -------------------------------------------------------------------------
>  <OUTSPH><rec.dms>

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