[Dock-fans] WriteDMS problem

Scott Brozell sbrozell at rci.rutgers.edu
Sun May 31 21:41:27 PDT 2009


Hi,

When I added the Write DMS Tool in Chimera option to this tutorial
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
the rec.dms produced by Chimera was read by sphgen, and sphgen
produced a rec.sph. 

I didn't see any .dms attachments to this thread.
If someone sends me the input files then I'll try them.

Scott

On Tue, May 26, 2009 at 01:17:07PM -0700, Eric Pettersen wrote:
> Hi John,
> 	I think the question is whether the Chimera-generated DMS file works 
> with sphgen or not.  If it doesn't then either Chimera or sphgen needs  
> fixing.  The whole point of having Chimera generate the file is so  
> that people don't have to download/compile/install DMS (and a  
> compilation environment).  If they have to use DMS anyway it kind of  
> defeats the purpose.  I was hoping you could try running the Chimera- 
> generated DMS file that had been attached through sphgen and see what  
> happens.  I would myself but I don't have Dock installed and have  
> never run sphgen in my life. :-)
> 
> --Eric
> 
> On May 22, 2009, at 11:34 AM, John J. Irwin wrote:
> 
> >Hi Seungwon & Eric
> >
> >We usually use dms as a standalone program to generate input for  
> >sphgen. As you are using chimera, the output may be subtly different  
> >(?).  I suggest running dms standalone as a control.
> >
> >Good luck
> >
> >John
> >
> >Eric Pettersen wrote:
> >>
> >>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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> >>Dock-fans at docking.org
> >>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >>
> 

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