[Dock-fans] WriteDMS problem

John J. Irwin jji at cgl.ucsf.edu
Fri May 22 11:34:20 PDT 2009


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 findany 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" fileusing thechimera's
>> WriteDMS program, which was todaynewly downloadedas 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"
>> Ithink thatmy 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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