[Dock-fans] WriteDMS problem

Eric Pettersen pett at cgl.ucsf.edu
Tue May 26 13:17:07 PDT 2009


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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>>

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