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## apbs-users

 [Apbs-users] Query about calculating distance from a given residue to the nearest electrostatic peak From: zhiya sheng - 2007-03-14 08:24:28 Attachments: Message as HTML ```Dear all, I’d like to calculate the distance from a given residue in a protein to the nearest electrostatic peak on its surface. Would you please help me to do this with APBS? I am wondering if I could generate a pdb-like file containing the electrostatic potential of each residue in a protein structure, or if I could get the locations (coordinates or something alike) of all electrostatic field peaks on the surface of a protein molecule and how I can do this. In addition, I have to calculate this distance in a number of structures. May I do this in the command-line way instead of running the electrostatics calculation one by one in the APBS Tool window in molecular graphics programs like PyMOL? Any help would be appreciated. Thanks a lot! Best wishes, Zhiya --------------------------------- Mp3疯狂搜-新歌热歌高速下 ```
 Re: [Apbs-users] Query about calculating distance from a given residue to the nearest electrostatic peak From: Nathan Baker - 2007-03-16 11:21:07 ```Hello -- > I=E2=80=99d like to calculate the distance from a given residue in a =20= > protein to the nearest electrostatic peak on its surface. This is an interesting question; however, you'll need to provide more =20= detail. What do you mean by "peak" on its surface? Are you looking =20 for some sort of local maximum/minimum? > Would you please help me to do this with APBS? I am wondering if I =20 > could generate a pdb-like file containing the electrostatic =20 > potential of each residue in a protein structure, or if I could get =20= > the locations (coordinates or something alike) of all electrostatic =20= > field peaks on the surface of a protein molecule and how I can do =20 > this. This should be feasible -- assuming the "peak" definition isn't too =20 complicated. Can I ask why you want to do this? > In addition, I have to calculate this distance in a number of =20 > structures. May I do this in the command-line way instead of =20 > running the electrostatics calculation one by one in the APBS Tool =20 > window in molecular graphics programs like PyMOL? Probably -- once I have a better idea of what you're looking for. Thanks, Nathan > Any help would be appreciated. Thanks a lot! > > Best wishes, > Zhiya > > Mp3=E7=96=AF=E7=8B=82=E6=90=9C-=E6=96=B0=E6=AD=8C=E7=83=AD=E6=AD=8C=E9=AB= =98=E9=80=9F=E4=B8=8B > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```
 [Apbs-users] =?gb2312?q?RE=A3=BA=20Re:=20=20Query=20about=20calculating=20?= =?gb2312?q?distance=20from=20a=20given=20residue=20to=20the=20nearest=20e?= =?gb2312?q?lectrostatic=20peak?= From: zhiya sheng - 2007-03-27 11:10:27 Attachments: Message as HTML ```Dear Prof. Baker, I am sorry for this delay! It is still hard for me to understand those papers about electrostatic peak. However, my supervisor advised me today to calculate the local maximum/minimum potential within a certain area on the protein surface (or inside several grids) around the given residue as peak. As it is reported, a shell is drawn on the FDPB grid, using solvent points that are second nearest neighbor to molecule points, where the molecule is described with a solvent re-entrant surface, and the peak potential I need to calculate is the local extremum within 5% or 10% of the shell closest to the centre of a given residue. And he also said that I might not need the distance, for I just need to obtain the peak or average potential within a certain distance to a given residue to describe the electrostatic property of that residue. Would you please help me to calculate the potential peak or give me some advice on how to extract the electrostatic property of a given residue from APBS output files? Thank you very much! I attached the titles of two papers about this peak here, just in case that you are interested or that I didn’t explain "peak" correctly: Bate P, Warwicker J. Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. Greaves R，Warwicker J. Active Site Identification through Geometry-based and Sequence Profile-based Calculations: Burial of Catalytic Clefts. Thanks again and best wishes to you! Sincerely yours, Zhiya --------------------------------- 抢注雅虎免费邮箱-3.5G容量，20M附件！ ```
 Re: [Apbs-users] =?utf-8?q?RE=EF=BC=9A_Re=3A__Query_about_calculating?= =?utf-8?q?_distance_from_a_given_residue_to_the_nearest_electrostatic_pea?= =?utf-8?q?k?= From: Nathan Baker - 2007-03-29 17:54:33 ```Hello -- > It is still hard for me to understand those papers about =20 > electrostatic peak. However, my supervisor advised me today to =20 > calculate the local maximum/minimum potential within a certain area =20= > on the protein surface (or inside several grids) around the given =20 > residue as peak. As it is reported, a shell is drawn on the FDPB =20 > grid, using solvent points that are second nearest neighbor to =20 > molecule points, where the molecule is described with a solvent re-=20 > entrant surface, and the peak potential I need to calculate is the =20 > local extremum within 5% or 10% of the shell closest to the centre =20 > of a given residue. I'd recommend looking at the Vacc class (http://apbs.sourceforge.net/=20 doc/programmer/html/group__Vacc.html) in APBS for these types of =20 functions. In particular, the Vacc_atomSurf function (http://=20 apbs.sourceforge.net/doc/programmer/html/group__Vacc.html#a8) will =20 return solvent-accessible surface discretizations for each atom. You =20= can use the Vgrid class (http://apbs.sourceforge.net/doc/programmer/=20 html/group__Vgrid.html) to obtain potential values at specific points =20= in space. Together, these two functions should probably do most of =20 what you're looking for. Some initial Python wrappings of the Vgrid functionality can be found =20= in the apbs/tools/python directory. Good luck! -- Nathan > And he also said that I might not need the distance, for I just =20 > need to obtain the peak or average potential within a certain =20 > distance to a given residue to describe the electrostatic property =20 > of that residue. > > Would you please help me to calculate the potential peak or give me =20= > some advice on how to extract the electrostatic property of a given =20= > residue from APBS output files? Thank you very much! > > I attached the titles of two papers about this peak here, just in =20 > case that you are interested or that I didn=A1=AFt explain "peak" =20 > correctly: > > Bate P, Warwicker J. Enzyme/non-enzyme discrimination and =20 > prediction of enzyme active site location using charge-based methods. > > Greaves R=A3=ACWarwicker J. Active Site Identification through = Geometry-=20 > based and Sequence Profile-based Calculations: Burial of Catalytic =20 > Clefts. > > Thanks again and best wishes to you! > > Sincerely yours, > Zhiya > > > =C7=C0=D7=A2=D1=C5=BB=A2=C3=E2=B7=D1=D3=CA=CF=E4-3.5G=C8=DD=C1=BF=A3=AC2= 0M=B8=BD=BC=FE=A3=A1 -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ```