Hello,
I'm trying to extract PDB/CIF files from a multi-structure SDF file. At the moment, I'm just writing out one at a time (based on molecule # using -f and -l command-line options). I have confirmed that the extract is correct by writing to an intermediate MOL file; however, the PDB file that is produced is quite incorrect, with improper connectivity, etc., and the corresponding CIF file is also incorrect. Here's the MOL snippet: Structure36 OpenBabel05300818252D 11 11 0 0 0 0 0 0 0 0999 V2000 1.2091 5.5646 0.0000 O 0 0 0 0 0 2.7394 6.4432 0.0000 C 0 0 0 0 0 1.2091 4.1920 0.0000 C 0 0 0 0 0 2.4182 3.4862 0.0000 C 0 0 0 0 0 0.0000 3.4862 0.0000 C 0 0 0 0 0 3.4957 4.1061 0.0000 C 0 0 0 0 0 2.4182 2.0725 0.0000 C 0 0 0 0 0 0.0000 2.0725 0.0000 C 0 0 0 0 0 4.6695 3.4251 0.0000 O 0 0 0 0 0 1.2091 1.3667 0.0000 C 0 0 0 0 0 1.2091 0.0000 0.0000 Br 0 0 0 0 0 1 2 1 0 0 0 1 3 1 0 0 0 3 4 2 0 0 0 3 5 1 0 0 0 4 6 1 0 0 0 4 7 1 0 0 0 5 8 2 0 0 0 6 9 1 0 0 0 7 10 2 0 0 0 8 10 1 0 0 0 10 11 1 0 0 0 M END What I am doing wrong? No matter what I do, I can't seem to get a vali PDB using OpenBabel, either directly from the SDF or the MOL file itself. However, I know the MOL output is valid, as I've used other tools that can successfully produce a PDB/CIF pair (e.g. PRODRG). Thanks in advance for any help. Roni ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
On dimanche 01 juin 2008, Roni Gordon wrote:
> I'm trying to extract PDB/CIF files from a multi-structure SDF file. At > the moment, I'm just writing out one at a time (based on molecule # > using -f and -l command-line options). I have confirmed that the > extract is correct by writing to an intermediate MOL file; however, the > PDB file that is produced is quite incorrect, with improper > connectivity, etc., and the corresponding CIF file is also incorrect. Could you supply an example sdf file and the exact command used that produces the invalid pdb and cif output ? And open a bug report on sf (see: http://sourceforge.net/tracker/?group_id=40728). What version of OB are you using ? -- Vincent Favre-Nicolin Université Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Roni Gordon
On May 30, 2008, at 6:28 PM, Roni Gordon wrote: > extract is correct by writing to an intermediate MOL file; however, > the > PDB file that is produced is quite incorrect, with improper > connectivity, etc., and the corresponding CIF file is also incorrect. I don't think translating to a CIF is a good idea here -- you're taking a MOL file with 2D coordinates only and expecting to have good fractional 3D coordinates. As far as PDB, I'd be curious to know what you mean by "quite incorrect." The PDB file I generate (attached) has connect records, HETATOM, etc. If you can be a bit more specific (e.g., version of Open Babel, etc. as mentioned previously) it would certainly help. Cheers, -Geoff ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
Well, I'm starting from an SDF file, which I presume has correct 3D
coordinates; the reason I used MOL as an intermediate was to use PRODRG to produce a "valid" PDB file that I know is correct (this was my previous procedure before I discovered OpenBabel). I've attached the two different PDB files from babel v2.1.1 vs prodrg using the same MOL input (in my case, I've included Hs, but it doesn't seem make a difference). My modeling software (Coot) doesn't connect the atoms in the same way, so I'm confused. Roni On Mon, 2008-06-02 at 12:55 -0400, Geoffrey Hutchison wrote: > On May 30, 2008, at 6:28 PM, Roni Gordon wrote: > > > extract is correct by writing to an intermediate MOL file; however, > > the > > PDB file that is produced is quite incorrect, with improper > > connectivity, etc., and the corresponding CIF file is also incorrect. > > I don't think translating to a CIF is a good idea here -- you're > taking a MOL file with 2D coordinates only and expecting to have good > fractional 3D coordinates. As far as PDB, I'd be curious to know what > you mean by "quite incorrect." The PDB file I generate (attached) has > connect records, HETATOM, etc. If you can be a bit more specific > (e.g., version of Open Babel, etc. as mentioned previously) it would > certainly help. > > Cheers, > -Geoff > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ![]() ![]() ![]() |
In reply to this post by Roni Gordon
Hi,
[Please answer to the ML so that all can help] On lundi 02 juin 2008, Roni Gordon wrote: > Sorry -- using OB v2.1.1 with the following commands: > > openbabel -isdf library.sdf -omol output.mol -f 36 -l 36 > > openbabel -isdf library.sdf -opdb output.pdb -f 36 -l 36 > > Unfortunately, I can't disclose the contents of the SDF file, it has > thousands of compounds. Could you extract a sub-file with just a few structures so that we can reproduce the problem ? And as Geoff mentioned - what do you mean by "quite incorrect" - wasn't the original data 2D ? -- Vincent Favre-Nicolin Université Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Geoffrey Hutchison
On mardi 03 juin 2008, Roni Gordon wrote:
> Well, I'm starting from an SDF file, which I presume has correct 3D > coordinates; the reason I used MOL as an intermediate was to use PRODRG > to produce a "valid" PDB file that I know is correct (this was my > previous procedure before I discovered OpenBabel). > > I've attached the two different PDB files from babel v2.1.1 vs prodrg > using the same MOL input (in my case, I've included Hs, but it doesn't > seem make a difference). My modeling software (Coot) doesn't connect > the atoms in the same way, so I'm confused. In the attached test.mol, only 2D coordinates are included ? This can't be the intermediate mol file used as input ? Unless prodrg does the 2D->3d transform ? -- Vincent Favre-Nicolin Université Joseph Fourier http://v.favrenicolin.free.fr ObjCryst & Fox : http://objcryst.sourceforge.net ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Roni Gordon
Dear all,
> Well, I'm starting from an SDF file, which I presume has correct 3D > coordinates; the reason I used MOL as an intermediate was to use PRODRG > to produce a "valid" PDB file that I know is correct (this was my > previous procedure before I discovered OpenBabel). > > I've attached the two different PDB files from babel v2.1.1 vs prodrg > using the same MOL input (in my case, I've included Hs, but it doesn't > seem make a difference). My modeling software (Coot) doesn't connect > the atoms in the same way, so I'm confused. The only difference I see is atoms order. To answer to Vincent, I think test.mol is already a 3D conformation, but the molecule is mostly planar. Prodrg doesn't transform from 2D to 3D. In my tests with openbabel 2.1.1 : - Sybyl doesn't read well test-babel.pdb (only 4 atoms are loaded) - Pymol is OK with test-babel.pdb, but all bonds are single (well, OK, it's normal) - Cactvs Browser is OK with test-babel.pdb, the cyclic bonds are correctly double/single - Mview (Chemaxon) reads well test-babel.pdb, but with "~" (any bond) connection Starting from a mol2 ligand, converted in pdb by openbabel or molconvert (Chemaxon): - Sybyl doesn't read well the ligand.pdb - Pymol (all single bond) and Cactvs browser (double bonds where needed) are OK - Mview is unable to load the ligand.pdb... Again, between ligand.pdb"openbabel" and ligand.pdb converted with sybyl (starting from mol2), I don't see any difference, apart from atom ordering. Hope these small comments could help. I wish Coot could read mol2, it would help a lot... By the way, when converting a ligand mol2 in cif, it lost the bond type information (openbabel 2.1.1). Is there a way to keep bond type in .cif file when converting with openbabel ? Because mol2->pdb->cif with eg pdb2cif program is not very useful... Regards, Pascal ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
On mercredi 4 juin 2008, Pascal Muller wrote:
> The only difference I see is atoms order. To answer to Vincent, I > think test.mol is already a 3D conformation, but the molecule is > mostly planar. Prodrg doesn't transform from 2D to 3D. In the test.mol and babel.pdb file, all non-H atoms have 0 as z-coordinate, but not in the prodrg: the -CH2-OH ligand has its OH group out of the ring plane, and the O-CH3 ligand has its methyl group out-of-plane. ... So there has been a 2D->3D transform, even if it does not really break the molecule, just reduces steric problems. btw rasmol reads both pdb's fine. And both molecules look fine too except for some steric problems in the original 2D structure. > By the way, when converting a ligand mol2 in cif, it lost the bond > type information (openbabel 2.1.1). Is there a way to keep bond type > in .cif file when converting with openbabel ? Because mol2->pdb->cif > with eg pdb2cif program is not very useful... Well, there is a _chemical_conn_bond_type CIF keyword which we could use for that. Of course it would require the software that reads the CIF to understand that keyword. Would that be OK ? (There is also a _geom_bond_multiplicity but that does seem to correspond to a number of bonds rather than a bond type.) See the definitions @ http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core.dic/index.html Vincent -- Vincent Favre-Nicolin http://vincefn.net Université Joseph Fourier http://www.ujf-grenoble.fr CEA/ Institut Nanosciences & Cryogénie http://inac.cea.fr ObjCryst & Fox http://objcryst.sourceforge.net ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Geoffrey Hutchison
Hi Vincent,
That does appear to be the case... I went back and checked the SDF to find all Z=0. PRODRG has the option for energy minimization, which gives a reasonable 3D structure with appropriate CIF constraints; but it's web-based. Are there any equivalent command line tools, or other ideas for producing 3D coordinates? Thanks again, Roni > On mardi 03 juin 2008, you wrote: > In the attached test.mol, only 2D coordinates are included ? This > can't be the intermediate mol file used as input ? Unless prodrg does > the 2D->3d transform ? > > -- > Vincent Favre-Nicolin > Université Joseph Fourier > http://v.favrenicolin.free.fr > ObjCryst & Fox : http://objcryst.sourceforge.net ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
This post was updated on .
Dear friends,
I have converted ZINC database SDF file to pdb with openbabel. Then I docked the molecule and checked the interaction with LigPlot, I found the bond order of oxygen were wrong. (Not like those of original ZINC molecule.) Similarly, when I visualize it with Marvin-sketch the bond order of oxygen were not correct. Please find the required file attached. ![]() Regards Jyoti |
In reply to this post by Roni Gordon
The article you have shared here very awesome
potty racers |
In reply to this post by Roni Gordon
The problem with converting sdf-> pdb you share quite well. I learned and understood many things from this problem. I hope you will have many articles to share with us.
vex 3 |
In reply to this post by Roni Gordon
It is a good and amazing article. Your information is very useful for me and for others. Thank you so much.
hotmail login |
In reply to this post by Roni Gordon
On this subject internet page, you'll see my best information, be sure to look over this level of detail
mutilate a doll 2 |
In reply to this post by Roni Gordon
Great info. I love all the posts, I really enjoyed, I would like more information about this, because it is very nice., Thanks for sharing.
basketball legends |
In reply to this post by Roni Gordon
something that is remarkable and should be learned. Thank you for providing this great information. driving directions
|
In reply to this post by Roni Gordon
very nice information you share with us. thanks for this.
gmail login |
Free forum by Nabble | Edit this page |