From: Angel H. <ang...@ua...> - 2006-06-28 13:09:29
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Hello, Inbal Which bonds are you missing? I see all bonds in Jmol 10.2 and 10.3.1, two are partial bonds (I guess dative bonds) Looks the same as in Rasmol, except in this the partial bonds ares oild, normal bonds. Is that youe problem? |
From: Inbal Tuvi-A. <in...@op...> - 2006-06-29 08:25:04
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Hello again, Thank you for the quick answers. I believe the pdb file is written correctly - it is a complex with Mo as the central atom, connected to 4 oxygen atoms and 2 nitrogen atoms. In Jmol 10.0 I do not see the bond between Mo and one of the nitrogen atoms, and the bond between Mo and one oxygen atoms is also missing. I do not have Rasmol, but I checked it with Gaussian View and it looks just fine there. I will try to upgrade Jmol as suggested. By the way, CONQUEST can create various types of molecular files, but I need pdb files for the application I'm working on. Best regards, Inbal =20 -----Original Message----- From: jmo...@li... [mailto:jmo...@li...] On Behalf Of Bob Hanson Sent: Wednesday, June 28, 2006 3:42 PM To: jmo...@li... Subject: Re: [Jmol-users] Problem with display of pdb file Inbal, you should contact the makers of CONQUEST and tell them that they are=20 not writing proper PDB files. They are putting too many connections on the CONECT lines. Specifically, CONECT 1 4 5 6 14 15 16 indicates two hydrogen bonds -- to atoms 15 and 16. This is what Jmol is displaying. If you want to get around this, add the following script to your load=20 command: connect (*) (*) single modify;wireframe 0.15 which says, "connect as a single bond any bond that already exists, and=20 display all bonds at the default bond size" Alternatively, what other output formats does CONQUEST have? I just=20 wrote a Tripos SYBYL mol2 reader for 10.x.16. You could try that instead. Bob Hanson Inbal Tuvi-Arad wrote: >Hello to all, > I have a problem with the way Jmol displays pdb files and hope someone >can help me. I downloaded a pdb file from the CSD. When I open it in >Jmol I can not see all the chemical bonds and some of the atoms are >disconnected. When I open it in Chime, or other chemical software I can >see all the bonds. What could be the reason? > >Following is a copy of the file. > >Sincerely, >Inbal Tuvi-Arad >__________________________________ >Dr. Inbal Tuvi-Arad >Department of Natural Sciences >The Open University of Israel >108 Ravutski St., POB 808,=20 >Raanana, 43107, Israel >Tel: 972-9-778-1773 >Fax: 972-9-778-0661 >Email: in...@op... >__________________________________ > >HEADER CSD ENTRY ADASMO >COMPND UNNAMED >AUTHOR GENERATED BY CONQUEST >CRYST1 10.533 18.217 10.817 90.00 103.08 90.00 P 21/c 2 >CONECT 1 4 5 6 14 15 16 > =20 > Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2006-06-29 13:11:02
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The PDB file is not proper format. See http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html I have forwarded this exchange of emails to CCDC. Bob Hanson Inbal Tuvi-Arad wrote: >Hello again, > Thank you for the quick answers. I believe the pdb file is written >correctly - it is a complex with Mo as the central atom, connected to 4 >oxygen atoms and 2 nitrogen atoms. In Jmol 10.0 I do not see the bond >between Mo and one of the nitrogen atoms, and the bond between Mo and >one oxygen atoms is also missing. I do not have Rasmol, but I checked >it with Gaussian View and it looks just fine there. I will try to >upgrade Jmol as suggested. >By the way, CONQUEST can create various types of molecular files, but I >need pdb files for the application I'm working on. > >Best regards, >Inbal > > >-----Original Message----- >From: jmo...@li... >[mailto:jmo...@li...] On Behalf Of Bob >Hanson >Sent: Wednesday, June 28, 2006 3:42 PM >To: jmo...@li... >Subject: Re: [Jmol-users] Problem with display of pdb file > > >Inbal, > >you should contact the makers of CONQUEST and tell them that they are >not writing proper PDB files. >They are putting too many connections on the CONECT lines. Specifically, > >CONECT 1 4 5 6 14 15 16 > >indicates two hydrogen bonds -- to atoms 15 and 16. >This is what Jmol is displaying. > >If you want to get around this, add the following script to your load >command: > >connect (*) (*) single modify;wireframe 0.15 > >which says, "connect as a single bond any bond that already exists, and >display all bonds at the default bond size" > >Alternatively, what other output formats does CONQUEST have? I just >wrote a Tripos SYBYL mol2 reader for 10.x.16. You could try that >instead. > >Bob Hanson > > >Inbal Tuvi-Arad wrote: > > > >>Hello to all, >> I have a problem with the way Jmol displays pdb files and hope >> >> >someone > > >>can help me. I downloaded a pdb file from the CSD. When I open it in >>Jmol I can not see all the chemical bonds and some of the atoms are >>disconnected. When I open it in Chime, or other chemical software I >> >> >can > > >>see all the bonds. What could be the reason? >> >>Following is a copy of the file. >> >>Sincerely, >>Inbal Tuvi-Arad >>__________________________________ >>Dr. Inbal Tuvi-Arad >>Department of Natural Sciences >>The Open University of Israel >>108 Ravutski St., POB 808, >>Raanana, 43107, Israel >>Tel: 972-9-778-1773 >>Fax: 972-9-778-0661 >>Email: in...@op... >>__________________________________ >> >>HEADER CSD ENTRY ADASMO >>COMPND UNNAMED >>AUTHOR GENERATED BY CONQUEST >>CRYST1 10.533 18.217 10.817 90.00 103.08 90.00 P 21/c 2 >>CONECT 1 4 5 6 14 15 16 >> >> >> >> > > >Using Tomcat but need to do more? Need to support web services, >security? >Get stuff done quickly with pre-integrated technology to make your job >easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache >Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |