[Jmol-users] CML visualization in Jmol
Dear All, I use Jmol to visualize CML files within HTML pages. These CML files are generated from Tripos mol2 files. This means that the CML files do countain the connectivities between the atoms. If you look at http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html The second molecule Fragment RA5 (for instance) presents a connection problem and a bond which should not exist is created. See the corresponding file @ http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml The P(2) atom is linked to O(3) and H(20) to O(19) (this is normal), but for instance O(3) should _not_ be linked to H(20). I am aware that this structure presents an un-normal distance (too short) between those O(3) and H(20) atoms. I can understand that Jmol calculates its own connectivities based on atom distances in the absence of connectivity information, but I would expect Jmol to follow the connectivities if the list of connections is provided in the CML file (and not to add new ones). Am I wrong ? Thanks, regards, Francois --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] CML visualization in Jmol
Hi Francois What you need is to deactivate autobonding. On a previos post http://sourceforge.net/mailarchive/message.php?msg_id=12416924 Miguel sayed: Jmol prerelease 10.00.21 is now available It includes support for: 2. set autobond off can be used before loading any file type to prevent auto-bonding. Explicit bonds with the file are retained This should fix your problem (I have not tested it) Good luck winmail.dat
Re: [Jmol-users] CML visualization in Jmol
Francois wrote: This means that the CML files do countain the connectivities between the atoms. [snip] I can understand that Jmol calculates its own connectivities based on atom distances in the absence of connectivity information, Correct. If no connectivity information is presented then Jmol will calculate connectivity. but I would expect Jmol to follow the connectivities if the list of connections is provided in the CML file (and not to add new ones). Am I wrong ? You are correct. The rule is that if connectivity information is present in the file then Jmol will respect that connectivity and will not add any more bonds. (Note that PDB files are an exception to this rule, because the PDB specification calls for optional CONECT records that specify connectivity in addition to the 'normal' bonds.) Regarding your issue Francois ... I have been doing some work to allow people to use scripting commands to add and delete specific bonds. This functionality will allow you to explicitly select the *incorrect* bond and delete it. I plan to release this code within a week. So you may want to test this new functionality before you go to the trouble of adding connectivity to your CML files. Miguel --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] CML visualization in Jmol
Hi Francois What you need is to deactivate autobonding. On a previos post http://sourceforge.net/mailarchive/message.php?msg_id=12416924 Miguel sayed: Jmol prerelease 10.00.21 is now available It includes support for: 2. set autobond off can be used before loading any file type to prevent auto-bonding. Explicit bonds with the file are retained This should fix your problem (I have not tested it) I may have misunderstood his question, but I do not think that this is going to solve the problem for Francois. If any connectivity information is in the file then Jmol will not perform autobonding (with the exception of PDB files). If a file has no connectivity, then Jmol will perform autobonding. Francois indicated that his CML files have no connectivity information. If he uses 'set autobond off' then he will have only atoms, with no bonds at all. If Francois explicitly adds bonds to his CML files then Jmol will not add any additional bonds. 'set autobond off' was implemented for those people who want to draw pictures or clouds of points using xyz files ... basically for applications where people are not displaying molecules. Miguel --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML visualization in Jmol
De: Miguel [EMAIL PROTECTED] Francois indicated that his CML files have no connectivity information. If he uses 'set autobond off' then he will have only atoms, with no bonds at all. In fact, his example contains bond informations: bondArray bond atomRefs2=1 2 order=1/ bond atomRefs2=1 11 order=1/ Apparently, Jmol doesn't understand them. For what I understand from the code of CMLReader, the reader expects to have the atom ids in the atomRefs attribute, not the atom numbers. Nico --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML visualization in Jmol
Quoting Miguel [EMAIL PROTECTED]: Oh oh, I am not sure you understood exactly what I wanted to say ;-) I _do_ have a list a connectivities in the CML file... Please see: http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml I can understand that Jmol calculates its own connectivities based on atom distances in the absence of connectivity information, Correct. If no connectivity information is presented then Jmol will calculate connectivity. OK but I would expect Jmol to follow the connectivities if the list of connections is provided in the CML file (and not to add new ones). Am I wrong ? You are correct. The rule is that if connectivity information is present in the file then Jmol will respect that connectivity and will not add any more bonds. The problem is that Jmol adds two new bonds _besides_ the list of connectivities already available in the CML file... See: http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml Details: The P(2) atom is linked to O(3) and H(20) to O(19) (this is normal), but for instance O(3) should _not_ be linked to H(20). I am aware that this structure presents an un-normal distance (too short) between those O(3) and H(20) atoms. Thanks, Francois --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML visualization in Jmol
Quoting [EMAIL PROTECTED]: In fact, his example contains bond informations: bondArray bond atomRefs2=3D=221 2=22 order=3D=221=22/ bond atomRefs2=3D=221 11=22 order=3D=221=22/ Apparently, Jmol doesn't understand them. For what I understand from the code of CMLReader, the reader expects to ha= ve the atom ids in the atomRefs attribute, not the atom numbers. My mistake, sorry... thanks a lot Nico. Regards, Francois --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML visualization in Jmol
Correct. If no connectivity information is presented then Jmol will calculate connectivity. OK but I would expect Jmol to follow the connectivities if the list of connections is provided in the CML file (and not to add new ones). Am I wrong ? You are correct. The rule is that if connectivity information is present in the file then Jmol will respect that connectivity and will not add any more bonds. The problem is that Jmol adds two new bonds _besides_ the list of connectivities already available in the CML file... Jmol will not do that. The problem is: * the connectivity information in the CML file is invalid * the file reader discards all of the invalid bond records * there is no connectivity information in the file * Jmol calculates *all* of the connectivity See: http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml Nico is correct. The atomRefs must contain references to atom ids. There is no concept of atom number. You have this: atom id=O3' elementType=O x3=-3.505024 y3=-1.071412 z3=1.676940scalar dictRef=jmol:charge-0.5387/scalar/atom atom id=P elementType=P x3=-4.285099 y3=-2.041241 z3=0.839733scalar dictRef=jmol:charge1.2162/scalar/atom ... bond atomRefs2=1 2 order=1/ You need this: bond atomRefs2=O3 P order=1 / Miguel --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid3432bid#0486dat1642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Need set autobonding in documentation
The word autobond does not occur in the Jmol script manual. Please add set autobond on|off to your list for the next manual update, Bob. Thanks, -Eric At 1/25/06, you wrote: Hi Francois What you need is to deactivate autobonding. On a previos post http://sourceforge.net/mailarchive/message.php?msg_id=12416924 Miguel sayed: Jmol prerelease 10.00.21 is now available It includes support for: 2. set autobond off can be used before loading any file type to prevent auto-bonding. Explicit bonds with the file are retained This should fix your problem (I have not tested it) Good luck Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
