Miguel & Jaim wrote: > Please send me the entire file so that I can look at it.
You indicated that the entire file was what was in your original message. I have included it below for reference purposes >> We find out that we're sending some incorrect data to Jmol, >> like a CONNECT with a non-existing atom name (see the example >> at the end). Yes, I see some 'extra' references. >> It turns out that Jmol is too nice with us and draws something. >> Since some of the conections are incorrect, I assume that the >> generated structure is not correct, but I had no other way of >> knowing about the incorrect data. > > That is *not* good. I misunderstood your original message ... >> We hope to fix the data soon, but I think is interesting to >> know what's the default behaviour of Jmol. >> >> Shall Jmol ignore errors and try to draw what's available? Yes, Jmol ignores file errors and makes a 'best efforts' attempt to draw whatever is in the file that is presented. Many people want to do things like cut out pieces of a .pdb file in order to show the structure. Therefore, extra references to atoms are ignored. > Clearly there is a bug in Jmol. It should not generate an image that is > incorrect. I thought that you were saying that Jmol was creating bonds where none existed. That is not the case. Jmol's rendering of the file below *is* correct. It has rendered exactly what you gave it. If the structure does not make sense chemically then you need to use another type of tool for structure verification. >> Shall Jmol report errors somehow and stop? > > Unfortunately, *many* files have errors. I do not think that Jmol should > stop ... other many people will never see anything :-) When errors are encountered Jmol does its best to keep moving and to display what it can. > But it should not draw bonds where none exist ... that is a bug. Jmol has not added any extra bonds to the file below. It draws what you gave it. Jmol does no checking to determine whether or not something makes sense chemically. An atom can have dozens of bonds with arbitrary lengths and Jmol will happily render it. Miguel ------------------ HEADER HEAD LIGAND FS4 HETATM 5763 FE1 FS4 A 733 0.671 35.798 101.733 HETATM 5764 FE2 FS4 A 733 1.708 33.346 101.586 HETATM 5765 FE3 FS4 A 733 2.845 35.141 103.255 HETATM 5766 FE4 FS4 A 733 3.166 35.443 100.573 CONECT 5763 4035 5764 5765 5766 CONECT 5763 5767 5768 5769 CONECT 5764 4125 5763 5765 5766 CONECT 5764 5767 5768 5770 CONECT 5765 4198 5763 5764 5766 CONECT 5765 5768 5769 5770 CONECT 5766 4057 5763 5764 5765 CONECT 5766 5767 5769 5770 CONECT 5767 5763 5764 5766 CONECT 5768 5763 5764 5765 CONECT 5769 5763 5765 5766 CONECT 5770 5764 5765 5766 END ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
