Bob Hanson wrote: > Miguel wrote: > >> The altLocs look like this >> >> ' ' >> ' ' >> 'A' >> 'A' >> 'B' >> 'B' >> ' ' >> ' ' >> 'A' >> 'A' >> 'A' >> 'B' >> 'B' >> 'B' >> ' ' >> ' ' >> >> and the branching looks like this >> ' ' >> ' ' >> 'A' 'B' >> 'A' 'B' >> ' ' >> ' ' >> 'A' 'B' >> 'A' 'B' >> 'A' 'B' >> ' ' >> ' ' >> >> >> So, the question is ... >> >> Q: In the general case, can the 'A' atoms from the first run/branch be >> paired with the 'B' atoms from the second run/branch? >> >> >> > not according to the CIF documentation and examples referred to in my > previous post. > >> Is this a valid confomation? >> ' ' >> ' ' >> 'A' >> 'A' >> ' ' >> ' ' >> 'B' >> 'B' >> 'B' >> ' ' >> ' ' >> >> >> > no, until proven otherwise. There is no mechanism within the CIF > structure to allow for this. > I am a bit late on this thread, but I was absent for two weeks and have to catch up with more than 400 emails in the Jmol-users and Jmol-developers list.
As far as I understand the current PDB format guide available at "http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html"; I don't think that Bob is right that the above conformation is not valid by definition. In the "ATOM" section of the guide the following is stated: "* If an atom is provided in more than one position, then a non-blank alternate location indicator must be used as the alternate location indicator for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator." This implies for me that the same alternate location indicator can be used in different residues for different conformations. Therefore all atoms of one residue with the same alternate location indicator are a "run" in Miguels terminology, which can theoretically (within the format specification) be combined with any other "run" to a valid conformation. Therefore I agree with Frieda that it can only be judged by further knowledge of the file content and the authors intentions if the above conformation would really make sense or not. Regards, Rolf ------------------------------------------------------- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
