Bob Hanson wrote: > Rolf Huehne wrote: >> Bob Hanson wrote: >>> load "1vwh" "alt/1VWH.cif" "alt/1VWH.cif";color altloc;restrict >>> none;select *;cartoon on >>> model 1001;conformation 1 >>> model 2001;conformation 2 >>> model 0 >>> >>> Do you see what that is doing? >>> >>> >> >> >> It first loads "1VWH.cif" twice as separate models, setting "1vwh" as >> the name displayed. >> Then it colors by altloc and displays only cartoon. >> With "conformation 1/2" the cartoon is calculated for both >> conformations. >> And finally both models are displayed simultaneously. >> >> Very nice! >> >> But I don't understand how the conformation commands are restricted to a >> specific model. > > because they are. They are designed to be restricted to the "current" > model. Otherwise, say you had 5 models loaded, the conformation > command would drive you crazy.
Q: Doesn't that break with the general rule that the current selection is the basis for any manipulation command? At first sight I don't think that I like this behaviour. And I don't think the usual behaviour would drive anyone crazy. It would just provide full control by setting the selection as desired prior to the "conformation" command. >> After loading the command "select *" selects all 4494 atoms from both >> models. > > correct > >> "model 1001" doesn't change the selection. > > correct > >> After "conformation 1" no atoms are selected any more. > > all of model 1001, conformation 1, are selected. Check this with > > color green > or > select selected > This is exactly what I did, a "select selected" after each command in the Jmol console. And Jmol reported "0 atoms selected" after "conformation 1". > >> "model 2001" doesn't change the selection. >> After "conformation 2" still no atoms are selected. > > oh yes, all of conformation 2 are selected. Same as above. >> Another question is how the conformation numbers "1","2" correspond to >> the altLoc indicators? > > 1 refers to the first found in the file, 2 to the next, .... > >> At least in the PDB format file they are "A","B" for 1VWH. Since I am >> not used to read mmCIF files I couldn't figure out yet if they were >> changed to "1","2" there. Since the following characters >> >> '*1234ABCDEFGHIJKLMNOPQRSTUVXYZ >> >> are currently used as altLoc indicators throughout the PDB database it >> would not be obvious how these are mapped to numbers. > > whatever order they are in the file, that maps to the 1 2 3 of the > conformations. Almost certainly this is ABCDE or 12345, so it should > be a pretty natural mapping. > > Hmm, you can have altloc "*", eh? Then we will have to take out > > %* > > and change that to > > %? > > But, really, this "*" and "'" business appears to have been abandoned > or maybe just never implemented. Jaime Prilusky has gathered > information for the ENTIRE PDB database at > http://bip.weizmann.ac.il/oca-bin/altloc and > http://bip.weizmann.ac.il/oca-docs/altLocations.txt, and they always > start with ABC or 123 or sometimes an odd alphabetic character. So the > statement, "are currently used as altLoc indicators throughout the PDB > database" is not quite correct. Do you know of cases where this is * > or '? (maybe outside the context of mmCIF?) > > My pivot table tells me there are 7174 models in the database with > altlocs. Of these, 78 are of the type "123", 7092 are of the type > "ABCDE", and 4 have a mix. Eric has looked, and many of these > numerical or odd ones are mistakes. Of the ABC type, the vast majority > are just "AB", a few more are "ABC", and then we have some others. > 1mx5 uses Y and Z only, for instance. So those would be "conformation > 1 (Y) and conformation 2 (Z). > > None use * or ', even though those might be officially allowed. My > guess is that they are NOT actually being allowed. > > We could write Jmol to allow * or ' when the bug report comes in. :) > > Bob > We have just started to include "altLoc" in our parsing of the entire PDB database, so I havn't looked yet into this in detail. My list above was just a distinct list of all altLoc indicators thast were reported by our parser. We use the PDB format files for parsing. Maybe Jaime used the mmCIF files instead and that could explain differences. After taking a look at some of those entries with "'" (1luh) and "*" (1d6d, 1esy, 1gt2, 1gy8, 1h86, 1vyr, 484d) I would agree that they look like mistakes. 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-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
