CIF behavior in FirstGlance

Preliminary Observations:
Behavior of CIF Files in FirstGlance in Jmol
Eric Martz with FG 0.99, April 2006.

CIF files are loaded by checking an Advanced Option accessed from the main page of FirstGlance, or by adding &cif=1 to the end of the URL.

TEST RESULTS IN BLACK WERE IN JMOL 10.00.48
TEST RESULTS IN MAGENTA WERE IN JMOL 10.00.60
All test results are in SIGNED Jmol.

If you make additional observations, or can explain some of the issues regarding CIF, please email

HETERO does not seem to exist as a selection term in CIF.

Multiple Model NMR files: FirstGlance shows all models for CIF, but only model 1 for PDB. ("All Models" shows all models for both CIF and PDB.) The pickCallback omits the model number

PDB ID Chains Ligand colors Ligand names, behavior

1d66 DNA =C,D in PDB but is A,B in CIF
Protein = A,B in PDB but is C,D in CIF
chains are blue, green, and yellow in both, but PDB magenta is pink in CIF.
Chain names and colors correct. Cd is gray in CIF vs. salmon in PDB.
Cd color correct. Cd is Cd
HOH is CD, can't hide it!

2hhd same id's and colors
Chains correct
Chain 0 reported for everything lacking a chain name, namely HOH. Fe is green in CIF vs. orange in PDB
Fe color correct.

1igt Chains correct.
Chains correct. carbohydrate OK OK All ligand is NAG in CIF. The FUC, MAN, GAL present in PDB become NAG in CIF.
SAME ERROR.

1pgb Secondary structure lost. Unnamed protein chain deemed chain 0, colored green. N/A. HOH OK.

1bkx single chain A of protein. One-residue nucleoside RNA chain remains invisible in Cartoon + Ligand (as with PDB file).
Ditto. Nonstandard residues color darker chain color in PDB but not in CIF.
Ditto. Nonstandard residues select as protein in both PDB and CIF.
Ditto.

1lcd CIF: Na is assigned to chain D, distinct from the true chains A,B, C. (In PDB, Na has no chain designation.
PDB protein is A, CIF protein is C.
PDB DNA is B,C. CIF is A,B.)
Chains correct, but unable to get pickCallback on cartoon of protein chain A. Na is blue in CIF vs. purple in PDB.
Na color correct. All HOH deemed Na (by pickCallback, and selection) not "sodium" and HOH is colored correctly. All models display when only model 1 should.
Only model 1 displays.

PDB ID	Chains	Ligand colors	Ligand names, behavior
1d66	DNA =C,D in PDB but is A,B in CIF Protein = A,B in PDB but is C,D in CIF chains are blue, green, and yellow in both, but PDB magenta is pink in CIF. Chain names and colors correct.	Cd is gray in CIF vs. salmon in PDB. Cd color correct.	Cd is Cd HOH is CD, can't hide it!
2hhd	same id's and colors Chains correct Chain 0 reported for everything lacking a chain name, namely HOH.	Fe is green in CIF vs. orange in PDB Fe color correct.
1igt	Chains correct. Chains correct.	carbohydrate OK OK	All ligand is NAG in CIF. The FUC, MAN, GAL present in PDB become NAG in CIF. SAME ERROR.
1pgb	Secondary structure lost. Unnamed protein chain deemed chain 0, colored green.	N/A.	HOH OK.
1bkx	single chain A of protein. One-residue nucleoside RNA chain remains invisible in Cartoon + Ligand (as with PDB file). Ditto.	Nonstandard residues color darker chain color in PDB but not in CIF. Ditto.	Nonstandard residues select as protein in both PDB and CIF. Ditto.
1lcd	CIF: Na is assigned to chain D, distinct from the true chains A,B, C. (In PDB, Na has no chain designation. PDB protein is A, CIF protein is C. PDB DNA is B,C. CIF is A,B.) Chains correct, but unable to get pickCallback on cartoon of protein chain A.	Na is blue in CIF vs. purple in PDB. Na color correct.	All HOH deemed Na (by pickCallback, and selection) not "sodium" and HOH is colored correctly.	All models display when only model 1 should. Only model 1 displays.