Hi everyone, It is my experience with Chimera on a Macintosh computer that the alternate designation must be case-sensitive. In other words: ~disp :42@.b - will NOT undisplay alternate location B atoms in residue 42 ~disp :42@.B - will undisplay alternate location B atoms in residue 42 YMMV, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62G, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 9/15/11 12:13 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Those A and B are "alternate location" identifiers, and they are part of standard PDB format. Now with higher-resolution structures, sometime more than one position can be identified in the density map, and this allows the depositors to report those multiple positions.
These are described in the "Intro to PDB Format" in the Chimera tutorials <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro .html> .. as well as at the PDB website <http://www.wwpdb.org/documentation/format33/sect9.html#ATOM>
In Chimera you can specify these on the command line as @[atoms].[altlocs] similar to the what we do for chains, :[residues].[chains]
Examples:
color red @.a - color all atoms with alternate location A red
~disp :42@.b - undisplay alternate location B atoms in residue 42
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 15, 2011, at 8:31 AM, Francesco Pietra wrote:
Hello:
Surely a naive question: While beginning to treat a multichain, engineered protein - downloaded from PDB web (1.94 A resolution) - with Chimera, I noticed that many amino acids have such feature as GLU 252 below. Same for many SER, ILE, HIS (two imidazole rings for the same residue number)
ATOM 2022 N GLU A 252 15.171 -45.532 45.115 1.00 26.12 N ATOM 2023 CA AGLU A 252 14.023 -44.631 45.214 0.50 26.30 C ATOM 2024 CA BGLU A 252 14.048 -44.592 45.252 0.50 26.30 C ATOM 2025 C GLU A 252 13.983 -43.654 44.050 1.00 25.90 C ATOM 2026 O GLU A 252 12.894 -43.403 43.470 1.00 25.36 O ATOM 2027 CB AGLU A 252 13.974 -43.909 46.559 0.50 26.93 C ATOM 2028 CB BGLU A 252 14.170 -43.759 46.533 0.50 26.77 C ATOM 2029 CG AGLU A 252 13.283 -44.741 47.629 0.50 29.02 C ATOM 2030 CG BGLU A 252 12.874 -43.673 47.313 0.50 29.14 C ATOM 2031 CD AGLU A 252 14.088 -45.948 48.051 0.50 33.10 C ATOM 2032 CD BGLU A 252 12.806 -44.716 48.426 0.50 31.91 C ATOM 2033 OE1AGLU A 252 13.481 -47.014 48.330 0.50 34.82 O ATOM 2034 OE1BGLU A 252 13.394 -44.454 49.504 0.50 31.18 O ATOM 2035 OE2AGLU A 252 15.333 -45.828 48.101 0.50 35.49 O ATOM 2036 OE2BGLU A 252 12.162 -45.782 48.231 0.50 33.14 O ATOM 2037 N GLU A 253 15.141 -43.133 43.683 1.00 24.58 N ATOM 2038 CA GLU A 253 15.225 -42.212 42.559 1.00 25.11 C ATOM 2039 C GLU A 253 14.838 -42.941 41.242 1.00 23.83 C ATOM 2040 O GLU A 253 14.142 -42.383 40.374 1.00 23.54 O ATOM 2041 CB GLU A 253 16.637 -41.603 42.476 1.00 26.18 C ATOM 2042 CG GLU A 253 17.033 -40.722 43.697 1.00 30.81 C ATOM 2043 CD GLU A 253 17.635 -41.491 44.915 1.00 36.16 C ATOM 2044 OE1 GLU A 253 17.540 -42.742 45.032 1.00 35.80 O ATOM 2045 OE2 GLU A 253 18.198 -40.809 45.801 1.00 40.87 O
About the protein: SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA; SOURCE 3 ORGANISM_TAXID: 300; SOURCE 4 GENE: TMOA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P58KABE;
The said residue are not among those not located in the experiment.
I am interested in channels, pores and so on in the protein, so that the above issue is of most concern for me.
Thanks for aid
francesco pietra
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