[Chimera-users] Double coordinates for same residue

Thu Sep 15 09:28:44 PDT 2011

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 at .b
- will NOT undisplay alternate location B atoms in residue 42

~disp :42 at .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 at 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 at .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
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>
>
>_______________________________________________
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu
>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users