How do I make the default label for metal atoms be upper and lower case? For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc. This is true for all two letter atom names. Thanks Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>>>
Hi Mike, Does the FE1 name come from a PDB or Mol2 file you opened? If that name appears in the file, one obvious approach is to change the file replacing FE1 with Fe1. I'm not sure if that will break code that expects FE1. I don't think there are any options in Chimera to manipulate the case of names displayed in labels. I believe Chimera just uses the capitalization of names it obtains from the file it read in. I guess Chimera could have some option to manipulate the case of atom names in labels. But it seems very specialized. Someone looking at a protein with a C-alpha atom named CA generally does not want Ca. This also indicates that it isn't possible to know if an atom name refers to an atomic element (e.g. Fe = iron, Ca = calcium) or something else (like C-alpha). Tom
How do I make the default label for metal atoms be upper and lower case?
For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc.
This is true for all two letter atom names.
Thanks Cheers, Mike
<<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <><
Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <mailto:mikeday@caltech.edu> <<< ------------------------------------------------------------------------>>>
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Hi Mike, I see your test file contains Cu1 and Chimera shows that in a label as CU1 with all upper case. That surprises me. Our expert on that Eric Pettersen can explain it next week. You may be right that Chimera knows the atomic elements and could selectively capitalize labels according to your preferences when the atom name matches the element symbol. Again it is something Eric can advise on. Tom
Tom,
Thanks for the reply.
The file is a PDB, a file with the first few lines is attached.
I was hoping that since Chimera understood atom names well enough to color them that there would be a file with atoms names used for labeling.
If this is something I can change in my installation, great, if not, no worries. I use a mac. I've already changes the python file to understand the non-sttandard space group P21/N.
Cheers, Mike
<<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <><
Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <mailto:mikeday@caltech.edu> <<< ------------------------------------------------------------------------>>>
On Feb 11, 2011, at 2:27 PM, Tom Goddard wrote:
Hi Mike,
Does the FE1 name come from a PDB or Mol2 file you opened? If that name appears in the file, one obvious approach is to change the file replacing FE1 with Fe1. I'm not sure if that will break code that expects FE1. I don't think there are any options in Chimera to manipulate the case of names displayed in labels. I believe Chimera just uses the capitalization of names it obtains from the file it read in.
I guess Chimera could have some option to manipulate the case of atom names in labels. But it seems very specialized. Someone looking at a protein with a C-alpha atom named CA generally does not want Ca. This also indicates that it isn't possible to know if an atom name refers to an atomic element (e.g. Fe = iron, Ca = calcium) or something else (like C-alpha).
Tom
How do I make the default label for metal atoms be upper and lower case?
For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc.
This is true for all two letter atom names.
Thanks Cheers, Mike
<<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125
<>< <>< <>< <>< <>< <>< <>< <>< <>< <><
Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <mailto:mikeday@caltech.edu> <<< ------------------------------------------------------------------------>>>
On Feb 11, 2011, at 4:20 PM, Tom Goddard wrote:
Hi Mike,
I see your test file contains Cu1 and Chimera shows that in a label as CU1 with all upper case. That surprises me. Our expert on that Eric Pettersen can explain it next week. You may be right that Chimera knows the atomic elements and could selectively capitalize labels according to your preferences when the atom name matches the element symbol. Again it is something Eric can advise on.
The upper-casing has been there since "time immemorial" (i.e. Greg doesn't remember why he wrote the code that way ;-) ). I could take it out in the 1.6 daily build and see what happens. It would only affect non-standard PDB files, since all RCSB PDB files use upper case exclusively. The possible negative consequence would be that if some program generates PDB files where the backbone atoms are "ca", "n", "c", etc. then Chimera would no longer recognize them as backbone and would not depict them with ribbons, would not automatically get their atom types correct, etc. Are there major programs out there that generate lower case atom names? Beats me. I can't think of any off the top of my head. If anyone can, please chime in! I guess I'll remove the upper casing (in the 1.6 build) if no one does... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Mike, I don't know if it would help, but you can label atoms by element (which would capitalize the atomic symbol correctly), for example: labelopt info element label ~H That wouldn't get you the full atom name, however. 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 Feb 11, 2011, at 10:24 AM, Michael Day wrote:
How do I make the default label for metal atoms be upper and lower case?
For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc.
This is true for all two letter atom names.
Thanks Cheers, Mike
participants (4)
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Elaine Meng -
Eric Pettersen -
Michael Day -
Tom Goddard