Chimera does not always recognise atom name in PDB ATOM records
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Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma@mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de
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Hi Christian, Here are the rules for atom names in correct PDB format, as I understand them: Atom names start with element symbols right-justified in columns 13-14 as permitted by the length of the name. For example, the symbol FE for iron appears in columns 13-14, whereas the symbol C for carbon appears in column 14. If an atom name has four characters, however, it must start in column 13 even if the element symbol is a single character (for example, some hydrogens). So while it is true that columns 13-16 are for atom names, just putting the names anywhere in that area does not mean the format is correct. The Chimera User's Guide includes some information on PDB format: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 17, 2009, at 6:57 AM, Christian Schudoma wrote:
Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers.
1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N
When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16.
I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc.
The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk...
(*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this.
Any comments on this?
Best regards, Christian Schudoma
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To supplement what Elaine said, without the column-positioning of the atom name it would be impossible to distinguish a carbon alpha (CA) from a calcium (CA). Though if you provide the element symbol in columns 77-78 then the atom name will be ignored for determining the element. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 17, 2009, at 8:41 AM, Elaine Meng wrote:
Hi Christian, Here are the rules for atom names in correct PDB format, as I understand them:
Atom names start with element symbols right-justified in columns 13-14 as permitted by the length of the name. For example, the symbol FE for iron appears in columns 13-14, whereas the symbol C for carbon appears in column 14. If an atom name has four characters, however, it must start in column 13 even if the element symbol is a single character (for example, some hydrogens).
So while it is true that columns 13-16 are for atom names, just putting the names anywhere in that area does not mean the format is correct.
The Chimera User's Guide includes some information on PDB format: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Mar 17, 2009, at 6:57 AM, Christian Schudoma wrote:
Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers.
1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N
When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16.
I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc.
The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk...
(*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this.
Any comments on this?
Best regards, Christian Schudoma
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Thanks Elaine and Eric, for your quick replies and clarification. Nevertheless, the "element column override" (s. below) doesn't work for me, regardless of where in the element record I place a single-character element symbol (neither placing it in column 77 nor in 78). Best regards, Christian Eric Pettersen wrote:
To supplement what Elaine said, without the column-positioning of the atom name it would be impossible to distinguish a carbon alpha (CA) from a calcium (CA). Though if you provide the element symbol in columns 77-78 then the atom name will be ignored for determining the element.
--Eric
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Hi Christian, Chimera is supposed to honor the element column and apparently it is not. I'll open a ticket in the Chimera Trac database for this bug and will put you on the CC list for it. It will definitely be fixed by the next release. Sorry it didn't work! --Eric On Mar 19, 2009, at 6:49 AM, Christian Schudoma wrote:
Thanks Elaine and Eric, for your quick replies and clarification. Nevertheless, the "element column override" (s. below) doesn't work for me, regardless of where in the element record I place a single- character element symbol (neither placing it in column 77 nor in 78).
Best regards, Christian
Eric Pettersen wrote:
To supplement what Elaine said, without the column-positioning of the atom name it would be impossible to distinguish a carbon alpha (CA) from a calcium (CA). Though if you provide the element symbol in columns 77-78 then the atom name will be ignored for determining the element.
--Eric
participants (3)
-
Christian Schudoma
-
Elaine Meng
-
Eric Pettersen