Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?: [cid:image001.png@01D90BDD.3983D7C0] I’d like to have this information in my own PDB files. Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Hello Matt, The full sequence of what was used in the experiment (crystallography, NMR, ...) comes from the SEQRES records in a PDB file: <https://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#...> Those residues included in the SEQRES but without corresponding atomic coordinates will automatically be shown with the black outline box in the sequence window. If you open a PDB file that doesn't have SEQRES records, the sequence window will only reflect what was read from the coordinates. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2022, at 11:47 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?:
<image001.png>
I’d like to have this information in my own PDB files. Thank you, Matt
Thanks Elaine, Do you know of an easy way to convert .fasta to the SEQRES format? Thanks, Matt On 12/9/22, 5:12 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: EXTERNAL EMAIL– Use caution with any links or file attachments. Hello Matt, The full sequence of what was used in the experiment (crystallography, NMR, ...) comes from the SEQRES records in a PDB file: <https://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#...> Those residues included in the SEQRES but without corresponding atomic coordinates will automatically be shown with the black outline box in the sequence window. If you open a PDB file that doesn't have SEQRES records, the sequence window will only reflect what was read from the coordinates. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 9, 2022, at 11:47 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hello ChimeraX Team, > What information in the PDB file specifies the unmodelled residues (in black box)?: > > <image001.png> > > I’d like to have this information in my own PDB files. > Thank you, > Matt This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Hi Matt, Sorry no, I do not. However, I just did a websearch on it out of curiosity and got the following, which I have not tried. <http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_pd...> I don't see how to do it with the top part of the page (PDB seqres isn't one of the output choices as far as I can tell,) but the bottom part of the page explains how to do it with biopython. Caveat emptor since I don't know if works. :-) Best, Elaine
On Dec 9, 2022, at 2:22 PM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Elaine,
Do you know of an easy way to convert .fasta to the SEQRES format?
Thanks, Matt
On 12/9/22, 5:12 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
EXTERNAL EMAIL– Use caution with any links or file attachments.
Hello Matt, The full sequence of what was used in the experiment (crystallography, NMR, ...) comes from the SEQRES records in a PDB file: <https://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#...>
Those residues included in the SEQRES but without corresponding atomic coordinates will automatically be shown with the black outline box in the sequence window. If you open a PDB file that doesn't have SEQRES records, the sequence window will only reflect what was read from the coordinates.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 9, 2022, at 11:47 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?:
<image001.png>
I’d like to have this information in my own PDB files. Thank you, Matt
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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participants (2)
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Elaine Meng -
Jaremko, Matt Joseph