Selecting residues with zones when reference is absent
Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver
Hello Carlos, Try these commands: select ligand & nucleic acid z<10 ~select protein z<10 I tried it on examples of nucleic acid structures with ligand and with and without protein: 6raw and 6gld, respectively. If you want just one line of commands, you can put them together with a semicolon between. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2019, at 11:52 AM, Carlos G. Oliver <cgoliver@protonmail.com> wrote:
Hello,
I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins.
The selection command I have so far is:
`select nucleic acid z<10 & protein z>10 & ligand`
This works for PDBs that contain both nucleic acids and protein.
However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand.
I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases.
Thanks!
Carlos G. Oliver
Hello Elaine, That is perfect. Thank you very much! Carlos Sent with ProtonMail Secure Email. ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Monday, September 16, 2019 1:44 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Carlos, Try these commands:
select ligand & nucleic acid z<10 ~select protein z<10
I tried it on examples of nucleic acid structures with ligand and with and without protein: 6raw and 6gld, respectively.
If you want just one line of commands, you can put them together with a semicolon between. I hope this helps, Elaine
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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2019, at 11:52 AM, Carlos G. Oliver cgoliver@protonmail.com wrote: Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver
participants (2)
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Carlos G. Oliver -
Elaine Meng