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A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). Note that you can get a complete list of jiffies with | A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). Note that you can get a complete list of jiffies with | ||
phenix.list | phenix.list | ||
You can join the [http://www.phenix-online.org/mailman/listinfo/phenixbb PHENIX bulletin board] and/or view its archives. | |||
The documentation below focuses on the non-GUI commandline tools and may not be complete, nor up-to-date or even correct. | The documentation below focuses on the non-GUI commandline tools and may not be complete, nor up-to-date or even correct. | ||
== Installation problem on NFS for Mac OSX (posting of 23 Jan 2015) == | == Installation problem on NFS for Mac OSX (posting of 23 Jan 2015) == | ||
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=== [http://www.phenix-online.org/documentation/reference/elbow.html phenix.elbow] - electronic Ligand Builder and Optimisation Workbench === | === [http://www.phenix-online.org/documentation/reference/elbow.html phenix.elbow] - electronic Ligand Builder and Optimisation Workbench === | ||
Using taxol as an example: this is also named Paclitaxel and one can easily obtain the [https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMILES SMILES string]. Then just watch [https://www.youtube.com/watch?v=8qVYTUVKlbQ this video on phenix.elbow]. | |||
But before you make restraints yourself, check whether it is already in the | |||
dictionary - search on http://ligand-expo.rcsb.org . Taxol should be [http://ligand-expo.rcsb.org/reports/T/TA1/index.html TA1]. | |||
This can then be used in elbow as a chemical component. This option provides more information than the SMILES string. | |||
phenix.elbow --chemical_components=TA1 | |||
== Model building and completion == | == Model building and completion == | ||
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definitions for unknown ligands. | definitions for unknown ligands. | ||
In that case, just running | In that case, just running | ||
phenix. | phenix.ready_set model.pdb | ||
will produce | will produce model.updated.pdb and model.ligands.cif, which may be fed to phenix.refine by | ||
phenix.refine model.pdb data.mtz | phenix.refine model.updated.pdb data.mtz model.ligands.cif ... | ||
If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file. | If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file. | ||
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are different - this turn the non-bonded interaction off so the residues | are different - this turn the non-bonded interaction off so the residues | ||
will get pushed apart. | will get pushed apart. | ||
==== Special positions ==== | |||
Single atoms on (or close enough to) a special position (i.e. on one or more 2-,3-,4- or 6-fold rotation axis/axes) are automatically restrained to stay on that special position. For anything else (like a ligand crossing a symmetry element) the trick is: reducing occupancy to 1/n for a n-fold rotation axis, and excluding atoms from non-bonded repulsions with their symmetry mates - see [[Phenix#Switching_off_specific_interactions]] . | |||
==== Bond across symmetry axis ==== | |||
There is a small hint at | |||
[https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles] | |||
For bonds to symmetry copies, specify the symmetry operation in xyz notation, for example: | |||
symmetry_operation = -x-1/2,y-1/2,-z+1/2 | |||
The whole .eff file might look like: | |||
refinement.geometry_restraints.edits { | |||
bond { | |||
action = *add delete change | |||
atom_selection_1 = chain A and resid 1199 and name O4 | |||
atom_selection_2 = chain A and resid 1196 and name C1 | |||
symmetry_operation = X-1/2,-Y+1/2,-Z | |||
distance_ideal = 1.439 | |||
sigma = 0.020 | |||
} | |||
} | |||
(this is from a posting of Oleg Sobolev to PHENIXBB on Wed, 27 May 2020 15:55:27 -0700) | |||
==== NCS ==== | ==== NCS ==== | ||
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* Automatic detection of NCS groups: | * Automatic detection of NCS groups: | ||
phenix.refine data.hkl model.pdb | phenix.refine data.hkl model.pdb ncs=True ncs_search.enabled=True | ||
* Manual specification of NCS groups: | * Manual specification of NCS groups: | ||
phenix.refine data.hkl model.pdb ncs_groups.params | phenix.refine data.hkl model.pdb ncs_groups.params | ||
where ncs_groups.params contains e.g.: | where ncs_groups.params contains e.g.: | ||
refinement.ncs.restraint_group { | refinement.ncs.restraint_group { | ||
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* run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | * run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | ||
http://skuld.bmsc.washington.edu/~tlsmd/ | http://skuld.bmsc.washington.edu/~tlsmd/ | ||
* or use <code>phenix.find_tls_groups</code> to find TLS groups, and to generate a tls_selections.def file. | |||
* use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/reference/refinement.html | * use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/reference/refinement.html | ||
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Alternatively, phenix.refine can identify TLS groups on-the-fly, using <pre>tls.find_automatically=True</pre> | Alternatively, phenix.refine can identify TLS groups on-the-fly, using <pre>tls.find_automatically=True</pre> | ||
At lower resolution than 1.5A if you run two consecutive refinements, first with TLS | At lower resolution than 1.5A if you run two consecutive refinements, first with TLS | ||
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* In specific (rare !) situations one wants to exclude specific interactions. The pdb_interpretation.custom_nonbonded_symmetry_exclusion=<selection> command line keyword was designed for this purpose. | * In specific (rare !) situations one wants to exclude specific interactions. The pdb_interpretation.custom_nonbonded_symmetry_exclusion=<selection> command line keyword was designed for this purpose. Example (either simply add this on the commandline, after setting the selection appropriately, or if using GUI, find this parameter in "All parameters", and type in atom selection): | ||
custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and sidechain" | |||
* To switch off the interaction between a specific atom and its environment, e.g. to obtain unbiased (by restraints) estimates of distances, see http://www.phenix-online.org/documentation/reference/refinement.html#anch80 - you just add restraints of the form: | * To switch off the interaction between a specific atom and its environment, e.g. to obtain unbiased (by restraints) estimates of distances, see http://www.phenix-online.org/documentation/reference/refinement.html#anch80 - you just add restraints of the form: | ||
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If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation: | If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation: | ||
* if the Phenix binary installer is not used: the Phenix source installer requires (on Fedora and RHEL) the openssl-devel, libXt-devel and bzip2-devel RPM to be installed on the system | * if the Phenix binary installer is not used: the Phenix source installer requires (on Fedora and RHEL) the openssl-devel, libXt-devel, libtiff, libtiff-devel and bzip2-devel RPM to be installed on the system | ||
* to re-compile Rosetta: go to the main/source directory and issue: | * to re-compile Rosetta: go to the main/source directory and issue: | ||
phenix.python scons.py bin mode=release extras=python -j 2 | phenix.python scons.py bin mode=release extras=python -j 2 |