modification of nonbonded geo restraints between symmetry mates
Dear PHENIX users, I wonder what is the 'correct' way of (re)defining geometric restraints among atoms. Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners? Thank you in advance for your help! -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185
Alejandro There are a number of options. The most direct is to use phenix.metal_coordination --use-default-bondlengths=1 model.pdb to get an "edits" file which contains a number of bond and angle directives for phenix.refine. Without the --use-default-bondlengths option, the bonds in the model.pdb are used as ideal distances. With the option, the ideal values are quantum chemical calculated distances. Always look in the edits file to make sure it contains the restraints you want. You can remove some (angles are the most likely candidates) and add if desired. You can also run phenix.ready_set model.pdb which will generate the "edits" file and add hydrogens to your model. Nigel On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
Dear PHENIX users,
I wonder what is the 'correct' way of (re)defining geometric restraints among atoms.
Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners?
Thank you in advance for your help!
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Thank you Nigel! I'll try this immediately. ...in the meantime, I still have a question for you : will this handle as well the coordination with atoms on symmetry-related protein neighbors? (don't see those in the elbow.edits that phenix.metal_coordination generates...or am I missing something silly here?) ale Nigel W Moriarty wrote:
Alejandro
There are a number of options. The most direct is to use
phenix.metal_coordination --use-default-bondlengths=1 model.pdb
to get an "edits" file which contains a number of bond and angle directives for phenix.refine. Without the --use-default-bondlengths option, the bonds in the model.pdb are used as ideal distances. With the option, the ideal values are quantum chemical calculated distances.
Always look in the edits file to make sure it contains the restraints you want. You can remove some (angles are the most likely candidates) and add if desired.
You can also run
phenix.ready_set model.pdb
which will generate the "edits" file and add hydrogens to your model.
Nigel
On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
Dear PHENIX users,
I wonder what is the 'correct' way of (re)defining geometric restraints among atoms.
Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners?
Thank you in advance for your help!
-- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185
sorry to bother! ...of course it was silly : the 'shared' Zn atoms are on special positions, so I guess the best way to go is to refine their positions with 0.5 occupancy and that's it (the bond distance with the symmetric of course already being taken into account on the ASU's contents!) best alejandro Alejandro Buschiazzo wrote:
Thank you Nigel!
I'll try this immediately.
...in the meantime, I still have a question for you : will this handle as well the coordination with atoms on symmetry-related protein neighbors? (don't see those in the elbow.edits that phenix.metal_coordination generates...or am I missing something silly here?)
ale
Nigel W Moriarty wrote:
Alejandro
There are a number of options. The most direct is to use
phenix.metal_coordination --use-default-bondlengths=1 model.pdb
to get an "edits" file which contains a number of bond and angle directives for phenix.refine. Without the --use-default-bondlengths option, the bonds in the model.pdb are used as ideal distances. With the option, the ideal values are quantum chemical calculated distances.
Always look in the edits file to make sure it contains the restraints you want. You can remove some (angles are the most likely candidates) and add if desired.
You can also run
phenix.ready_set model.pdb
which will generate the "edits" file and add hydrogens to your model.
Nigel
-- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185
...of course it was silly : the 'shared' Zn atoms are on special positions, so I guess the best way to go is to refine their positions with 0.5 occupancy and that's it (the bond distance with the symmetric of course already being taken into account on the ASU's contents!)
phenix.refine takes the multiplicity of the special position into account. I.e. you probably want to keep the occupancy at 1.0, unless you think the Zn really isn't fully occupied. Is the Zn covalently bound? (That may need a little attention.) Ralf
Alejandro Currently you have to have LINK records in your model.pdb that contain the symmetry details and use phenix.link_edits to generate the correct "edits". I'll have to look into putting the smarts into the metal_coordinate code. Nigel On 2/3/09 9:26 AM, Alejandro Buschiazzo wrote:
Thank you Nigel!
I'll try this immediately.
...in the meantime, I still have a question for you : will this handle as well the coordination with atoms on symmetry-related protein neighbors? (don't see those in the elbow.edits that phenix.metal_coordination generates...or am I missing something silly here?)
ale
Nigel W Moriarty wrote:
Alejandro
There are a number of options. The most direct is to use
phenix.metal_coordination --use-default-bondlengths=1 model.pdb
to get an "edits" file which contains a number of bond and angle directives for phenix.refine. Without the --use-default-bondlengths option, the bonds in the model.pdb are used as ideal distances. With the option, the ideal values are quantum chemical calculated distances.
Always look in the edits file to make sure it contains the restraints you want. You can remove some (angles are the most likely candidates) and add if desired.
You can also run
phenix.ready_set model.pdb
which will generate the "edits" file and add hydrogens to your model.
Nigel
On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
Dear PHENIX users,
I wonder what is the 'correct' way of (re)defining geometric restraints among atoms.
Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners?
Thank you in advance for your help!
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
participants (3)
-
Alejandro Buschiazzo -
Nigel W Moriarty -
Ralf W. Grosse-Kunstleve