syntax and alternate conformations
Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \ occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }
Hi Mark, Which version of phenix.refine do you have? (phenix.version) With the current release (both full Phenix and CCI Apps released yesterday), you should get what you seem to expect automatically, _without_ the four "group = ..." atom selections. It should also work with CCI Apps 2008_04_25_1421 or later. Let me know if that's not what you observe. Ralf
Hi Mark, 1) I see from the parameters file that you are using an outdated version of the program where there was a bug in occupancy refinement. Please install the latest version. 2) As Ralf mentioned, in the latest version the constraints for occupancies of atoms in alternative conformations are built automatically based on input PDB file. You don't need to change any parameter for this and you don't need to give selections too. Pavel. On 5/27/2008 12:08 PM, Mark Collins wrote:
Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark
refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \
occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }
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Thank you both, I am currently upgrading from 1.3b-rc6 to 1.3-rc2. From both your responses I take it that there is no longer a group_occupancies option but any pdb file containing residues with alternate conformations will be recognized automatically the group_occupancies refined? Mark On May 27, 2008, at 9:00 PM, Pavel Afonine wrote:
Hi Mark,
1) I see from the parameters file that you are using an outdated version of the program where there was a bug in occupancy refinement. Please install the latest version.
2) As Ralf mentioned, in the latest version the constraints for occupancies of atoms in alternative conformations are built automatically based on input PDB file. You don't need to change any parameter for this and you don't need to give selections too.
Pavel.
On 5/27/2008 12:08 PM, Mark Collins wrote:
Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark
refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \
occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }
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------------------------------------------------------------------------ ---------------------- The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...' Isaac Asimov (1920 - 1992) ------------------------------------------------------------------------ ---------------------- Mark Collins Columbia University Dept. of Biochemistry & Molecular Biophysics Hendrickson Lab, Black Building 259/201 Office/Lab 212 305 1951 (work) [email protected]
Hi Mark,
From both your responses I take it that there is no longer a group_occupancies option but any pdb file containing residues with alternate conformations will be recognized automatically the group_occupancies refined?
There still are selections (individual and group), but hopefully you won't need them anymore. Ralf
Hi Mark, yes, group_occupancies is no longer there. By default, phenix.refine will refine occupancies of all atoms in alternative conformations (the constraints on occupancies are built automatically based on input PDB file). On top of it, you can specify your own selections for group and individual occupancy refinement. However note, there will be no constraints applied to user selected occupancies. For example, if you do: group = chain A and resid 113 there will be one occupancy refined per residue 113 in chain A. If you specify multiple groups they will be treated independently. Pavel. On 5/27/2008 9:28 PM, Mark Collins wrote:
Thank you both, I am currently upgrading from 1.3b-rc6 to 1.3-rc2. From both your responses I take it that there is no longer a group_occupancies option but any pdb file containing residues with alternate conformations will be recognized automatically the group_occupancies refined?
Mark
On May 27, 2008, at 9:00 PM, Pavel Afonine wrote:
Hi Mark,
1) I see from the parameters file that you are using an outdated version of the program where there was a bug in occupancy refinement. Please install the latest version.
2) As Ralf mentioned, in the latest version the constraints for occupancies of atoms in alternative conformations are built automatically based on input PDB file. You don't need to change any parameter for this and you don't need to give selections too.
Pavel.
On 5/27/2008 12:08 PM, Mark Collins wrote:
Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark
refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \
occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }
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---------------------------------------------------------------------------------------------- The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...' Isaac Asimov (1920 - 1992) ----------------------------------------------------------------------------------------------
Mark Collins Columbia University Dept. of Biochemistry & Molecular Biophysics Hendrickson Lab, Black Building 259/201 Office/Lab 212 305 1951 (work) [email protected] mailto:[email protected]
------------------------------------------------------------------------
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The new download works like a dream. The occupancy of residues with alternate conformations now sum to 1, using *occupancy in my script. Thank you once again, Mark On May 28, 2008, at 12:28 AM, Mark Collins wrote:
Thank you both, I am currently upgrading from 1.3b-rc6 to 1.3-rc2. From both your responses I take it that there is no longer a group_occupancies option but any pdb file containing residues with alternate conformations will be recognized automatically the group_occupancies refined?
Mark
On May 27, 2008, at 9:00 PM, Pavel Afonine wrote:
Hi Mark,
1) I see from the parameters file that you are using an outdated version of the program where there was a bug in occupancy refinement. Please install the latest version.
2) As Ralf mentioned, in the latest version the constraints for occupancies of atoms in alternative conformations are built automatically based on input PDB file. You don't need to change any parameter for this and you don't need to give selections too.
Pavel.
On 5/27/2008 12:08 PM, Mark Collins wrote:
Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark
refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \
occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }
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---------------------------------------------------------------------- ------------------------ The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...' Isaac Asimov (1920 - 1992) ---------------------------------------------------------------------- ------------------------
Mark Collins Columbia University Dept. of Biochemistry & Molecular Biophysics Hendrickson Lab, Black Building 259/201 Office/Lab 212 305 1951 (work) [email protected]
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participants (3)
-
Mark Collins -
Pavel Afonine -
Ralf W. Grosse-Kunstleve