Thanks for your reply, I am going to run as you said and I will tell you if it works. Best regards Fulvio Saccoccia Il giorno lun, 03/09/2012 alle 11.06 -0700, Jeff Headd ha scritto:

Hi Fulvio,

The crash in phenix.den_refine that you are seeing is because you do not have individual_sites active in your refinement parameters. If you change your den.params file to read:

refine { strategy = *individual_sites rigid_body individual_adp \ group_adp tls occupancies group_anomalous *den }

the refinement should work just fine.

I will add a check to make sure that this behavior is more clear.

Thanks, Jeff

On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia wrote: Dear Phenix users,

here you have an error occurred during a DEN refinement cycle on a twinned structure. Please, help me in order to overcome the problem.

This is the command line I used to run phenix: phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50 convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4 secondary_structure_restraints=true optimize_xyz_weight=true optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb use_geometry_restraints=true den.params fix_rotamers=true

den.params is attached

I was running phenix dev-1145 on a 64bit Debian machine.

This is the error message:

Running DEN torsion optimization on 4 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 100.0 ...trying gamma 0.2, weight 100.0 ...trying gamma 0.0, weight 300.0 ...trying gamma 0.2, weight 300.0 Traceback (most recent call last): File "/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module> den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:]) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py", line 113, in run customized_master_params=master_phil) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py", line 1532, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py", line 830, in refinement_machine log=log) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 88, in __init__ "serious error; please contact [email protected].") % so) RuntimeError: DEN weight optimization failed: DEN cycle 1 rfree at start of SA cycle: 0.4642 k_rep = 1.00 tardy_tree summary: number of vertices: 16570 number of edges: 16855 find cluster loops: 0 repeats number of fixed vertex lists: 0 number of fixed vertices: 0 number of clusters: 7857 merge clusters with multiple connections: 1 pass number of hinge edges: 7857 number of loop edges: 0 number of loop edge bendings: 0 number of fixed hinges: 0

CAUGHT EXCEPTION: (argument #0) ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0) Traceback (most recent call last): File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py", line 155, in __call__ result = O.func(arg) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 227, in try_den_weight_torsion call_back_after_step=False) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 228, in run reduced_geo_manager=reduced_geo_manager) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 86, in __init__ O.weights = target_weights.xyz_weights_result AttributeError: 'NoneType' object has no attribute 'xyz_weights_result'

This is a serious error; please contact [email protected].

Thanks in advance

Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

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Hi Fulvio, I'm sorry that you're still having trouble. I was able to run a test refinement with your den.params input file when adding individual_sites as a refinement strategy. Can you send me your most recent set of parameters and perhaps any .log file that was generated directly to my email (not the list) and I will take closer look. Jeff On Tue, Sep 4, 2012 at 4:14 AM, fulvio saccoccia < [email protected]> wrote:

Dear all, I performed den refinement as suggested by Jeff Headd but it does not work. Just the: phenix.den_refine data.hkl model.pdb (without options at all for den refinement) works. All attempt to use a den_refine.params file (edited in such a way that parameters are different from default ones) were unsuccesful.

Any advices is welcome

Thanks

Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

Il giorno lun, 03/09/2012 alle 11.06 -0700, Jeff Headd ha scritto:

...

Hi Fulvio,

The crash in phenix.den_refine that you are seeing is because you do not have individual_sites active in your refinement parameters. If you change your den.params file to read:

refine { strategy = *individual_sites rigid_body individual_adp \ group_adp tls occupancies group_anomalous *den }

the refinement should work just fine.

I will add a check to make sure that this behavior is more clear.

Thanks, Jeff

On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia wrote: Dear Phenix users,

here you have an error occurred during a DEN refinement cycle on a twinned structure. Please, help me in order to overcome the problem.

This is the command line I used to run phenix: phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50 convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4 secondary_structure_restraints=true optimize_xyz_weight=true optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb use_geometry_restraints=true den.params fix_rotamers=true

den.params is attached

I was running phenix dev-1145 on a 64bit Debian machine.

This is the error message:

Running DEN torsion optimization on 4 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 100.0 ...trying gamma 0.2, weight 100.0 ...trying gamma 0.0, weight 300.0 ...trying gamma 0.2, weight 300.0 Traceback (most recent call last): File

"/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module>

...

den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:]) File

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py",

...

line 113, in run customized_master_params=master_phil) File

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py",

...

line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py", line 1532, in run ncs_manager = self.ncs_manager) File

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py",

...

line 830, in refinement_machine log=log) File

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line

...

88, in __init__ "serious error; please contact [email protected].") % so) RuntimeError: DEN weight optimization failed: DEN cycle 1 rfree at start of SA cycle: 0.4642 k_rep = 1.00 tardy_tree summary: number of vertices: 16570 number of edges: 16855 find cluster loops: 0 repeats number of fixed vertex lists: 0 number of fixed vertices: 0 number of clusters: 7857 merge clusters with multiple connections: 1 pass number of hinge edges: 7857 number of loop edges: 0 number of loop edge bendings: 0 number of fixed hinges: 0

CAUGHT EXCEPTION: (argument #0) ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0) Traceback (most recent call last): File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py", line 155, in __call__ result = O.func(arg) File

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line

...

227, in try_den_weight_torsion call_back_after_step=False) File

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",

...

line 228, in run reduced_geo_manager=reduced_geo_manager) File

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",

...

line 86, in __init__ O.weights = target_weights.xyz_weights_result AttributeError: 'NoneType' object has no attribute 'xyz_weights_result'

This is a serious error; please contact [email protected].

Thanks in advance

Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Hi Fulvio, There's no reason that I'm aware of why you can't use the same phenix installation in multiple concurrent sessions, and I've just tried the scenario you described and it worked fine, even with both jobs writing to the same directory. Are you still getting the same error message, or is it a different error? Jeff On Fri, Sep 7, 2012 at 12:35 AM, fulvio saccoccia < [email protected]> wrote:

Dear Jeff, I am sorry for the delay in reply you. The error can be overcome by running phenix.den_refine (with parallelization) but alone. I mean: it is not possible to run multiple phenix.den_refine tasks, for example in two different console. This would probably occupy the .py subroutine whose error were reported.

What do you think about this explanation? If I run phenix.den_refine with any parameters in den_refine.parameter file, it runs fine.

Bye

Fulvio

Il giorno mar, 04/09/2012 alle 09.42 -0700, Jeff Headd ha scritto:

...

Hi Fulvio,

I'm sorry that you're still having trouble. I was able to run a test refinement with your den.params input file when adding individual_sites as a refinement strategy. Can you send me your most recent set of parameters and perhaps any .log file that was generated directly to my email (not the list) and I will take closer look.

Jeff

On Tue, Sep 4, 2012 at 4:14 AM, fulvio saccoccia wrote: Dear all, I performed den refinement as suggested by Jeff Headd but it does not work. Just the: phenix.den_refine data.hkl model.pdb (without options at all for den refinement) works. All attempt to use a den_refine.params file (edited in such a way that parameters are different from default ones) were unsuccesful.

Any advices is welcome

Thanks

Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

Il giorno lun, 03/09/2012 alle 11.06 -0700, Jeff Headd ha scritto:

> Hi Fulvio, > > > The crash in phenix.den_refine that you are seeing is because you do > not have individual_sites active in your refinement parameters. If you > change your den.params file to read: > > > refine { > strategy = *individual_sites rigid_body individual_adp \ > group_adp tls occupancies group_anomalous *den > } > > > the refinement should work just fine. > > > I will add a check to make sure that this behavior is more clear. > > > Thanks, > Jeff > > On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia > wrote: > Dear Phenix users, > > here you have an error occurred during a DEN > refinement cycle on a > twinned structure. Please, help me in order to overcome the > problem. > > This is the command line I used to run phenix: > phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l > output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50 > convert_to_isotropic=true xray_data.high_resolution=3.6 > nproc=4 > secondary_structure_restraints=true optimize_xyz_weight=true > optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb > use_geometry_restraints=true den.params fix_rotamers=true > > den.params is attached > > I was running phenix dev-1145 on a 64bit Debian machine. > > This is the error message: > > Running DEN torsion optimization on 4 processors... > Running torsion simulated annealing > ...trying gamma 0.0, weight 100.0 > ...trying gamma 0.2, weight 100.0 > ...trying gamma 0.0, weight 300.0 > ...trying gamma 0.2, weight 300.0 > Traceback (most recent call last): > File >

"/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module>

...

> den_refine.run(command_name="phenix.den_refine", > args=sys.argv[1:]) > File >

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py",

...

> line 113, in run > customized_master_params=master_phil) > File >

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py",

...

> line 146, in run > call_back_handler=call_back_handler) > File > "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py", > line 1532, in run > ncs_manager = self.ncs_manager) > File >

"/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py",

...

> line 830, in refinement_machine > log=log) > File >

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line

...

> 88, in __init__ > "serious error; please contact [email protected].") % > so) > RuntimeError: DEN weight optimization failed: > DEN cycle 1 > rfree at start of SA cycle: 0.4642 > k_rep = 1.00 > tardy_tree summary: > number of vertices: 16570 > number of edges: 16855 > find cluster loops: 0 repeats > number of fixed vertex lists: 0 > number of fixed vertices: 0 > number of clusters: 7857 > merge clusters with multiple connections: 1 pass > number of hinge edges: 7857 > number of loop edges: 0 > number of loop edge bendings: 0 > number of fixed hinges: 0 > > CAUGHT EXCEPTION: (argument #0) > ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0) > Traceback (most recent call last): > File > "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py", > line 155, in __call__ > result = O.func(arg) > File >

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line

...

> 227, in try_den_weight_torsion > call_back_after_step=False) > File >

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",

...

> line 228, in run > reduced_geo_manager=reduced_geo_manager) > File >

"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",

...

> line 86, in __init__ > O.weights = target_weights.xyz_weights_result > AttributeError: 'NoneType' object has no attribute > 'xyz_weights_result' > > This is a serious error; please contact > [email protected]. > > Thanks in advance > > Fulvio Saccoccia > PhD student > Dept. of Biochemical Sciences > Sapienza University of Rome > +390649910556 > > > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb

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