Yes, this trivial combination of two commands will do it: phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb then do --show-adp-statistics phenix.pdbtools protein_only.pdb --show-adp-statistics phenix.pdbtools rna_only.pdb --show-adp-statistics phenix.pdbtools water_only.pdb --show-adp-statistics Pavel. On 4/27/10 9:08 AM, Raja Dey wrote:

Hi, I need the values of B factors for Protein and DNA part separately in a Protein-DNA complex to prepare Table 1. I am not sure if PHENIX is doing that calculation. Can anyone tell me how I can get those values? Thanks...

Raja

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Hi Young-Jin,

Let me ask a similar but different question. I have two molecules (A and B). I was trying to put A molecule with neighbor waters or inside A waters only while excluding B or B molecule neighbored waters: Let me simplify if we can make separate A and B pdb files while have waters only 5A near to A or B molecules?

I did from Pymol before, but wondering if phenix can do in simpler way.

no easy way exposed to the user-level for doing this in PHENIX. It would take me 10 minutes to write a custom Python script that will use CCTBX tools for this. Pavel.

You can optimise the geometry with eLBOW. One of the most frequent problems is the quality of the input. The better chemical representation of the molecule, the better eLBOW will work. GIGO. If you are able, send me the input file directly and I'll help you with the optimisation. Nigel On 4/27/10 11:09 AM, r n wrote:

Hi all

I do have crystal structure of my ligand and trying to optimise the geometry using phenix.elbow. It entirely rotate one of the ring bond to other side and in result of breaking the ring geometry. Ring contain sulphur and other heavy metal.

Is it any way to optimize with current geometry in phenix.elbow so that it wont ruin the molecule? Thanks ram

------------------------------------------------------------------------

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ooh ooh ooh--I know this! Look in the .geo file On 13 May 2010, at 5:34 PM, Maia Cherney wrote:

Dear phenixbb, how to get listed all dihedral angles from a ligand after refinement. (Not ideal cif files, but actual dihedral angles).

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

--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif? Maia Nigel Moriarty wrote:

As Patrick correctly stated you should look in the .geo. All the geometry information is written there and it is instructive to look there. There is, however, an alternative if you wish to get more info about a ligand. You can type

phenix.reel lig,cif model.cif

choose "Geometry transfer". You can then compare the ideal and the actual values of all of the restraints listed in the CIF restraints file. You may have to choose the pull-down menu View->List geometry values depending on your version.

Nigel

On Thu, May 13, 2010 at 2:35 PM, Patrick Loll wrote:

...

ooh ooh ooh--I know this!

Look in the .geo file

On 13 May 2010, at 5:34 PM, Maia Cherney wrote:

...

Dear phenixbb, how to get listed all dihedral angles from a ligand after refinement. (Not ideal cif files, but actual dihedral angles).

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

--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA

(215) 762-7706 [email protected]

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I got the error Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/phenix-1.6.1-357/reel/reel/command_line/main.py", line 20, in <module> reel_frame.ProcessArguments(args, options) File "/usr/local/phenix-1.6.1-357/reel/reel/ReelFrame.py", line 1935, in ProcessArguments overlay=options.overlay, File "/usr/local/phenix-1.6.1-357/reel/reel/ReelFrame.py", line 1124, in LoadFile overlay=overlay, File "/usr/local/phenix-1.6.1-357/reel/reel/MoleculeNotebook.py", line 127, in ReadFile if atom1.unique_residue_key==atom2.unique_residue_key: AttributeError: AtomClass instance has no attribute 'unique_residue_key' Maia Nigel Moriarty wrote:

That should be model.pdb, the final model from the refinement.

Sorry

Nigel

On Thu, May 13, 2010 at 4:32 PM, Maia Cherney wrote:

...

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif?

Maia

Nigel Moriarty wrote:

...

As Patrick correctly stated you should look in the .geo. All the geometry information is written there and it is instructive to look there. There is, however, an alternative if you wish to get more info about a ligand. You can type

phenix.reel lig,cif model.cif

choose "Geometry transfer". You can then compare the ideal and the actual values of all of the restraints listed in the CIF restraints file. You may have to choose the pull-down menu View->List geometry values depending on your version.

Nigel

On Thu, May 13, 2010 at 2:35 PM, Patrick Loll wrote:

...

ooh ooh ooh--I know this!

Look in the .geo file

On 13 May 2010, at 5:34 PM, Maia Cherney wrote:

...

Dear phenixbb, how to get listed all dihedral angles from a ligand after refinement. (Not ideal cif files, but actual dihedral angles).

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

--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA

(215) 762-7706 [email protected]

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Maia You can save a CIF file from REEL using a pull-down menu under File. However, I'm a little unclear on what you are trying to achieve. Can you elaborate? Nigel On Thu, May 13, 2010 at 9:25 PM, Maia Cherney wrote:

Hi Nigel, The phenix.reel worked, even with the error message (Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory).

I got all dihedrals in the reel window, now how can I save them?

Maia

Nigel Moriarty wrote:

...

That should be model.pdb, the final model from the refinement.

Sorry

Nigel

On Thu, May 13, 2010 at 4:32 PM, Maia Cherney wrote:

...

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif?

Maia

Nigel Moriarty wrote:

...

As Patrick correctly stated you should look in the .geo.  All the geometry information is written there and it is instructive to look there.  There is, however, an alternative if you wish to get more info about a ligand.  You can type

phenix.reel lig,cif model.cif

choose "Geometry transfer".  You can then compare the ideal and the actual values of all of the restraints listed in the CIF restraints file. You may have to choose the pull-down menu View->List geometry values depending on your version.

Nigel

On Thu, May 13, 2010 at 2:35 PM, Patrick Loll wrote:

...

ooh ooh ooh--I know this!

Look in the .geo file

On 13 May 2010, at 5:34 PM, Maia Cherney wrote:

...

Dear phenixbb, how to get listed all dihedral angles from a ligand after refinement. (Not ideal cif files, but actual dihedral angles).

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

--------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA  19102-1192  USA

(215) 762-7706 [email protected]

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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

Maia I can add a feature to write all the columns in some simple text format. I'll let you know when its in the release. Nigel On Fri, May 14, 2010 at 9:19 AM, Maia Cherney wrote:

Hi Nigel,

I have the ADP and methyl-ATP ligands in my complexes. I see that some torsion angles that are common for both ligands are very different. I want to give a table in my paper with the most changed torsion angles. They should be actual angles after refinement, not from the ideal cif files. Right now I just do screen shots (png files) to save the information from different complexes, but it's very inconvenient. If I could get a list of torsions as a table in a text file that would be most convenient.

Maia

Nigel Moriarty wrote:

...

Maia

You can save a CIF file from REEL using a pull-down menu under File. However, I'm a little unclear on what you are trying to achieve.  Can you elaborate?

Nigel

On Thu, May 13, 2010 at 9:25 PM, Maia Cherney wrote:

...

Hi Nigel, The phenix.reel worked, even with the error message (Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory).

I got all dihedrals in the reel window, now how can I save them?

Maia

Nigel Moriarty wrote:

...

That should be model.pdb, the final model from the refinement.

Sorry

Nigel

On Thu, May 13, 2010 at 4:32 PM, Maia Cherney wrote:

...

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif?

Maia

Nigel Moriarty wrote:

...

As Patrick correctly stated you should look in the .geo.  All the geometry information is written there and it is instructive to look there.  There is, however, an alternative if you wish to get more info about a ligand.  You can type

phenix.reel lig,cif model.cif

choose "Geometry transfer".  You can then compare the ideal and the actual values of all of the restraints listed in the CIF restraints file. You may have to choose the pull-down menu View->List geometry values depending on your version.

Nigel

On Thu, May 13, 2010 at 2:35 PM, Patrick Loll wrote:

> > ooh ooh ooh--I know this! > > Look in the .geo file > > On 13 May 2010, at 5:34 PM, Maia Cherney wrote: > > > > >> >> Dear phenixbb, >> how to get listed all dihedral angles from a ligand after >> refinement. >> (Not ideal cif files, but actual dihedral angles). >> >> Maia >> _______________________________________________ >> phenixbb mailing list >> [email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> > > > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA  19102-1192  USA > > (215) 762-7706 > [email protected] > > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > > > >

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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

Nigel, I am getting different numbers for dihedrals from reel and from coot or pymol. This is one of my ligands, ADP. If you run reel and compare with manual measurement, some numbers are the same, but most of them are different. For example, var1 and var2 are the same, but var3 to var6 are different. Here is the comparison first number, pymol; second number, reel) (hydrogens are removed). var3 -75.8; 28.6 var4 129.6; -117.6 var5 -169.1; 154.1 var6 136.7; -151.7 etc. What is the problem? Is it a different way to measure the torsions? Maia Nigel Moriarty wrote:

Maia

I can add a feature to write all the columns in some simple text format. I'll let you know when its in the release.

Nigel

On Fri, May 14, 2010 at 9:19 AM, Maia Cherney wrote:

...

Hi Nigel,

I have the ADP and methyl-ATP ligands in my complexes. I see that some torsion angles that are common for both ligands are very different. I want to give a table in my paper with the most changed torsion angles. They should be actual angles after refinement, not from the ideal cif files. Right now I just do screen shots (png files) to save the information from different complexes, but it's very inconvenient. If I could get a list of torsions as a table in a text file that would be most convenient.

Maia

Nigel Moriarty wrote:

...

Maia

You can save a CIF file from REEL using a pull-down menu under File. However, I'm a little unclear on what you are trying to achieve. Can you elaborate?

Nigel

On Thu, May 13, 2010 at 9:25 PM, Maia Cherney wrote:

...

Hi Nigel, The phenix.reel worked, even with the error message (Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory).

I got all dihedrals in the reel window, now how can I save them?

Maia

Nigel Moriarty wrote:

...

That should be model.pdb, the final model from the refinement.

Sorry

Nigel

On Thu, May 13, 2010 at 4:32 PM, Maia Cherney wrote:

...

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif?

Maia

Nigel Moriarty wrote:

> As Patrick correctly stated you should look in the .geo. All the > geometry information is written there and it is instructive to look > there. There is, however, an alternative if you wish to get more info > about a ligand. You can type > > phenix.reel lig,cif model.cif > > choose "Geometry transfer". You can then compare the ideal and the > actual values of all of the restraints listed in the CIF restraints > file. You may have to choose the pull-down menu View->List geometry > values depending on your version. > > Nigel > > On Thu, May 13, 2010 at 2:35 PM, Patrick Loll > wrote: > > > > >> ooh ooh ooh--I know this! >> >> Look in the .geo file >> >> On 13 May 2010, at 5:34 PM, Maia Cherney wrote: >> >> >> >> >> >>> Dear phenixbb, >>> how to get listed all dihedral angles from a ligand after >>> refinement. >>> (Not ideal cif files, but actual dihedral angles). >>> >>> Maia >>> _______________________________________________ >>> phenixbb mailing list >>> [email protected] >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >>> >>> >> --------------------------------------------------------------------------------------- >> Patrick J. Loll, Ph. D. >> Professor of Biochemistry & Molecular Biology >> Director, Biochemistry Graduate Program >> Drexel University College of Medicine >> Room 10-102 New College Building >> 245 N. 15th St., Mailstop 497 >> Philadelphia, PA 19102-1192 USA >> >> (215) 762-7706 >> [email protected] >> >> _______________________________________________ >> 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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