On Mon, Feb 14, 2011 at 7:48 AM, Ed Pozharski wrote:

Note that original request was sent to both phenix and ccp4 bulletin boards.  And I think most reasonable people have agreed in the past that advertising phenix on ccp4bb is OK (at the least on the freedom of speech grounds :)  So I guess the reverse must also be true

Yes, none of us here actually mind this - it was a legitimate answer. Occasionally this also provides useful insight into what features Phenix is lacking, or aren't intuitive enough (although, in this case, I still find phenix.pdbtools easier to use). -Nat

This seems very flexible and general indeed, but for the specific job of making an MR model, it could be very tedious to code which atoms to keep for which residues, where to delete, and how to renumber. Chainsaw does all of that for you. With the "keep atoms in common", it deletes all atoms that don't exist in the target structure- for example if the real protein has a glycine, it doesn't make much sense to trim the model to alanine. On the other hand if the protein has asp and the model glu, you might want to keep Cg as well. And based on the alignment you give it, which is the only input other than the model pdb, it will decide where to delete residues and renumber to the target sequence taking into account gaps and inserts. Which you can control by editing the alignment. Pavel Afonine wrote:

Hi,

as Jeff pointed out last week, using phenix.pdbtools you can be very selective in what you keep/remove. Just a few examples:

- remove all waters: phenix.pdbtools model.pdb remove=water

- remove all waters and DNA/RNA: phenix.pdbtools model.pdb remove="water or dna or rna"

- remove all protein sidechains: phenix.pdbtools model.pdb remove="protein and sidechain" or equivalently: phenix.pdbtools model.pdb keep="all and not (protein and sidechain)"

- keep only oxygens: phenix.pdbtools model.pdb keep="element O"

- keep only nitrogens in protein sidechains: phenix.pdbtools model.pdb keep="protein and sidechain and element N"

- keep only backbone in chain A and in chain C: phenix.pdbtools model.pdb keep="(chain A and backbone) or (chain C and backbone)"

- remove residues in chain A from number 3 to 25: phenix.pdbtools model.pdb remove="chain A and resseq 3:25"

... and so on.

To get more familiar with atom selection syntax you can practice by running the command

phenix.pdb_atom_selection model.pdb ATOM_SELECTION_STRING

for example:

phenix.pdb_atom_selection model.pdb "chain A and resseq 1:100"

which will output the selected atoms to the screen. Some examples of atom selection syntax can be found here: http://phenix-online.org/documentation/refinement.htm#anch88

Pavel.

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Hi phenixers, I just installed the version phenix-1.7-650 on ubuntu 9.4 and tried a test run. My previous version runs fine. The new version gives me this error =============================== refinement start ============================== Traceback (most recent call last): File "/usr/local/phenix-1.7-650/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/driver.py", line 1207, in run call_back_handler = call_back_handler) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 220, in refinement_machine xray_structure = model.xray_structure,) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 124, in extract_from_pdb_header xray_structure = xray_structure) File "/usr/local/phenix-1.7-650/cctbx_project/mmtbx/f_model.py", line 327, in __init__ twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character: NULL ^ Please, take a look at the error and advise me how to fix it. Maia

Delete the entire REMARK section at the start of the PDB file, and the error should go away. On Tue, Mar 1, 2011 at 8:39 AM, Maia Cherney wrote:

Hi phenixers,

I just installed the version phenix-1.7-650 on ubuntu 9.4 and tried a test run. My previous version runs fine. The new version gives me this error

=============================== refinement start ==============================

Traceback (most recent call last):  File "/usr/local/phenix-1.7-650/phenix/phenix/command_line/refine.py", line 11, in <module>   command_line.run(command_name="phenix.refine", args=sys.argv[1:])  File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/command_line.py", line 89, in run   call_back_handler=call_back_handler)  File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/driver.py", line 1207, in run   call_back_handler       = call_back_handler)  File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 220, in refinement_machine   xray_structure = model.xray_structure,)  File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 124, in extract_from_pdb_header   xray_structure = xray_structure)  File "/usr/local/phenix-1.7-650/cctbx_project/mmtbx/f_model.py", line 327, in __init__   twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character:  NULL  ^ Please, take a look at the error and advise me how to fix it.

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

Hi Maia, this should be fixed in the latest nightly build: http://www.phenix-online.org/download/nightly_builds.cgi otherwise Nat's suggestion would fix this problem. Pavel. On 3/1/11 8:39 AM, Maia Cherney wrote:

Hi phenixers,

I just installed the version phenix-1.7-650 on ubuntu 9.4 and tried a test run. My previous version runs fine. The new version gives me this error

=============================== refinement start ==============================

Traceback (most recent call last): File "/usr/local/phenix-1.7-650/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/driver.py", line 1207, in run call_back_handler = call_back_handler) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 220, in refinement_machine xray_structure = model.xray_structure,) File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py", line 124, in extract_from_pdb_header xray_structure = xray_structure) File "/usr/local/phenix-1.7-650/cctbx_project/mmtbx/f_model.py", line 327, in __init__ twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character: NULL ^ Please, take a look at the error and advise me how to fix it.

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