Dear Nat, Thank you, I'm trying to do a refinement in GUI and had to look up something in docs. Actually, I was looking for how to select say, chain A with residues 1-10 and all chain C for anisotropic ADP refinement in GUI? It seems that I can select only one chain with certain residues but not two.. Could you point me to the right direction, please? Best wishes, Alex On 21 Mar 2012, at 17:55, Nathaniel Echols wrote:

On Wed, Mar 21, 2012 at 8:52 AM, Alexander Batyuk wrote:

...

Is there any particular reason for missing documentation file in phenix-dev-1008 and up (it could not be found on the website as well)? dev-1005 is fine.

I think this was my fault - I was trying to make it possible to install to a path containing spaces, and it did not work as well as I hoped. Will fix ASAP. (I'm pretty sure there haven't been any documentation changes in the last few days, however.)

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

Dear Nat, Does that mean in your selection example that both chain A and chain C will be refined with anisotropic ADP or either one or another? I'm a bit confused with selection operator "or". And I was trying to put "and", which did not work. Best wishes, Alex On 21 Mar 2012, at 18:55, Nathaniel Echols wrote:

On Wed, Mar 21, 2012 at 10:48 AM, Alexander Batyuk wrote:

...

Thank you, I'm trying to do a refinement in GUI and had to look up something in docs. Actually, I was looking for how to select say, chain A with residues 1-10 and all chain C for anisotropic ADP refinement in GUI? It seems that I can select only one chain with certain residues but not two.. Could you point me to the right direction, please?

Hmm, not sure why this wouldn't work. Are you using the graphical editor or typing in the selection manually? The editor seems to work fine in "select range" mode (see image attached). The selection syntax is pretty simple too:

(chain A and resseq 1:10) or (chain C)

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

-- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

Dear Ralf, Now it's clear. Thank you! Best wishes, Alex On 22 Mar 2012, at 10:08, Ralf Grosse-Kunstleve wrote:

These are boolean "and" and "or". "chain A and resid 1" selects all atoms with resid 1 in chain A, but not any atoms in chain B. "chain A or chain B" selects all atoms in chain A and (regular language) all atoms in chain B. Once you get use to it it makes total sense. Ralf

On Thu, Mar 22, 2012 at 1:04 AM, Alexander Batyuk wrote:

Dear Nat,

Does that mean in your selection example that both chain A and chain C will be refined with anisotropic ADP or either one or another? I'm a bit confused with selection operator "or". And I was trying to put "and", which did not work.

Best wishes,

Alex

On 21 Mar 2012, at 18:55, Nathaniel Echols wrote:

...

On Wed, Mar 21, 2012 at 10:48 AM, Alexander Batyuk wrote:

...

Thank you, I'm trying to do a refinement in GUI and had to look up something in docs. Actually, I was looking for how to select say, chain A with residues 1-10 and all chain C for anisotropic ADP refinement in GUI? It seems that I can select only one chain with certain residues but not two.. Could you point me to the right direction, please?

Hmm, not sure why this wouldn't work. Are you using the graphical editor or typing in the selection manually? The editor seems to work fine in "select range" mode (see image attached). The selection syntax is pretty simple too:

(chain A and resseq 1:10) or (chain C)

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

-- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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

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