Dear Chimera Users, I am trying to add missing residues to the protein with the ID: 1u54 But unfortunately for chain A, I cannot do the adding. I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works. Best Wishes, Armin -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul
Hi Armin, This problem turns out to be kind of complicated to fix, but rather easy to work around. Until I have time to actually fix the problem you can work around the problem by running this command (Favorites->Command Line) after opening 1u54 and before doing the modeling: setattr r isHet false :ptr I will open a ticket in our bug database for this issue with you on the recipient list, so you will know when it is actually fixed. —Eric
On Jan 29, 2018, at 1:49 PM, ARMIN HODAEI <ahodaei15@ku.edu.tr> wrote:
Dear Chimera Users,
I am trying to add missing residues to the protein with the ID: 1u54 But unfortunately for chain A, I cannot do the adding.
I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works.
Best Wishes, Armin -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric, Thank you very much for your time and attention. I do appreciate your kind reply. Best Wishes, Armin On Tue, Jan 30, 2018 at 3:07 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Armin, This problem turns out to be kind of complicated to fix, but rather easy to work around. Until I have time to actually fix the problem you can work around the problem by running this command (Favorites->Command Line) after opening 1u54 and before doing the modeling: setattr r isHet false :ptr I will open a ticket in our bug database for this issue with you on the recipient list, so you will know when it is actually fixed.
—Eric
On Jan 29, 2018, at 1:49 PM, ARMIN HODAEI <ahodaei15@ku.edu.tr> wrote:
Dear Chimera Users,
I am trying to add missing residues to the protein with the ID: 1u54 But unfortunately for chain A, I cannot do the adding.
I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works.
Best Wishes, Armin -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
-- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul
Dear UCSF-Chimera, I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended. But my question is: if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment? I have tried but it seems that I can't go back. Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ? Thank you, Best H.
Hi Hernando, This is possible, but the only (non-Python) way I can think of to do it is kind of a pain. You would use the Attribute Calculator (Tools->Structure Analysis) to define a residue attribute named ‘saveHelix’ using the formula ‘residue.isHelix’ and then the same with ‘saveStrand’ and ‘residue.isStrand’. After the secondary assignments were later changed, you could revert to the originals by again using the Attribute Calculator, but by defining isHelix/isStrand with the formula residue.saveHelix/saveStrand. Ugly. Also, the saveHelix/Strand won’t be remembered in sessions unless you get tonight’s daily build. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 30, 2018, at 12:38 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera,
I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended. But my question is: if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment? I have tried but it seems that I can't go back. Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ?
Thank you,
Best
H.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Hernando, Here’s another way, slightly less painful … make aliases to save and restore the secondary structure, commands: alias ^sskeep sel strand;namesel ostrand;sel helix;namesel ohelix;~sel alias ^ssrestore setattr r isHelix false;setattr r isStrand false;setattr r isHelix true ohelix;setattr r isStrand true ostrand <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html> Each alias command should be entered as one long line (even though the mailing-list software may decide to display them broken into multiple lines). Then in Chimera, you have new commands “sskeep” and “ssrestore” that can be typed or run from the Aliases menu, and they are saved in the preferences file automatically so they should be available in later uses of Chimera. You would run sskeep one time before changing any assignments and then ssrestore any time you want to restore the ones that were saved with sskeep. Matchmaker with “computeSS true” changes secondary structure assignments by running “ksdssp”, which you could also run separately. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#options> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> The named selections (saved sets of residues) created by the aliases are saved in session files. The approach outlined above just saves/restores secondary structure for all open models together. A fancier appraoch would save different names for different models so they could be saved/restored independently, but that would probably require python (possibly could be done with “perframe” command) and I did not try it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2018, at 3:54 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Hernando, This is possible, but the only (non-Python) way I can think of to do it is kind of a pain. You would use the Attribute Calculator (Tools->Structure Analysis) to define a residue attribute named ‘saveHelix’ using the formula ‘residue.isHelix’ and then the same with ‘saveStrand’ and ‘residue.isStrand’. After the secondary assignments were later changed, you could revert to the originals by again using the Attribute Calculator, but by defining isHelix/isStrand with the formula residue.saveHelix/saveStrand. Ugly. Also, the saveHelix/Strand won’t be remembered in sessions unless you get tonight’s daily build. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 30, 2018, at 12:38 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera, I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended. But my question is: if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment? I have tried but it seems that I can't go back. Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ? Thank you, Best H.
participants (4)
-
ARMIN HODAEI -
Elaine Meng -
Eric Pettersen -
Hernando J Sosa