Stepping through model in secondary structure element steps (ISOLDE)
Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP - Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org>
Hi Matthias, I'm afraid I retired the "per-secondary-structure-element" stepping mode some time back - it was always just a bit too flaky for my liking. I guess it wouldn't be too difficult to add a command with the equivalent functionality... but could you expand on what you dislike about the new mode? There are a couple of options to the "isolde step" command that might help you tweak it more to your liking: "interpolateFrames {integer}" will set the number of frames used in the "sliding" animation - the default is 15; I often set it to 5 when working through a big model; 1 will cause it to simply jump instantly to the next residue. "viewDistance {float}" will set the distance in Angstroms between residue and camera (default is 10). For both of these it will remember the last value you set. Best, Tristan On Sun, Nov 24, 2024 at 12:54 PM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time.
Many thanks in advance, Matthias
Sent from Outlook for Android <https://aka.ms/AAb9ysg> --- *Matthias Kopano Vorländer* Postdoc matthias.vorlaender@imp.ac.at
Plaschka Lab IMP – Research Institute of Molecular Pathology - imp.ac.at
Part of Vienna BioCenter. www.viennabiocenter.org _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Tristan, Thanks a lot for the reply and the helpful command options. The primary reason for preferring the secondary structure steps over the single amino acid steps is the time it takes to go systematically through large models (>10 000 residues). I also find it sometimes easier to see more residues in context rather than focusing on a single one – the distance argument you mentioned is helpful there. In case there is a chance for reviving the secondary structure steps I would be happy to hear about it 😊 Best wishes, Matthias From: Tristan Croll <tcroll@altoslabs.com> Date: Tuesday, November 26, 2024 at 10:43 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Stepping through model in secondary structure element steps (ISOLDE) Hi Matthias, I'm afraid I retired the "per-secondary-structure-element" stepping mode some time back - it was always just a bit too flaky for my liking. I guess it wouldn't be too difficult to add a command with the equivalent functionality... but could you expand on what you dislike about the new mode? There are a couple of options to the "isolde step" command that might help you tweak it more to your liking: "interpolateFrames {integer}" will set the number of frames used in the "sliding" animation - the default is 15; I often set it to 5 when working through a big model; 1 will cause it to simply jump instantly to the next residue. "viewDistance {float}" will set the distance in Angstroms between residue and camera (default is 10). For both of these it will remember the last value you set. Best, Tristan On Sun, Nov 24, 2024 at 12:54 PM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP – Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hello, If navigating by secondary structure is too flaky, maybe a more reliable solution could be to add an option to "isolde step" called, say, byResidues (with default of 1). This option would make "isolde step" move by this number of residues when set, instead of the default of 1 residue. And it would persist until changed, but reset to the default in a new session (like viewDistance). If one could choose by how many residues to move with one step, and with viewDistance set to look from further away, one could get something pretty close to navigating by secondary structure. Cheers, Guillaume On 26 Nov 2024, at 15:51, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Tristan, Thanks a lot for the reply and the helpful command options. The primary reason for preferring the secondary structure steps over the single amino acid steps is the time it takes to go systematically through large models (>10 000 residues). I also find it sometimes easier to see more residues in context rather than focusing on a single one – the distance argument you mentioned is helpful there. In case there is a chance for reviving the secondary structure steps I would be happy to hear about it 😊 Best wishes, Matthias From: Tristan Croll <tcroll@altoslabs.com<mailto:tcroll@altoslabs.com>> Date: Tuesday, November 26, 2024 at 10:43 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Cc: ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Stepping through model in secondary structure element steps (ISOLDE) Hi Matthias, I'm afraid I retired the "per-secondary-structure-element" stepping mode some time back - it was always just a bit too flaky for my liking. I guess it wouldn't be too difficult to add a command with the equivalent functionality... but could you expand on what you dislike about the new mode? There are a couple of options to the "isolde step" command that might help you tweak it more to your liking: "interpolateFrames {integer}" will set the number of frames used in the "sliding" animation - the default is 15; I often set it to 5 when working through a big model; 1 will cause it to simply jump instantly to the next residue. "viewDistance {float}" will set the distance in Angstroms between residue and camera (default is 10). For both of these it will remember the last value you set. Best, Tristan On Sun, Nov 24, 2024 at 12:54 PM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP – Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
participants (3)
-
Guillaume Gaullier -
Tristan Croll -
Vorländer,Matthias Kopano