render by attribute displacement of a NMA
Hy, I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute? Thanks in advance for you rhelp! Giorgio -- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.
Hi Giorgio, I don't know exactly what's in your file, but if it opens as multiple models (e.g. #0.1, #0.2, #0.3 similar to when you open an NMR structure such as 1g1p, or as #0, #1, #2 ...): (1) first check: are the structures shown as a ribbon? (like spaghetti, all same radius) If Chimera can show it as the spaghetti-like ribbon, it can show it as a worm. If not (only dots) it cannot show it as a worm. (2) show the sequence of any one, doesn't matter which one since they all have the same sequence (menu: Favorites... Sequence, choose which model) (3) in the sequence window menu, (a) choose Structure... Associations, and in the resulting dialog make all of the structures associate with that same single sequence (b) choose Headers... RMSD:ca to show the histogram of RMSD values (4) choose which model you want to represent as worm, hide all of the others (e.g. with Model Panel "S" checkboxes) (4) in Render by Attribute, choose attributes of residues, then choose attribute: mavRMSDca, use Worms tab, etc. Click the Help buttons on tools to see their detailed instructions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2021, at 9:07 AM, Giorgio Giardina <giorgio.giardina@uniroma1.it> wrote:
Hy,
I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute?
Thanks in advance for you rhelp! Giorgio
Thank you very much Elaine!! it worked nicely. I attached the image I rendered. Thanks again, stay safe, Giorgio [image: NMA-worms-displacement.png] On Sun, 14 Mar 2021 at 18:15, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Giorgio, I don't know exactly what's in your file, but if it opens as multiple models (e.g. #0.1, #0.2, #0.3 similar to when you open an NMR structure such as 1g1p, or as #0, #1, #2 ...):
(1) first check: are the structures shown as a ribbon? (like spaghetti, all same radius) If Chimera can show it as the spaghetti-like ribbon, it can show it as a worm. If not (only dots) it cannot show it as a worm.
(2) show the sequence of any one, doesn't matter which one since they all have the same sequence (menu: Favorites... Sequence, choose which model)
(3) in the sequence window menu, (a) choose Structure... Associations, and in the resulting dialog make all of the structures associate with that same single sequence (b) choose Headers... RMSD:ca to show the histogram of RMSD values
(4) choose which model you want to represent as worm, hide all of the others (e.g. with Model Panel "S" checkboxes)
(4) in Render by Attribute, choose attributes of residues, then choose attribute: mavRMSDca, use Worms tab, etc.
Click the Help buttons on tools to see their detailed instructions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2021, at 9:07 AM, Giorgio Giardina < giorgio.giardina@uniroma1.it> wrote:
Hy,
I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute?
Thanks in advance for you rhelp! Giorgio
-- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.
Great! Thanks for sharing, your image looks nice. Elaine
On Mar 15, 2021, at 12:53 AM, Giorgio Giardina <giorgio.giardina@uniroma1.it> wrote:
Thank you very much Elaine!!
it worked nicely. I attached the image I rendered.
Thanks again, stay safe, Giorgio <NMA-worms-displacement.png>
On Sun, 14 Mar 2021 at 18:15, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Giorgio, I don't know exactly what's in your file, but if it opens as multiple models (e.g. #0.1, #0.2, #0.3 similar to when you open an NMR structure such as 1g1p, or as #0, #1, #2 ...):
(1) first check: are the structures shown as a ribbon? (like spaghetti, all same radius) If Chimera can show it as the spaghetti-like ribbon, it can show it as a worm. If not (only dots) it cannot show it as a worm.
(2) show the sequence of any one, doesn't matter which one since they all have the same sequence (menu: Favorites... Sequence, choose which model)
(3) in the sequence window menu, (a) choose Structure... Associations, and in the resulting dialog make all of the structures associate with that same single sequence (b) choose Headers... RMSD:ca to show the histogram of RMSD values
(4) choose which model you want to represent as worm, hide all of the others (e.g. with Model Panel "S" checkboxes)
(4) in Render by Attribute, choose attributes of residues, then choose attribute: mavRMSDca, use Worms tab, etc.
Click the Help buttons on tools to see their detailed instructions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2021, at 9:07 AM, Giorgio Giardina <giorgio.giardina@uniroma1.it> wrote:
Hy,
I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute?
Thanks in advance for you rhelp! Giorgio
-- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: L’arte e la scienza sono libere e libero ne è l’insegnamento
________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Giorgio Giardina