Save multiscale model as PDB?
Hi Elaine, Hope you're well! I'm working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I've tried looking in the Help documentation, but can't find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak@petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
Hi Maja! The multiscale model is initially shown with low-resolution surfaces only; except for the original structure, the atomic coordinates of all the copies are not loaded. This is because the atomic copies take more memory and may make the program slow to respond (e.g. rotate). …this is mentioned at the very bottom of the page... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/multiscale.html#loading> However, you can force loading all atomic copies if you need them for display or to save as PDB files. For example, in the Multiscale Models dialog, top section Select chains: "All" and then in the middle section, Act on selected chains, Style: “Show… ribbons” It will take a while for all the atomic copies to be loaded and for all the chains to appear as ribbons. Then you can save PDB of all chains. 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 24, 2019, at 5:12 PM, Divjak Maja <Maja.Divjak@petermac.org> wrote:
Hi Elaine, Hope you’re well! I’m working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I’ve tried looking in the Help documentation, but can’t find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja
Hi Elaine, Thank you so much- works perfectly! Also, I made another Ras morph and that worked beautifully too. Have a lovely day, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research Phone +61 3 8559 5961 Email maja.divjak@petermac.org 305 Grattan Street Melbourne Victoria 3000 www.petermac.org -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 26 March 2019 3:29 AM To: Divjak Maja <Maja.Divjak@petermac.org> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Save multiscale model as PDB? Hi Maja! The multiscale model is initially shown with low-resolution surfaces only; except for the original structure, the atomic coordinates of all the copies are not loaded. This is because the atomic copies take more memory and may make the program slow to respond (e.g. rotate). …this is mentioned at the very bottom of the page... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/multiscale.html#loading> However, you can force loading all atomic copies if you need them for display or to save as PDB files. For example, in the Multiscale Models dialog, top section Select chains: "All" and then in the middle section, Act on selected chains, Style: “Show… ribbons” It will take a while for all the atomic copies to be loaded and for all the chains to appear as ribbons. Then you can save PDB of all chains. 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 24, 2019, at 5:12 PM, Divjak Maja <Maja.Divjak@petermac.org> wrote:
Hi Elaine, Hope you’re well! I’m working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I’ve tried looking in the Help documentation, but can’t find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja
Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.
participants (2)
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Divjak Maja -
Elaine Meng