How to update the bonding status in a molecular trajectory?
Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran@ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000
Hi Ran, There is no need to send the same question to the mailing list three times within minutes of one another. It looks like the bonds are between the wrong pairs of atoms. Assuming your trajectory is model #1, these commands should fix it: "~bond; bond #1". --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 8, 2022, at 6:03 PM, 洪冉 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. <image.png>
Ran hong hongran@ahpu.edu.cn <mailto:hongran@ahpu.edu.cn> Anhui polytechnic university Wuhu, China, 241000
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Hi Eric, It looks like I went into an internet connecting issue so three same questions were posed on the mailing list yesterday, I do apologize. By using your method "~bond; bond #1", the problem was indeed solved, thank u very much. 洪冉 E_mail: hongran@ahpu.edu.cn 安徽工程大学 化学与环境工程学院 安徽芜湖北京中路8号 241000 发件人：Eric Pettersen <pett@cgl.ucsf.edu> 发送日期：2022-09-09 23:18:52 收件人："洪冉" <hongran@ahpu.edu.cn> 抄送人：ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> 主题：Re: [chimerax-users] How to update the bonding status in a molecular trajectory? Hi Ran,There is no need to send the same question to the mailing list three times within minutes of one another. It looks like the bonds are between the wrong pairs of atoms. Assuming your trajectory is model #1, these commands should fix it: "~bond; bond #1". --Eric Eric Pettersen UCSF Computer Graphics Lab On Sep 8, 2022, at 6:03 PM, 洪冉 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. <image.png> Ran hong hongran@ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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