Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. I have attached a photo where the left one is the selected residue (Thr) and the right photo is the residue when it is changed to Ile. [image: Screen Shot 2023-06-30 at 5.38.22 PM.png] Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. I have attached a photo of the settings. [image: Screen Shot 2023-06-30 at 5.39.01 PM.png] Thank you so much for your help! Best, Bani Kaur
Hi Bani, I don't know why the Ile residue is not shown when you use Rotamers to change it. When I use Rotamers and choose to change the residue type, its sidechain atoms are displayed immediately. However, the new sidechain is NOT selected. So you need to select the residue again or else only the backbone is selected -- maybe that is your problem. So the first thing to try is to make sure you select the residue again after mutating it to Ile. Then command show sel ...will show the atoms of the selected residue including the sidechain. Secondly, in the Clashes tool you should turn on the "Reveal atoms of interacting residues" option or else any clashing atoms that are currently hidden will stay hidden regardless of whether they are clashing. Thirdly, how do you know that the residue has clashes? Maybe it does not have any clashes. Look in the Log after you do the clashes calculation. If there are no clashes, it will say so in the Log. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2023, at 5:39 PM, Bani Kaur via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. I have attached a photo where the left one is the selected residue (Thr) and the right photo is the residue when it is changed to Ile. <Screen Shot 2023-06-30 at 5.38.22 PM.png> Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. I have attached a photo of the settings. <Screen Shot 2023-06-30 at 5.39.01 PM.png> Thank you so much for your help!
Best, Bani Kaur
participants (2)
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Bani Kaur -
Elaine Meng