- ChimeraX-users - RBVI Mailing Lists

How to update the bonding status in a molecular trajectory?
by 洪冉 12 Sep '22

12 Sep '22

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(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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Failure in installing daily build version
by jq 10 Sep '22

10 Sep '22

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morphed model
by Krishnan Raman 09 Sep '22

09 Sep '22

How do we get the morph player after reopening the saved session with a prexisting morphed model ? thanks Krishnan Raman CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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2D plots and graphs for protein-ligand interactions
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ Many thanks in advance! Cheers Enrico

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Create Complete Oligomers
by Samuel Kyobe 09 Sep '22

09 Sep '22

Dear ChimeraX We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6). Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. We would like to use the complete structure for MD studies. Thank you Samuel

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Visualization of the carbon - Cl bond in a small molecule
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I have an issue with the visualization of the small molecule obtained from the tleap module of the amber tools. First of all in vmd and pymol everything looks OK. In the ChimeraX there is no bond between atom CL of the ligand and the aromatic C atom. I've tried to change atom type for the CL: setattr :lig@CL1 atoms idatm_type CL show :lig@* but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico

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How to update the bonding status in a molecular trajectory?
by 洪冉 08 Sep '22

08 Sep '22

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(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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image
by 洪冉 08 Sep '22

08 Sep '22

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(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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Moving one map in a session while keeping the other/s inactive
by mailman-bounces＠cgl.ucsf.edu 08 Sep '22

08 Sep '22

Dear All, This question might have been answered before but could you let me know how to move 1 map from one position to another without disturbing the other map/s (as we inactivate the maps in Chimera). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] [Chimera-users] How to caluculate buried surface area
by Elaine Meng 07 Sep '22

07 Sep '22

Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users(a)cgl.ucsf.edu (different than chimera-users(a)cgl.ucsf.edu) The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> So, maybe something like command: measure buriedarea protein with ligand ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead: measure buriedarea protein with :UNK You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera > > I am sorry to interrupt your busy schedule. > > My name is Matsui, and I am a second-year master's student at a Japanese university. > Thank you for taking time out of your busy schedule to respond to my question the other day. > > We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. > > For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. > > What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. > > In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. > > I tried to check and tried , but it did not work. > > 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html > > 2.Try to use measure blob using chimera X. > Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea > > However, I didn't know how to solve this command. > Command ;ui mousemode right "pick blobs > > Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology　M2 > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > > <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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