- Chimera-users - RBVI Mailing Lists

how to perform minimize structure for enzyme+NADPH complex
by 朱鑫鑫 28 Aug '22

28 Aug '22

Hello everyone I have a question, how to perform minimize structure for enzyme+NADPH complex. Thank you very much. Xinxin Zhu 27/8/2022

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A problem on minmize structure
by 朱鑫鑫 28 Aug '22

28 Aug '22

Hello everyone I want to conduct a minimize structure using a protein complex model, but a error appears during this process. It reminds me to assign the hydrogen geometry info to NADP, and I click these options, but, it next will report a error. And I DONT know how to sovle this problem. I hope some suggestions I will obtain. Thank you very much. Xinxin Zhu 27/8/2022

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POV-RAY rendering and labels
by Francesco Pietra 26 Aug '22

26 Aug '22

Hello In my hands, with CHIMERA (v 1.15 Linux64 X11), POV-RAY rendering does not reproduce labels, only an interrogation mark in their place. Thanks for advice francesco pietra

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Re: [Chimera-users] Chimera ac Im command not working
by Tom Goddard 26 Aug '22

26 Aug '22

Hi Wayne, Chimera crashes usually are caused by graphics driver bugs or running out of memory. How large is your map? By the way, we stopped developing Chimera more than 6 years ago and you would be better off using ChimeraX which is the modern version of Chimera which we actively develop. Tom > On Aug 26, 2022, at 4:51 AM, Wayne Lim <wayne.lim(a)student.manchester.ac.uk> wrote: > > Dear Tom, > > I just tried this and over multiple times chimera 1.6 crashed and returned this error message: > > chimera exited abnormally, the exit code was: -1073741819 > > Not sure why it's doing that, any ideas as to what that code means? > > BW, > > Wayne > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, August 25, 2022 11:50 PM > To: Wayne Lim <wayne.lim(a)student.manchester.ac.uk> > Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera ac Im command not working > > Hi Wayne, > > I guess you mean you tried the current Chimera version 1.16. To change the sign of the map values use command > > vop scale #0 factor -1 > > I don't know what is wrong if the graphics is black after that, but I would start looking at the histogram in the Volume Viewer window and see if the yellow brightness curve is in the right place. Below is an image with Chimera 1.16 and map EMDB 1273 showing the histograms for the original and inverted map and it displays correctly on my Mac. > > Tom > > <invertmap.png> >> On Aug 25, 2022, at 8:39 AM, Wayne Lim via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera team, >> >> I am using Chimera to view the surface pane of my TEM images in attempts to see the features of the image in 3D. Since I stained it positively, I have to invert the map values so I can properly view it under “surface”. However, when I do so in Chimera 1.5, it displays an “unexpected python error”. When tried in Chimera 1.6, the result is simply a black screen. I am stumped as to how to solve this issue. A colleague of mine done it and I followed the same procedure he has done, but to no avail. >> >> Best, >> >> Wayne >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Query Regarding processing protein in Chimera
by asetiya 26 Aug '22

26 Aug '22

Sir/Ma'am, I have query regarding chimera, through command line I want to select a particular residue and delete the remaining protein and save in the .mol2 file for further processing for my project.I used the following command to select the residue: select :30 for selecting the desired residue. Can you give me an insight as to how to delete the remaining protein and save in the .mol2 format. That will be very helpful. Thanks & Regards Anjali Setiya ------------------------------------------------------------------------------------------------------------ [ C-DAC is on Social-Media too. Kindly follow us at: Facebook: https://www.facebook.com/CDACINDIA & Twitter: @cdacindia ] This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------

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Chimera ac Im command not working
by Wayne Lim 25 Aug '22

25 Aug '22

Dear Chimera team, I am using Chimera to view the surface pane of my TEM images in attempts to see the features of the image in 3D. Since I stained it positively, I have to invert the map values so I can properly view it under “surface”. However, when I do so in Chimera 1.5, it displays an “unexpected python error”. When tried in Chimera 1.6, the result is simply a black screen. I am stumped as to how to solve this issue. A colleague of mine done it and I followed the same procedure he has done, but to no avail. Best, Wayne

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Fwd: How to display hydrohobic area
by Elaine Meng 23 Aug '22

23 Aug '22

> > From: Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> > Subject: How to display hydrohobic area > Date: August 22, 2022 at 9:17:37 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Dear Chimera > Thank you for taking the time to answer my question the other day. > I'm Kenji Matsui, a second-year master's student at a national university in Japan. > > I would like to display the hydrophobicity of the protein around the ligand like the first picture, but I couldn't do it. > How can I do this? > When I actually did it, it turned out to be the second picture. > > I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me. > > First photo > > > Second photo > > Hi Kenji, If I understand correctly, you want to show the amino acid hydrophobicity coloring on the ribbon and sticks, not the molecular surface. When you open the structure, it may already be displayed as ribbon and sticks. Do not show the surface. (Or, if you already are showing the surface, you can hide it with menu: Select... Clear Selection, menu: Actions... Surface... hide) Then you can use the "rangecolor" command to color protein ribbons/sticks by hydrophobicity: rangecolor kdHydrophobicity min dodger blue 0 white max orange red See rangecolor help <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> That command is part of the tutorial for surface coloring: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#h…> However, when the surface is not shown, you can see that this comand also colors the other representations (ribbons and sticks). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Geometric objects
by Reza Khayat 18 Aug '22

18 Aug '22

Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Question regarding RMSD
by ALI, MUNIRA (PGT) 16 Aug '22

16 Aug '22

Good morning, I have conducted a superposition between two of the same protein where one was obtained by X ray and the other was predicted by alphafold. I wanted to use the RMSD value of the alignment rather then just have qualitative results but I am unsure of how to interpret the values given by chimera. When I get the output of for example: RMSD between 189 pruned atom pairs is 1.164 angstroms; (across all 553 pairs: 10.750), what exactly do these two outputs mean, which one should I be using and how exactly do I interpret this? Kind regards, Munira

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Trouble generating surface
by Heilman, Destin 12 Aug '22

12 Aug '22

Hi, I’m trying to generate a square surface between 4 markers to trace an atomic plane. I’ve created a marker file (attached) with the positions of the 4 atoms and when I select all markers and use the Volume Tracer tool to generate the surface, I see it show up in the Model Panel but it is not visible (see screen shot - I’m trying this in a random PDB file to test). The Volume Tracer tool also says “No surface” despite the Traced surface showing up in the Model Panel. I notice that there is no color next to the traced surface as well. It’s likely something silly I’m missing but I would appreciate help with this. Thanks. DH Destin Heilman, Ph.D (he/him/his) Professor of Chemistry and Biochemistry Chair, Undergraduate Studies Director, UMass MQP Project Center Department of Chemistry and Biochemistry Worcester Polytechnic Institute 100 Institute Road, Worcester MA 01609-2280 Goddard Hall 103B Office: 508-831-5396 Lab: 508-831-5386 [cid:787efcd6-e2fa-4b91-a11d-7b66c303cbed@prod.exchangelabs.com]

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