May 2022 - Chimera-users - RBVI Mailing Lists

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

4 4

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 4

Blast not working
by Antonio Díaz Quintana 02 Jun '22

02 Jun '22

3 3

Re: [Chimera-users] HBONDS comparing GROMACS and CHIMERA
by Elaine Meng 31 May '22

31 May '22

----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco Forwarding to the list so that somebody who knows more about the code can answer... > On May 30, 2022, at 1:23 AM, Sourpis, Anastasios <asourpis(a)uni-mainz.de> wrote: > > Dear Elaine, > > I would like to ask you if > CHIMERA is openned source. > > And if yes how can I have access to the Hbonds > class/funtion to understand better how it works? > > Kind regards, > Tasos > > > > On May 25, 2022, at 11:32 AM, Elaine Meng via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > > > Dear Tasos Sourpis, > > > It is not surprising that different programs give (partially) different results, because each program uses somewhat different methods and/or parameters to identify H-bonds. There is no universally accepted exact method. However, my guess is that they would agree in the majority of cases. > > > > > > The method used by Chimera is described in the help page: > > > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhb…> > > > > > > To summarize, there are several different distance and angle cutoffs depending on the atom types (element and hybridization state) of both the donor and acceptor. The diagram of how the angle is defined would also depend on both of those types. > > > > > > So probably what you are interested in are the exact diagrams for the different donor-acceptor pair types and the cutoff values for distances and angles. These are in the figures and tables of the paper cited in the link above, namely > > > > > > Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. > > > > > > Then Chimera allows adding tolerance values to the cutoffs of distances and angles from the paper, because they were defined on very high-resolution crystal structures, but used on structures that may not be so precise. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Chimera(X) team > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > > > >> On May 25, 2022, at 2:57 AM, Sourpis, Anastasios via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > >> > > >> Dear All, > > >> > > >> I would like to ask about the hydrogen bonds' built-in configuration > > >> of CHIMERA. > > >> > > >> Can I possibly have some insight into how it works? > > >> > > >> Regarding the distance and angle constraints do you have any > > >> graphical representation of the conditions. > > >> > > >> I would like to attach a figure and ask if this is the correct > > >> applying configuration regarding the distance and the angle > > >> (hbonds_lst.pdf). > > >> > > >> > > >> Also, I would like to share with you the output > > >> when I compare gmx hbond using GROMACS and > > >> chimera. > > >> > > >> ATTENTION: using gmx hbond I have the connected atoms > > >> via hydrogen, but the two configurations are essentially > > >> different (chimera_(molecules).tga and gromacs_atomonly.tga). > > >> > > >> Thank you in advance. > > >> Kind regards, > > >> Tasos Sourpis > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 2

how to solve the problem of topology
by Kenji MATSUI 31 May '22

31 May '22

Dear Chimera Thank you for your support the other day. I also apologize for contacting you outside of business hours due to the time difference. Excuse me, I have a question about the issue of ligand topology for the docking study. ligand: 25-hydroxy cholesterol The topology did not match when I used this ligand for the docking study. Could you tell me how to solve this problem? The thing I tried 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html 2. I tried to change the conformation of the C23-24 part, but the situation won't be changed. Reference:< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.… > --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

2 2

Drawing a set of spheres describing a pocket in a protein
by svle＠tiscali.it 30 May '22

30 May '22

Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

3 6

Fwd: [chimerax-users] relative position of a marker
by C.J. 25 May '22

25 May '22

Thank you both Tom and Elaine. I just test the command but it doesn't work. See attached picture. Elaine Meng <meng(a)cgl.ucsf.edu> 于2022年5月25日周三 11:45写道： > Hi Jianhao, > It depends what you mean by relative position. If you mean distance, one > way would be to place a marker at the map center and then measure distance > between it and the marker you already have. > > You can place a marker at map center with "measure center" and the "mark > true" option: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center> > > ....or at specific coordinates such as 0,0,0 with "marker" and the > "position" keyword to specify a point: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html#create> > > Then you can select the two markers (same as atoms) with Ctrl-click, > Shift-Ctrl-click and then use command "distance sel": > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > > Or regardless of whether you wanted to measure any distances, you can save > the marker(s) to file and just look at the file with a text-editor to see > what its coordinates are: > <https://rbvi.ucsf.edu/chimerax/docs/user/markers.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 25, 2022, at 7:54 AM, C.J. via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > I place a marker in a cryoEM map with "Volume Tracer" tool. How can I > know the relative position of the marker to the origin or center of the > map? Thank you! > > Best, > > Jianhao > >

2 1

HBONDS comparing GROMACS and CHIMERA
by Sourpis, Anastasios 25 May '22

25 May '22

Dear All, I would like to ask about the hydrogen bonds' built-in configuration of CHIMERA. Can I possibly have some insight into how it works? Regarding the distance and angle constraints do you have any graphical representation of the conditions. I would like to attach a figure and ask if this is the correct applying configuration regarding the distance and the angle (hbonds_lst.pdf). Also, I would like to share with you the output when I compare gmx hbond using GROMACS and chimera. ATTENTION: using gmx hbond I have the connected atoms via hydrogen, but the two configurations are essentially different (chimera_(molecules).tga and gromacs_atomonly.tga). Thank you in advance. Kind regards, Tasos Sourpis

2 1

Place Objects output to mrc
by Ricardo Righetto 20 May '22

20 May '22

Hi, Regarding https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-March/018516.html I stumbled upon this thread somewhat late, so here is my approach to do what Pranav asked, just in case: 1. Use the "Place Objects" plugin to map back your particles into the tomogram, using STL files to represent the average 2. Generate an MRC volume made up entirely of "ones", exactly the same size as your tomogram. For example, for a volume that is 928x928x464 voxels one can do this in EMAN using: $ e2proc3d.py :928:928:464:1 ones_bin4.mrc You could obviously use some other program to do the same thing, or Python, MATLAB, etc. 3. Load this "ones" volume in your Chimera session. Make sure all regions are loaded in step 1, e.g. vol #2 style surface step 1 level 0.5 region all (the volume doesn't have to be visible, though) 4. Mask your "ones" volume using the surface of the mapbacks from "Place Object", e.g.: mask #1 #2 fullmap true 5. Save the new, masked volume as an MRC file The result is essentially a binary volume (well, not exactly because of the masking interpolation) where voxels of your mapped-back particles are 1 and the rest is 0. This is quite useful to compose segmentations and mapbacks on tomograms in Chimera or ChimeraX having full control like we do with any MRC volume (unlike e.g. STL or COLLADA objects). Note you may get some artifacts on the edges, so you might have to play a bit with the thresholds both when creating the STL of your subtomogram average and when displaying your new volume "sculpted" by the mapbacks, to minimize those. The results however have been good enough in my experience, working with low-resolution averages :-) Hope this helps! Best wishes, -- Ricardo Diogo Righetto

2 1

Allocating GPUs
by Giono Matteo (PSI) 19 May '22

19 May '22

Dear all, Does anyone know if it’s possible to make Chimera use GPUs instead of CPUs? I have a 2021 Macbook Pro with 12-core GPUs and knowing that all the work is done by the CPU make all these GPUs kind of useless. Best, MG

5 5