- Chimera-users - RBVI Mailing Lists

Help Coordinating Metal Atom to an Amino Acid (Cysteine)
by Sydney Marchi 01 Aug '22

01 Aug '22

Hello Chimera Software Developers, I am having a lot of trouble coordinating a metal atom (using Zinc in place of Cr) to the nitrogen, oxygen, and potentially sulfur atom on cysteine. The two main problems that I am having are getting the geometry I need, which is octahedral, where the metal is also coordinated to two-three water molecules as well as eventually the N-7 of guanine. I am trying to build and minimize the Zn-Cysteine model first though before incorporating it into a DNA oligo. I can't seem to get the geometry I need but beside from that, I have tried to minimize the structure using Amber with an undesired geometry just to test if it will run, and it doesn't let me. I have read the reply log and I believe this is due to the atom labeling on cysteine being the issue. But changing the atoms names is a coding problem, and I don't know anything about coding. I tried building cysteine on my own as a potential fix in place of using the prebuilt model but ran into the same problem where it would not minimize my structure. I need this model for my dissertation, so any help would be greatly appreciated. I can attach any files that you may need, set up a zoom meeting, whatever is easiest for you. I know this is probably not the most conventional use for this software, but I really need to figure this out, and I don't have enough knowledge to tinker with it on my own anymore. Thank you for any feedback. Best Regards, Sydney Marchi PhD Candidate, Chemistry Office: Shelby Hall, 3043 University of Alabama

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Question about equivalent command in Chimera
by Thu Nguyen 28 Jul '22

28 Jul '22

Good afternoon, I want to ask if we have any command in Chimera that is similar to the command "volume cover" in ChimaraX. My goal is to create a map and pdb file of individual chains from the whole structure. For example: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 > save 12554_A1.mrc models #3 Could you tell me how I can do this using Chimera commands? Thank you very much. Best regards, Thu

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Re: [Chimera-users] How to show hydrophobility clearly
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Kenji In this latest message, you are using one method that shows the pocket surface only, like in the tutorial. Your image after step 1 of what you tried looks OK to me: But if you are not happy with that, I am guessing you do not want this method. If you want it to look more like this example image with the labeling "hydrophobic pocket" and "allosteric tunnel" ...then you need to use a DIFFERENT method that includes clipping: showing the whole surface of the protein and then using clipping to slice. We already discussed this method, and you were already using this method the first time you asked the question: <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html> With that method, all you can do is to move and rotate the structure and move the clipping (either global clipping plane with Side View tool or surface-only clipping with Per-Model Clipping, both mentioned in previous replies) to try to get a good view. However, different pockets are different shapes and depending on the shape of your pocket it may not be possible to make an image that clearly shows what you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> wrote: > > 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 am looking at ligand-protein interactions and how they affect binding affinity. > > Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure(third) > > If you know of any, could you please let us know? > > I tried to show what you mentioned in your email.(clip off, mclip) > > I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me. > > <image.png> <image.png> > > The picture I want to show > <image.png> > > Tried thing > 1. clip off +~ribbon > <1edf41f0-9f2e-4921-92fe-19399979fd97.png> > > 2.m clip > <image1.png> > > > > > . > --------------------------------------------------------------------------- > > > 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 > <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>

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Help with Fetch ID from UNIProt
by Tina Wright 26 Jul '22

26 Jul '22

Hi there, I have worked my way through the majority of the Chimera tutorials and thought I would try to Fetch ID of Human SP-B (P07988) from UNIProt but unlike the tutorials, it will not upload an image. Can you please help? Many thanks Tina Wright

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How to examine the hydrophobicity and hydrophilicity around the ligand
by Kenji MATSUI 21 Jul '22

21 Jul '22

Dear Chimera Thank you for taking the time to answer my question the other day. I also apologize for contacting you outside of business hours due to the time difference. I'm Kenji Matsui, a second-year master's student at a national university in Japan. I am looking at ligand-protein interactions and how they affect binding affinity. Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure below（second photo,）. [image: image10.png] [image: image.png] second photo Methods Tried select→ligand→Focus This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand. [image: image.png] Please confirm. --------------------------------------------------------------------------- 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

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VolumeViewer in python
by Yumeng Yan 20 Jul '22

20 Jul '22

Hi all, I tried to fit some models into a large density map using python script for chimera. Do you know how to set the VolumeViewer module in python script to show all the surface of the density map like command line” volume #1 style surface region all level 0.15 step 1”? Here is my python code: Import chimera import FitMap import VolumeViewer model_list = chimera.openModels.open("test.pdb") em_map = VolumeViewer.open_volume_file("test.mrc")[0] “python code ” for “volume #1 style surface region all level 0.15 step 1” model = chimera.selection.ItemizedSelection([model_list[0]]) listfit = FitMap.fitcmd.fitmap(model, em_map, resolution=5.0, metric="correlation") Thanks and best wishes, Yumeng

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imod
by Aaran Vijayakumaran 13 Jul '22

13 Jul '22

Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say? Thank you in advance for any assistance. Bests, Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623(a)cam.ac.uk<mailto:Av623@cam.ac.uk> [A picture containing text, screenshot Description automatically generated] [cid:image001.png@01D84DAF.64335190]

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IOError for non-existing ViewDock_Accelerator.py when executing Chimera
by 夏前程 07 Jul '22

07 Jul '22

Hi, Recently I've received an error message from CLI each time I executed chimera as before. Although it does not affect the normal use of chimera, I am still curious what's the issue and how to get rid of it? The error message is as below: Error executing accelerators file $HOME/Downloads/Chimera/ViewDock_Accelerator.py: IOError: [Errno 2] No such file or directory: '$HOME/Downloads/Chimera/ViewDock_Accelerator.py' File "$HOME/opt/UCSF-Chimera64-1.15rc/share/Accelerators/__init__.py", line 103, in load_accelerators execfile(path, dict) See reply log for Python traceback. With Regards, Qiancheng Xia, 2022/07/07

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Coloring model by b-factor
by 师扬 07 Jul '22

07 Jul '22

Dear developer, I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range. Best wishes, Yang

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Mask Question in windows Chimera
by Zhang, Ruojing 04 Jul '22

04 Jul '22

To whom it may concern, Hello, this may sound like a silly question. May I ask how to use Mask in Volume? For some unknown reasons, I could not find the Mask button in Volume Viewer and neither in the tool taskbar. The input files are pdb and mrc file. I used Fit in Map to align structure and map. Then I selected the whole structure. When I went back to mask the map, I could not find the Mask button in Volume Viewer. When I tried to run in the command line (mask), it shows "missing required arguments: Volume, SurfaceSpec". Could you please help? Thank you Jing

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ChimeraX Version 1.4 on CentOS/RHEL 7
by Long Gui 01 Jul '22

01 Jul '22

Dear Chimera community, We are interested in the new version of the ChimeraX/1.4 but we could not find the installation file of ChimeraX/1.4 on our CentOS/RHEL 7 system. Only ChimeraX/1.3 supports CentOS/RHEL 7. So we would like to ask if there is a way to install ChimeraX/1.4 on our CentOS/RHEL 7 system? In addition, our computational source would prefer to install the program using docker. Currently I only find this docker file supports ChimeraX/1.3 https://github.com/maduprey/chimerax-docker/ ? Have anyone tried it for ChimeraX/1.4 yet? Thanks! Long Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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AutoDock Vina error on Chimera
by Utkarsh Narsaria 30 Jun '22

30 Jun '22

Dear Team, I am using chimera for a typical protein-ligand docking study. The ligands were prepared in chimera itself using the dockprep options using gasteiger charges and amber ff14SB force field. While docking the same using AutoDock Vina function in Chimera , we encountered few errors for some of the ligands. The errors are explained as follows : 1. "" Ho" is not a valid dock type AutoDock atom types are case-sensitive." 2. Autodock Vina Error on Chimera: "ValueError: Could not find an atomic number for Hc Hc" Any inputs regarding these will be helpful in resolving the issues. Regards, Utkarsh

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Save trajectory file to PDB
by Yan Yi Li 24 Jun '22

24 Jun '22

Hello, I have a question about saving specific frame from trajectory file to PDB. Instead of using MD movie, is there any module/command available so that I can convert the file format directly with python script? Regards

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How to show hydrophobic interactions
by Kenji MATSUI 17 Jun '22

17 Jun '22

Dear Chimera Thank you for taking the time to answer my question the other day. I also apologize for contacting you outside of business hours due to the time difference. I'm Kenji Matsui, a second-year master's student at a national university in Japan. I have shown hydrophobic interactions between ligands and amino acid residues, how should I display them? I refer to these methods. But, I did not know where to find Examine residues. Therefore, could you please tell me the location of Examine residues? If possible, we would appreciate it if you could attach a diagram after the operation so that we can confirm the operating procedure. *A:Find hydrophobic interactions* Select >> Residue(s) (either in entire structure or within a selected set (see above $ or %)) >> Amino acid category >> hydrophobic >> Action >> Atoms/Bonds >> Show >> Examine residues >> Mouse over atoms or Left click on them to identify them --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士 2年〒184-8588 東京都小金井市中町2-24-16 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

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New residues for swap commands
by Rodrigo Galindo-Murillo 15 Jun '22

15 Jun '22

Hello! Is it possible to add new amino acids to the swapaa and new nucleotides for the swapna commands? Thank you! Rodrigo.

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Discrepancies Between Running Python Script From Terminal and GUI
by Rafi Brent 06 Jun '22

06 Jun '22

To whom it may concern, I have a set of about 20,000 pdb files to which I would like to add Hydrogens, add partial charges, and convert to the mol2 format. I have written a python script to perform these tasks, which it does without issue when opened from the GUI using the "open" option in the top left corner. However, as soon as the script start srunning, I become unable to interact with the Chimera GUI and my computer warns that the application is not responding. While it continues to iterate through the pdb files and convert them to mol2 files, this process slows down drastically over time, from one file per second to over 30 seconds between files, a rate that is prohibitively slow. It is not clear to me why these issues are occurring, as there is nothing about the way my script is written that should increase the computational load over time. Based on the unresponsiveness of the Chimera application, I assumed that the slowdown might have something to do with the GUI, so I instead ran my script from the terminal, using chimera -- nogui python_script.py . This resulted in a rate of file conversion that was much faster than the GUI even before its slowdown, but it raised an error that was never a problem in the GUI: Cannot properly run "/Applications/Chimera.app/Contents/Resources/bin/amber18/bin/sqm -O -i sqm.in -o sqm.out". This only occurred on nonstandard amino acid residues, but the error was not solely determined by the residue's identity, as many carboxylated lysine residues were processed properly before the system encountered one particular file whose KCX residue caused it to crash. However, the error is consistent, meaning that the same KCX residue on that particular file always causes the program to crash. I have had no luck searching for the error online, but I am happy to include the entire error message in context if that would be helpful. More generally, I don't understand why running the exact same python script through the GUI and through the terminal window gives such different results. I'm happy to do it either way as long as the operation can be completed successfully within a day or two, and I would be very thankful for any advice you may have. Sincerely, Rafi Brent

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Downloading Trouble
by Harman Thind 02 Jun '22

02 Jun '22

To whom it may concern, I have a problem opening up Chimera. Every time I run the app the error message found in the image shows up. I have tried reinstalling the app and restarting my laptop... however, that hasn't accomplished much. What steps should I take next? Thank you for your time. - Harman T. [image: image.png]

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Fatal error during Energy minimization
by Saousen Diaf 02 Jun '22

02 Jun '22

Dear all, I am using structure minimize tool in UCSF Chimera to minimize a glycosylated structure, but I get a fatal error: *Failure running ANTECHAMBER for residue BMA+MAN+NAG+MAN+NAG+PHE+MAN+ASN* *Check reply log for details* *any idea on how to resolve the issue.* *Thank you in advance for your help.* *Best* *Saousen*

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Blast not working
by Antonio Díaz Quintana 02 Jun '22

02 Jun '22

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Re: [Chimera-users] Blast not working
by Tom Goddard 01 Jun '22

01 Jun '22

Hi Antonio, Glad to hear the new Chimera 1.16 version is working. Tom > On Jun 1, 2022, at 3:25 AM, Antonio Díaz Quintana <antonio.diaz(a)iiq.csic.es> wrote: > > Hello Tom, > > Thankyou. It worked. > > Best, > > Antonio > > El 01/06/2022 a las 07:07, Tom Goddard escribió: >> Hi Antonio, >> >> The error "ImportError: No module named replyobj" means Chimera cannot find its message logging module called "replyobj". That suggests that your Chimera installation is broken, and does not appear to be a problem specifically with BLAST. I would suggest installing the current Chimera version 1.16. >> >> If that does not fix it, use the Report a Bug... button that should appear when this error message is shown. Or if that button does not appear use Chimera menu entry Help / Report a Bug.... >> >> Tom >> >> >>> On May 31, 2022, at 8:05 AM, Antonio Díaz Quintana via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>> >>> Dear all, >>> >>> Recently, I stopped being able to perform a BLAST search from the SEQUENCE tool in UCSF Chimera. Is there anything I could do to fix this? >>> >>> Log message follows: >>> >>> Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence >>> Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service <http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service> >>> Opal job URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1654009255276130143… <http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1654009255276130143…> >>> Traceback (most recent call last): >>> File "C:\Program Files\Chimera 1.15rc\share\chimera\tasks.py", line 179, in runStatusCB >>> task.statusCBList[0]() >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\ParserBlastP.py", line 434, in _statusCB >>> self.finishCB(self.params, output) >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 424, in _finish >>> self.fetchColumnValues() >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 449, in fetchColumnValues >>> info = fetch_pdb_info(pdb_ids) >>> File "C:\Program Files\Chimera 1.15rc\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info >>> import replyobj >>> ImportError: No module named replyobj >>> >>> Best, >>> >>> Antonio >>> >>> -- >>> Dr. Antonio J. Díaz Quintana >>> Instituto de Investigaciones Químicas >>> Universidad de Sevilla - CSIC >>> Avda. Americo Vespucio 49 >>> 41092 Sevilla >>> Spain >>> >>> Phone: +34 954 48 9631 >>> _______________________________________________ >>> 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> >> > -- > Dr. Antonio J. Díaz Quintana > Instituto de Investigaciones Químicas > Universidad de Sevilla - CSIC > Avda. Americo Vespucio 49 > 41092 Sevilla > Spain > > Phone: +34 954 48 9631

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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

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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

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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…..

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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 > >

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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

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