June 2022 - Chimera-users - RBVI Mailing Lists

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.

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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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Chimera-users June 2022