- Chimera-users - RBVI Mailing Lists

CHIMERA scripting
by chiarini＠takisbiotech.it 31 Jan '24

31 Jan '24

Dear Responsible, I am trying to acquaint myself with "chimera --nogui --script" mode in order to automatize some pdb processing for a pipeline. I manage to search for pdb, to open the file, to select residues and to calculate COM for the selection. On the shell, I get the COM coordinates but I would like to print or store them to write them elsewhere. So the question is how can I print the replylog from shell to a text file, under the --nogui mode? I have tried with saveReplyLog but it doesn't seem to work...Any suggestions are appreciated. This is an excerpt from what I'm writing so far: import os from chimera import runCommand as rc from chimera import replyobj from chimera import saveReplyLog #change to the folder containing the pdb files os.chdir("xxx/yyy/zzz/ABC.pdb") def find_string_with_substring(string, substring): for s in strings: if substring in s: return s return None # list_files contain only the .pdb files list_pdb_files = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # specify the characters 'HLA' you want the filenames contain HLA_characters = HLA file_pdb_HLA = fins_string_with_substring(list_pdb_files, HLA_characters) print(list_pdb_files) print(file_pdb_HLA) nome = file_pdb_HLA replyobj.status(Processing " + nome) rc ("open " + nome) rc ("select :1.232") rc("measure center sel") saveReplyLog("~/reply-log.txt") Thank you so much -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

2 3

Intune Deployment
by CLIFFORD RAYMOND 31 Jan '24

31 Jan '24

Hi, My name is Clifford Raymond and I'm a manager in the tech department at East Brunswick Public Schools in New Jersey. I would like to know if you have the Chimera software in a MSI format for ease of installation? I'm currently trying to push the software out to my teachers through Microsoft Intune and the installer fails for unknown reasons. If you can assist I would greatly appreciate it. Clifford Raymond Senior Manager of Desktop Support Admin Building 760 Route 18N 732-613-6735 clifford.raymond(a)ebnet.org<mailto:clifford.raymond@ebnet.org> ________________________________ CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. Email received by or sent to school district officials/employees is subject to the Open Public Records Act [OPRA]. Consider alternate avenues of communication should you have concerns about the contents of your email being read by someone other than the person(s) you are contacting. ________________________________

3 5

Nucleic acid "mutation"
by Samo Lešnik 30 Jan '24

30 Jan '24

Dear Madam/Sir, I was wondering if it possible to "mutate" a base pair in nucleic acid (e..g A-->C), in the same way as can very elegantly be done for proteins with the rotamere function. Thank you and best regards, Samo

2 2

PDB file breaking down
by NCdt In Gue Chang 30 Jan '24

30 Jan '24

Good Afternoon, I'm currently a master's student using chimera but I have a problem and I was wondering if you guys have a solution for it. When the original PDB file is loaded onto chimera, I can see different alpha and beta chains however, when I run optimization using gaussian program and load the fchk file or pdb file converted from chk file, the chains are gone and I'm left with just atoms. When I convert the chk file to pdb file in gaussian, it does the same and I was wondering if you guys know a solution or tips to bypass this. If you could help me out, it would be great! Thank you ASLt / Ens 2 In Gue Chang Royal Military College of Canada Canadian Armed Forces s29459(a)rmc-cmr.ca / Tel: 778-828-1252 Collège militaire royal du Canada Forces armées canadiennes s29459(a)rmc-cmr.ca / Tél: 778-828-1252

2 1

CHIMERA scripting
by chiarini＠takisbiotech.it 30 Jan '24

30 Jan '24

Dear Responsible, I am trying to acq -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

1 0

Inquiry regarding file opening issue
by LEE JIA QI . 26 Jan '24

26 Jan '24

Dear Ms/Mr, I hope this email finds you well. I am writing to bring to your attention an issue I am experiencing with your software. I have been attempting to open my protein file using Chimera, but unfortunately I have encountered difficulties. The file opened with nothing, but I can open it last time I will send my file here, and I would appreciate it if you could provide guidance for me as soon as possible. I look forward to your assistance in resolving this issue. Best regards Jia Qi -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

2 1

RMSD related query
by Dhindwal, Poonam 16 Jan '24

16 Jan '24

Hello, I was wondering if there is a way in Chimera to generate RMSD values for individual C alpha after structure alignment. I want to plot a graph of RMSD vs individual Amino acids. I performed 'Matchmaker' to generate the structure alignment and in the output tab, I can see rmsd bars on top of aligned sequences but I am unable to get the exact values of RMSD. Any help would be greatly appreciated. Thank you, Poonam Dhindwal, Ph.D. Post-doctoral fellow Department of Veterinary Microbiology Western College of Veterinary Medicine University of Saskatchewan 52 Campus drive Saskatoon SK S7N5B4 Phone: 639-317-4702 Email: pod898(a)usask.ca

2 2

CAN NOT RECORD VIDEO
by akmalyati sulong 16 Jan '24

16 Jan '24

Dear Sir or Madam, I am trying to record a movie in Chimera 1.17.2, but I consistently get the following error without a proper error message: "An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ". Please help me to solve the problem Regards, Akmalyati email : nays5098(a)gmail.com

2 1

Query on the force field for energy minimization
by Prabuddha Bhattacharya 15 Jan '24

15 Jan '24

Dear Sir I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file. Thank you Kind regards *Prabuddha Bhattacharya * [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 13/01/24, 15:02:51

2 2

LIGAND ENERGY MINIMIZATION
by DR. SHAZIA DAWOOD 12 Jan '24

12 Jan '24

Dear Sir , I want to minimize ligand and protein energy (pre docking step) . which chimera should be downloaded. I have an ucsf chimera for windows but currently it is not working. mention me chimera for my laptop windows 10. Thanking You -- *Dr. Shazia Dawood* Assistant Professor Pharmacy And Allied Health Sciences M.Phil. PhD. Biochemistry (UOK) North Karachi Campus, Plot No. 204-205 Sector 7B/1, North Karachi, Karachi, Pakistan. 7580 03319764733 +9221-36723221-6/111-11-IQRA shazia.dawood(a)iqra.edu.pk <saad.saleem(a)iqra.edu.pk> --

2 3

how to play trajectory frames ?
by Mitch Murphy 11 Jan '24

11 Jan '24

i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "*'coordsets' has no suffix*" error message. and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "*Expected a keyword*". how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.

2 1

Chimera export morph animation to 3D software
by Rebekah Moore 09 Jan '24

09 Jan '24

Hi, I was wondering if it's possible to export a morph animation to a 3D software like C4D, Maya, or Blender? I don't wish to render a "movie" in Chimera, as I would like to add the protein morph to a 3D scene in C4D with other animated objects and render it using Redshift. Is this possible? I've tried exporting in vrml xmd and glb formats, which in theory can have animation data, but when I import the files into C4D or Blender the protein has no keyframes and is static. Thanks for your help! Best, Rebekah

2 1

Finding interacting residues between receptor and ligand
by Prathvi Singh 04 Jan '24

04 Jan '24

Hi Elaine, I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy. Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site. Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them? Thanks in advance, Prathvi

4 4

Need help using AutoDock Vina with Chimera on Mac
by Kush Unadkat 04 Jan '24

04 Jan '24

Greetings I am a student and I just got a new Mac and I am having a difficult time using AutoDock Vina in Chimera on my Mac. When working with two proteins (.mol2) format, I use AutoDock Vina in tools, input the required values and describe the path to “vina” using the browse button but instead of getting a pop up with the docking possibilities, I get an error like this: [Errno 30] Read-only file system: ‘docking.receptor.pdb’ I tried to look into the problem and if I can understand this correctly, I has something to do with Mac not allowing users to Write on the disk but I’m not sure. Can you please tell me what I’m doing wrong or how I can solve this issue? I am currently working on a project and I have a deadline so it is really important that I find a solution soon. Thank you. Your assistance is really valuable to me.

2 2

Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

2 3

Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

1 0

Highlighting residues
by Henen, Morkos 18 Dec '23

18 Dec '23

Hello, I'm running into an issue with using Chimera. When I move with the cursor over a protein residue or particular atom, it is used to show the name/number of this residue or atom. Now, for some reason, this option doesn't work. It has to be something I disabled by mistake, but I can't find that. Could you kindly guide me on what I can do to fix that? Thanks a lot Morkos Morkos Henen, Ph.D. Assistant Professor - Research University of Colorado-Anschutz Medical Campus Denver, USA

2 1

Distance between centroids
by Francesco Pietra 17 Dec '23

17 Dec '23

Hello with candidate version 1.15, linux64, X11 I want to measure the distance between the centroids of two aromatic stacking rings. The usual way of measuring distances does not work (clicking as needed has no effect), contrary to what the manual says. And I should have done successfully that measurement in the past. Also between one of the centroids and a regular atom: same issue. Distance between regular atoms works correctly. thanks for advice francesco pietra

2 2

A Software bug
by yongsheng_zhao 12 Dec '23

12 Dec '23

Hello, I installed the latest version of UCSF CHIMERA 1.17.3 on my win11 computer. After the installation, a window of related Settings kept coming up, and the EDGE browser was automatically opened to go to the CHIMERA help website. May I ask why? Now as long as you use this software, it keeps popping up small Windows, and the EDGE browser has been playing websites, like a virus, and it can't be used at all. | | yongsheng_zhao | | yongsheng_zhao2023(a)163.com |

3 3

[chimera] modeller.SequenceMismatchError
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. ) However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

3 8

Changing threshold value of attributes
by Abril Gijsbers 28 Nov '23

28 Nov '23

Dear community, I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. [image: image.png] When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( ui tool show "Render By Attribute" Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 759, in _set_value_cb self._redraw_cb() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right ValueError: operands could not be broadcast together with shapes (0,) (157,) ValueError: operands could not be broadcast together with shapes (0,) (157,) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right *See log for complete Python traceback.* Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb self._move_cur_marker(v) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker self._active_markers._update_plot() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot self._update_marker_coordinates() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1207, in _update_marker_coordinates x, y = self._scene_xy(m.xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy return self.histogram._scene_xy(abs_xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) TypeError: object of type 'function' has no len() TypeError: object of type 'function' has no len() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) *See log for complete Python traceback.*

2 1

saving selected residues
by Dieter Blaas 27 Nov '23

27 Nov '23

Hi, I selected several residues in an icosahedral viral capsid and want to save the corresponding pdb. However, whatever name I try to give this selection I receive the error "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". Can you please give me an example of a valid name! The viral subunits are 6sk5.pdb1 (#0.1), 6sk5.pdb1 (#0.2), and so on. I have no clue what I should call this selection for it being accepted. Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 4

recording a movie as series of PNGs with a transparent background
by Eugene Valkov 20 Nov '23

20 Nov '23

Hi folks, Per instructions ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html) I'm trying to make a movie with a series of PNGs with a transparent background to make into a GIF afterward. However, I get an error below. Any help would be appreciated! Thanks, Eugene Eugene Valkov Stadtman Investigator RNA Biology Laboratory National Cancer Institute This works: movie record size 1000,1000 format PNG supersample 4 directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop This doesn't work: movie record size 1000,1000 format PNG supersample 4 transparentBackground true directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop and I get this error: "Expected a keyword". Saving individual PNGs with a transparent background works fine. My version is 1.6.1 (2023-05-09).

2 2

Announcement: Release of DOCK 6.11
by Scott Brozell 16 Nov '23

16 Nov '23

We are pleased to announce the release of DOCK 6.11. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.11 is available for download and free for academic users at http://dock.compbio.ucsf.edu/DOCK_6/index.htm This is a release of the new descriptor-driven de novo design method DOCK_D3N which takes advantage of the integration of the open source toolkit RDKit into DOCK6. DOCK_D3N tailors ligand growth towards desirable regions of chemical space by calculating cheminformatic descriptors at each stage of ligand construction. For full information on what is new in DOCK 6.11, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.11.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

Unable run Modeller: [Errno 13] Permission denied
by naghmehn85＠gmail.com 27 Oct '23

27 Oct '23

Hello, I was trying to use the Modeller (run it locally) on Chimera UCSF but I encountered this error: Unable run Modeller: [Errno 13] Permission denied. I, as well, received this error when I wanted to load PDB files from my local MacOs. Would you mind please telling me what the issue is? Thank you so much.

3 2