- Chimera-users - RBVI Mailing Lists

Can I import the molecule Cellulose in Chimera?
by Mazin Nasralla 19 Mar '24

19 Mar '24

Hello, I would like to open a molecule of cellulose https://en.wikipedia.org/wiki/Cellulose in Chimera. I go to Open Fetch ID and open the Pubchem option and input the id and I get this error. [cid:image001.png@01DA7784.1097E770] I can import cellobiose which is a two monomer β-Glucose. If I could import something with say 6 monomers that would be fine. Is there a way to do it? Thanks, Mazin

2 1

APBS OpenDX file conversion to XYZ
by Scott Bembenek 05 Mar '24

05 Mar '24

Is it possible to use Chimera to convert an APBS OpenDX grid to coordinates: x,y,x, grid point value?

3 4

volume image intensity 1 vs 0.99
by Tyler Luchko (Lists) 05 Mar '24

05 Mar '24

Hello, I’m trying to fine tune the intensity of my volume image, but there is a large discontinuity between an intensity of 0.99 and 1 that is causing me problems. Using the following script, I get volume #1 style image volume #1 colormapongpu true volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,0.99 color orange Changing the last list to volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,1 color orange I get The last level goes from barely visible to completely opaque. I don’t know if this is the intended behavior or not, but I would like to have a smooth transition to full intensity. Is this possible? I notice that for levels between 0 and 1, the intensity seems to work as I expected. It is only for levels greater than 1 that I notice this behavior. I am on a Mac using version 1.7.1. The MRC file is 59 MB, so I have not included it. If it helps, the visualization is trying to show the water density around methanol (not shown) relative to bulk. Black (0) is zero density, white (1) is bulk density, blue (2) is 2 times bulk density, and orange (4) is 4 time bulk density. Thank you, Tyler

2 1

Rview in UCSF Chimera
by Richardson, Cory 05 Mar '24

05 Mar '24

Hi, I am new to chimera and would like to use 'rview' in UCSF Chimera. I have UCSF Chimera version 1.17.3 installed and would like to use 'rview' as it is not currently listed under Tools as an option to select. May you please provide guidance on how I may get UCSF Chimera to recognize and integrate 'rview'? Respectfully, Cory Richardson Sr., Systems Engineer Developing Brain Institute Diagnostic Imaging and Radiology Children’s National Hospital O: (202) 476-3866 F: (202) 476-6833 S: DevelopingBrainReserachLab [Description: cnmc_logo_sig2] “Scientists study the world as it is, engineers create the world that never has been.” Theodore von Kármán 1962 National Medal of Science Recipient Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 1

how to select atoms without substituents?
by Sara Luz Gomez Maya 05 Mar '24

05 Mar '24

Hi all, Is there any way to select (or directly remove) atoms without substituents? The situation is that I have to cut a region of a system. So, after selecting by zone *without* including the entire residues, I save the selection and I get some single atoms that I would like to get rid of. For example, in the attached file I got H atoms, C atoms, and also C2 chains that do not have any sense even if I complete their valences by adding H. Notice that in such a way they will become H2, CH4 and CH3CH3, respectively, which are very strange molecules for my system that actually contains phospholipids, ibuprofen, and water. I would like to know if there is any automatic tool to do it, for example defining an attribute or using the command line. Any help is appreciated. Regards, Sara

2 1

Dock problem selenium atom
by turgut şekerler 11 Feb '24

11 Feb '24

Dear Chimera Team, I hope this message finds you well. I am writing to inquire about an issue I encountered while attempting to perform docking with a selenium atom using the Dock Prep module in Chimera. My goal is docking selenium atom and my target protein. But ı always get a error message : cant prepare ligand. I have been utilizing Chimera's Dock Prep module to prepare ligands for docking with proteins, and it has been an effective tool thus far. However, I have encountered difficulties when attempting to prepare a ligand containing a selenium atom. It seems that the Dock Prep module is unable to handle the selenium atom properly, resulting in errors during ligand preparation. I have attempted to troubleshoot this issue by researching error codes and exploring potential solutions, but I have been unable to find a resolution. As such, I am reaching out to inquire if there are any specific recommendations or alternative approaches that could be used to successfully prepare a ligand containing a selenium atom for docking in Chimera. I understand that Chimera utilizes standard force field parameters for ligand preparation, but given the unique properties of selenium, it may be necessary to consider additional or specialized parameters to ensure accurate docking results. Any guidance or assistance you could provide on this matter would be greatly appreciated. I am eager to resolve this issue and continue utilizing Chimera for my docking studies. Thank you for your attention to this matter. I look forward to your response. Sincerely,

2 1

Trouble in Creating Peptide bond
by Vignesh Nandhagopal 06 Feb '24

06 Feb '24

Dear Chimera Help Team, I want to create a peptide bond. I followed this manuscript which I have attached along with this mail. I followed the steps of the manual I have used and I have seen a slight change in build structure. Kindly help me with this I am getting an error in the unrecognized protein code. Kindly help me with the steps.

2 3

polymer formation
by Kainaat Mahzaib 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

2 1

polymer formation
by Kainaat Mahzaib John 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

1 0

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 31 Jan '24

31 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 12 Jan '24

12 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 05 Jan '24

05 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