- Chimera-users - RBVI Mailing Lists

Problem downloading PDBs in Chimera
by Clarke, Oliver 10 Mar '25

10 Mar '25

Hi, Since this weekend, I have been unable to download PDBs from within Chimera (using "open" or Fetch by ID). The same PDBs load fine in ChimeraX or when downloaded manually. Cached PDBs load fine. Cheers Oli

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Setting partial charges to a protein gives same charges in both Gasteiger and AM1-BCC methods. Is that corrects?
by teralexei＠proton.me 03 Mar '25

03 Mar '25

Dear colleagues, calculation of partial charges in Chimera looks to work improperly in my hands. After addcharge or dokprep procedures, independent on method used (am1-bcc or Gasteiger), mol2 files are just the same: @<TRIPOS>MOLECULE .... PROTEIN AMBER ff14SB @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... The problem persist in both Chimera 1.17.3 and ChimeraX. The latter gives even "NO_CHARGES" comment in both (am1-bcc and Gasteiger) cases: @<TRIPOS>MOLECULE .... PROTEIN NO_CHARGES @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... I am not an expert in molecular modeling, sorry. But I think that I am doing something wrong. Could you please help me with setting charges properly? Thank you in advance! PS. I am a newbie here. Please don't hurt me too much. Yours sincerely, Al.

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registration
by YELIZ KAYA 27 Feb '25

27 Feb '25

Dear Sir, As I have attached the image, I registered to the Chimera program. However, I did not receive any e-mail. Can you help me with this? Thank you. Assoc. Prof. Dr. Yeliz KAYA IUC Chemistry Department -- *İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA <https://www.iuc.edu.tr/tr/_>* Yasal Uyarı: <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…> Bu e-posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafından alınması amaçlanan yetkili gerçek ya da tüzel kişinin kullanımı içindir. Eğer söz konusu yetkili alıcı değilseniz bu e-postanın içeriğini açıklamanız, kopyalamanız, yönlendirmeniz ve kullanmanız kesinlikle yasaktır ve bu e-postayı derhal silmeniz gerekmektedir. İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA bu e-postanın içerdiği bilgilerin doğruluğu veya eksiksiz olduğu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne şekilde olursa olsun içeriğinden, iletilmesinden, alınmasından ve saklanmasından sorumlu değildir. Bu e-postadaki görüşler yalnızca gönderen kişiye aittir ve İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA'nın görüşlerini yansıtmayabilir. *ISTANBUL UNIVERSITY-CERRAHPASA <https://www.iuc.edu.tr/tr/_>* Disclaimer <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…>: This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient you are hereby notified that any dissemination, forwarding, copying or use of any of the information is strictly prohibited, and the e-mail should immediately be deleted. ISTANBUL UNIVERSITY-CERRAHPASA makes no warranty as to the accuracy or completeness of any information contained in this e-mail and hereby excludes any liability of any kind for the information contained therein or for the information transmission, reception, storage or use of such in any way whatsoever. The opinions expressed in this e-mail may belong to the sender alone and may not necessarily reflect the opinions of ISTANBUL UNIVERSITY-CERRAHPASA.

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UCSF chimera problems when fetching PDB id's
by Charles-Alexandre Mattelaer 26 Feb '25

26 Feb '25

Hi all I just wanted to ask if it is normal my Chimera installs have begun throwing errors when fetching PDB’s by ID (eg 1EHZ)? It does work for other PDB codes, eg 6NP2. I used to do this regularly but since a few days I have noticed these errors pop up. It typically returns: “Error reading $PDBcode: No such id: $PDBcode” I am aware Chimera is deprecated and not supported anymore, but I used it for simple tasks eg Autodock Vina which is not supported in ChimeraX and teaching thereof. Kind regards Charles-Alexandre

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I would like to inquire about the way to make the ligand file pdbqt.
by Healer Choi 20 Feb '25

20 Feb '25

Dear UCSF Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea. I'm inquiring about a problem in the process of making a pdbqt file during the research project. First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed. As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking. I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux. Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3)

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script for clashes
by valerio chiarini 18 Feb '25

18 Feb '25

Dear Responsible, I am working on a script that should iterate through several structures, check the structures for clashes among all atoms, and eliminate the pdb in any clashes are found. Here is what I have worked out so far: # -*- coding: utf-8 -*- import os from chimera import runCommand as rc from chimera import replyobj import chimera # Specify folder folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" # String to be found search_string = "xxx" # List of files in the folder file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] print("File trovati nella cartella:" + str(file_names)) # Loop on every file containing 'search_string' in the name for pdb_file in file_names: if search_string in pdb_file: pdb_path = os.path.join(folder_path, pdb_file) # Open the PDB rc("open {}".format(pdb_path)) # Calculates clashes rc("findclash") rc("wait") # Verify if any clashes are found clashes = chimera.clashClashList() if clashes: # If clashes are found eliminates the file os.remove(pdb_path) print("Clash trovati, il file {} è stato eliminato.".format(pdb_file)) else: # If no clash, exit normally print("Nessun clash trovato per {}.".format(pdb_file)) But no analisys is done at all. I have been searching through the script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in order to found some clue on this function but so far I have found none. Could you help me on this issue? Thank you in advance Valerio Chiarini

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smart boards or mobile devices
by Wendy Tomamichel 13 Feb '25

13 Feb '25

Good afternoon. We have a VIBE board that we would like to utilize your software for. The only issue is that it is a smart board that can't download traditional software. Do you have a software download that I could try to see if it could work? Thank you! Wendy -- Wendy Tomamichel DePauw Chemistry Lab Manager Julian Science and Mathematics Center 2 E. Hanna St. Room 348 Greencastle, IN 46135 765-658-4606

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Chimera 1.X PDB downloads are broken
by Eric Pettersen 12 Feb '25

12 Feb '25

Hi all, The RCSB made a change to their web site this morning that broke the fetching of PDB files by ID code in Chimera. We have committed a fix to Chimera that re-enables PDB fetching, and that fix will be in tomorrow's daily build. Note that this problem only really affects you if you are trying to access PDB files you've never used before, because Chimera caches fetched PDB files on your machine. We hope to make a production release that incorporates this fix sooner rather than later, but aren't yet sure exactly when that will be. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Contributor
by Roy, Raj (MU-Student) 12 Feb '25

12 Feb '25

Dear Concern, I have used chimera for a long time, and I was wondering if I can contribute with some scripts/python code that can make chimera more beneficial to others. Regards, Raj Shekhor Roy PhD Student Electrical Engineering and Computer Science (EECS) Department University of Missouri - Columbia Email: rsr3gt(a)umsystem.edu Phone (Cell): 573-814-9512

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script for clashes
by chiarini＠takisbiotech.it 12 Feb '25

12 Feb '25

Dear Responsible, I am working on a script that should iterate through several structures, check the structures for clashes among all atoms, and eliminate the pdb in any clashes are found. Here is what I have worked out so far: # -*- coding: utf-8 -*- import os from chimera import runCommand as rc from chimera import replyobj import chimera # Specify folder folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" # String to be found search_string = "xxx" # List of files in the folder file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] print("File trovati nella cartella:" + str(file_names)) # Loop on every file containing 'search_string' in the name for pdb_file in file_names: if search_string in pdb_file: pdb_path = os.path.join(folder_path, pdb_file) # Open the PDB rc("open {}".format(pdb_path)) # Calculates clashes rc("findclash") rc("wait") # Verify if any clashes are found clashes = chimera.clashClashList() if clashes: # If clashes are found eliminates the file os.remove(pdb_path) print("Clash trovati, il file {} C( stato eliminato.".format(pdb_file)) else: # If no clash, exit normally print("Nessun clash trovato per {}.".format(pdb_file)) But no analisys is done at all. I have been searching through the script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in order to found some clue on this function but so far I have found none. Could you help me on this issue? Thank you in advance -- 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._

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