May 2021 - Chimera-users - RBVI Mailing Lists

What do you do for comparative modeling if the pdb is so new it's not in UniProt?
by Ralph Loring 24 May '21

24 May '21

Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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excluded bilayer in chimera
by Yanhe Zhao 22 May '21

22 May '21

To whom may concern, This is Yanhe Zhao, from UT Southwestern Medical Center. I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input. Best regards, Yanhe

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Measuring rotation
by JAVAD KARIMBAYLI 18 May '21

18 May '21

Greetings dear sir/madam I was trying to measure the rotation of my protein before vs after activation using the "measure rotation #0 #1" command, which worked smoothly. Then I wanted to check the rotation of specific residues. However, when I tried to specify residues, for example, residue 45 of model0 vs model1, the code didn't work. I have gone through Chimera documentation but didn't really find how to solve the issue. So, I kindly ask for your suggestions about how I may get residue-specific rotations. Thank you in advance Javad Karimbayli

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Covalent bond making and docking
by Zhang, Bixia 14 May '21

14 May '21

Good evening, I was trying to make a man made side chain, which is serine plus uracil. I used the command "bond sel" to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of "poor connection". I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model? Thank you, Bixia

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Question about error: "the exit code was: -1073731819"
by Sergio Garay 13 May '21

13 May '21

Dear Chimera Users My name is Sergio Garay, I have installed chimera-1.15-win64.exe on Windows 10pro 64bit. But when the program starts to run, the system gives me the following error message and the program closes: chimera exited abnormally; the exit code was: -1073731819. use the -- debug command line option for the full error message I tried installing the two previous versions of the program, with the same result. My PC has a Radeon RX 580 series videocard, and the system uses a WDDM 2.7 video controller. Could you give me any advice on how to fix this problem? Sincerely -- *Prof. Dr. Sergio Garay* *Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Enquiry regarding application
by Prem Rajak 13 May '21

13 May '21

Dear Sir/madam, I have a query regarding the use of UCSF Chimera for molecular docking studies. I am a faculty at an University and would like to analyse my molecular docking research studies using UCSF Chimera. Moreover, I would like to publish the images thus analysed in national/international standard journals. Publications may be multiauthored. Therefore, please let me know whether I can use the software free of cost or I have to purchase the licence. Looking forward to your reply. Thanks and regards, Dr. Prem Rajak Kazi Nazrul University West Bengal, India

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Help for Chimera launch fail
by 黄华 12 May '21

12 May '21

Dear Eric Pettersen, This is a Chimera User in South China Normal University(Guang zhou, China).  Now, I found I can not start the Chimera even after I reinstalled. Would you tell me how could I fix this problem? This is the message after I launch Chimera-debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 Press return or enter to to exit thanks for your help! hua ------------------ Hua Huang Principal Investigator School of Life Science South China Normal University Guangzhou, China 黄华华南师范大学M邮箱/未归类/生命科学学院/教职工/办公华南师范大学始建于1933年，是一所学科门类齐全的国家“211 工程”重点建设大学。 “艰苦奋斗、严谨治学、求实创新、为人师表 ”是华南师范大学校训。  

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] S33C .mrc file
by Elaine Meng 11 May '21

11 May '21

Dear Neha, Now you tell me that you opened 1qwa as the pdb (atomic structure) file, so this mrc file is completely irrelevant. I believe you just used the wrong steps to save the pdb. You need to use menu: File... Save PDB, and in that dialog "Save models" area, choose the atomic structure model. (Hiding the map does not matter, centering the view does not matter, it is only what you choose in the dialog). Then as Tom already said, you also have to turn on the "Save relative to model" option and chose the map model as the one you want to save the PDB relative to. Here is the help for the Save PDB dialog: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> 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 10, 2021, at 9:15 PM, Neha Goel <nehagoel24march(a)gmail.com> wrote: > Dear Elaine, > Thank You. Here I .mrc is attached. I was using a reference pdb like 1qwa from pdb database. > Regards > Neha Goel

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Unable to save file in pdb
by Neha Goel 10 May '21

10 May '21

Dear Chimera, I have a .mrc file. I reopened the file in chimera and would like to save it in pdb. I am unable to save it. It needed the molecular model pdb. Kindly guide me the way to save it. Regards Neha Goel

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