- Chimera-users - RBVI Mailing Lists

measure rotation
by Jesse M. Hansen 11 May '20

11 May '20

hi I repeatedly have this issue and no idea how to fix it. I send the same files to colleague and they cannot reproduce it. We cannot figure out whether it's some minor detail I am doing, or it's my version of chimera. When I try "measure rotation #1 #2" the axis ends up either pretty off center or WAY far away (like 20 protein widths away). have tried: * centering volume and resaving, fitting models into map and resaving. Opening and all looks correct. * tried opening pdb first then maps, or maps first then pdb. Both seem to give different results but neither are precisely down the actual axis of my helical protein despite having centered it. * adding "coordinateSystem #" to the command has no effect. The axis that appears is now as long as my box, but it's still not centered thanks Jesse

3 3

Re: [Chimera-users] How to save a pdb which moved by mouse
by Elaine Meng 11 May '20

11 May '20

On May 11, 2020, at 8:55 AM, 李雄俊 <lixiongjun(a)mail.sysu.edu.cn> wrote: > > Hello Dr Meng: > > I tried to dock a partial thread pdb file to a mrc file with UCSF-Chimera,as the tutorial recommanded，I clicked "Favorites ——> Model Panel",and inactivated mrc, and then dragged the pdb to dock the volume data. But I found that I cannot save this moved pdb, I mean, even though I save the pdb in a new file, when I open this file in Chemira, it shows that the pdb still be the original position, didn't move anywhere. If I want to change it's position, I need use "Tools/Movement/Transform Coodinates" to get a really moved pdb, but I cannot get precise displacement parameters, Could you please help me to solve this problem: How to save a dragged pdb's coordinates? Thank you very much. Hello, You can of course save a dragged PDB in its new location. Just make sure that when you save it, you save it "relative to" the map model. There is a choice for that in the File... Save PDB dialog. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> The chimera-users(a)cgl.ucsf.edu address (CC'd here) is recommended for asking questions, to ensure you get an answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

problems opening multiple pdb files
by Domenico Raimondo 09 May '20

09 May '20

Hi, I am using chimera on a Mac (10.15.4 verison). My problem is that every time I open a pdb file with a double click it opens it in a new window of chiemera. In this way I cannot have multiple pdb structures in a single chimera window using the double click method to open the files. Thanks. Domenico Raimondo. -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

2 3

ChimeraX on Twitter
by Tom Goddard 09 May '20

09 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

1 0

Question about vop maximum
by Reyhan Muhammad 08 May '20

08 May '20

Dear Chimera Users, I am new to Chimera and cryoEM. For my project, I would like to create a single map (which will be used as a mask) for six 3D classes. To achieve that, I have aligned all my six maps using Chimera 'Fit in Map' and used vop maximum (vop maximum #0,#1,#2,#3,#4,#5) to generate a new map that is supposed to 'cover' all the other maps. My question is, when I look at the vop output map (green map in the file attachment), why do we still see some densities from input maps (salmon color) outside the vop output map? I have also adjusted the contour level of all map to 0.04 (volume all step 1 level 0.04). I hope someone could help me to clarify my understanding of vop maximum. Thank you for your help. Best wishes, Reyhan <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

Conformation Search in Chimera
by Maj Krumberger 07 May '20

07 May '20

Hello, We are currently developing an educational exercise in Chimera for building different inhibitors in different proteases, using Chimera and then using AutoDock Vina for finding potential docking sites. I was wondering if there is a function in Chimera for doing a conformational search that we could do to find the lowest energy conformer before running AutoDock Vina? Thank you, Maj Krumberger Graduate Student - Nowick Group Department of Chemistry maj.krumberger(a)uci.edu University of California, Irvine 4302 Natural Sciences I Irvine, CA 92697-2025

2 2

MD simulation
by Александр Харченко 06 May '20

06 May '20

Good afternoon, dear Chimera team! My name is Dr. Pavlo V. Zadorozhnii I am trying to simulate the molecular dynamics of a protein. Started with a simple tripeptide RGD, but I have a number of problems: 1) after starting the energy minimization, the molecular dynamics simulation starts automatically, I can't do it step by step; 2) as soon as the conugate gradient minimazation step is started, the structure of the RGD tripeptide disappears; 3) after the calculation, the structure of the tripeptide does not appear and I can not analyze the data. All graphs and charts are blank. I used Chimera version 1.14. Print Screen is in the app. Please help me with the problem I have. Sincerely, Dr. Pavlo V. Zadorozhniy. -- реклама ----------------------------------------------------------- Поторопись зарегистрировать самый короткий почтовый адрес @i.ua https://mail.i.ua/reg - и получи 1Gb для хранения писем

2 1

Matching a small ligand to another
by Divjak Maja 06 May '20

06 May '20

Hi Elaine, Hope you're well! I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org 305 Grattan Street Melbourne Victoria 3000 www.petermac.org Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

2 2

Questions regarding UCSF Chimera
by THEVASHREE A/P RAJANDERAN 04 May '20

04 May '20

Dear Sir/Madam/Mr./Ms./Mrs./Dr. I am Thevashree Rajanderan from Sunway University, Malaysia. I had been using UCSF Chimera for months now but recently i am unable to conducts works on this software. At first i was unable to conduct AutodockVina, but now my projects keeps on freezing during the minimization process. May i know whether the server is down or is there anything new that i must download to further support the system. Thanks and regards. "All students are issued with an iMail email account. This is the official method by which Sunway will communicate with you on a range of administrative and academic matters. When corresponding with Sunway via email, you must use your iMail email account. Using the iMail email account helps to ensure your identity and validity of the communication."

2 1

in the docking process this message appear and does not continue, opal:vina_1.1.2 unavailable what i should do
by Ahmed Tawfeek 04 May '20

04 May '20

Dear Professors and Doctors, I need the help I am trying to learn the work on chimera for the purpose of checking my compounds as organic chemist but i could not continue, because at the docking stage, the autodock vina does not work and this message appear, the message " opal:vina_1.1.2 unavailable" what is the solution Best Regards Ahmed Tawfik

3 4