- Chimera-users - RBVI Mailing Lists

Can't connect to your website
by Ilona Nudelman 22 Jan '20

22 Jan '20

Hi, I am trying to connect to the UCSF Chimera website at https://www.cgl.ucsf.edu/chimera/ and it is not available with the error message "The server at www.cgl.ucsf.edu is taking too long to respond" I spoke with the IT department of my university to see if it was perhaps due to our firewall, but they say the problem is on your end. Are you guys aware of this issue? Thanks, Ilona

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save selected region to .mrc file: box size changed?
by jingchuansun 20 Jan '20

20 Jan '20

Hello, after segmentation, I can save a selected region to a .mrc file, but the box size is changed. Can I keep the original box size (and the relative position in original map)? Thanks! Jim ---------------------------------- http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/framecore.html Segment Map Save selected regions to .mrc file... save density map masked by the selected segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)

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Problem with autodock vina in chimera
by De campos, Luana J 17 Jan '20

17 Jan '20

Hi, I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Placing a model at 0,0,0?
by Divjak Maja 14 Jan '20

14 Jan '20

Hi there, I'm not sure this is possible, but what I would like to do is edit molecules in Chimera, position them at 0,0,0, save the PDB and then import the molecules into Maya, so that they are positioned at 0,0,0 in the viewport, instead of in some random position away from the work grid. I can actually edit molecules, then position them by eye in the Chimera viewport and save as PDB, which will position them near the grid in roughly the right orientation when imported into Maya. So what I'm looking for is a way of setting the molecules exactly to 0,0,0 in Chimera, so that they appear at 0,0,0 when imported into Maya. I'm not sure this is actually a valid concept in Chimera? Thanks so much for your help and best wishes, Maja 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.

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Issues with writesel
by Kevin Wang 14 Jan '20

14 Jan '20

Hi, I am trying to use the writesel command: writesel test. However, Chimera is not saving a list anywhere and I do not get an error message. Am I missing something in the command? Best, Kevin

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Chimera X commands
by Andrew Waight 14 Jan '20

14 Jan '20

Hello all, I've been an exclusive Chimera user for over 15 years. I have been scripting a lot in python lately and am super excited to learn that ChimeraX is written in python3. I totally want to import some chimera functions into my programs. Problem is, the ChimeraX command syntax seems all new (i can't even really figure out how to select properly, is there a ChimeraX command index that I am missing and is ChimeraX for me? ChimeraX looks beautiful by the way. Thanks you guys are amazing! Drew

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Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 13 Jan '20

13 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Placing a model at 0,0,0?
by Divjak Maja 13 Jan '20

13 Jan '20

Hi there, I'm not sure this is possible, but what I would like to do is edit molecules in Chimera, position them at 0,0,0, save the PDB and then import the molecules into Maya, so that they are positioned at 0,0,0 in the viewport, instead of in some random position away from the work grid. I can actually edit molecules, then position them by eye in the Chimera viewport and save as PDB, which will position them near the grid in roughly the right orientation when imported into Maya. So what I'm looking for is a way of setting the molecules exactly to 0,0,0 in Chimera, so that they appear at 0,0,0 when imported into Maya. I'm not sure this is actually a valid concept in Chimera? Thanks so much for your help and best wishes, Maja 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.

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Selecting multiple residues in one chain
by Yehuda Halfon 12 Jan '20

12 Jan '20

HI all, I want to select and color multiple residues in one chain. When I use select #1: 15, 18, 20 .B It select 15, 18 and 20 in all the chains. But when I use select #1: 15.B, 18.B, 20.B It select 15, 18 and 20 in chain B. Is there another way to select residues in one chain without adding .B after each one? It makes the script much bigger and less clean. Yehuda

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Re: [Chimera-users] Chimera on macOS Catalina (10.15)
by Chiara Rapisarda 10 Jan '20

10 Jan '20

Hello, I arrive a bit late to the discussion. After the Catalina upgrade, the open button in chimera is greyed out and I cannot open more than one file at any one time. Would anybody have any idea what is wrong? I have downloaded the latest build of chimera. Thank you for your help. Best, Chiara

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