January 2020 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

5 6

MD chimera bug
by Fabian Glaser 31 Jan '20

31 Jan '20

Dear Chimera developers, I think I have found abug in the MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case 96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script Best, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

2 3

conjugate moiety to protein PDB
by Michael Scott Bowers 30 Jan '20

30 Jan '20

Hi power users, I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file. Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file. I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond. Much thanks to everyone in advance. Best, Scott

3 2

Auto-associate define attribute/render by attribute
by Healey, Joseph 24 Jan '20

24 Jan '20

Hi Chimera team, I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins. Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence. Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment? Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

3 13

Fourier transform
by Angus McDonald 23 Jan '20

23 Jan '20

I am having trouble using the fourier transform tool in Chimera. I have tried looking for it in the Tools/Volume Data menu and I don't see it. I have also tried the start fourier which returned an error message. I suspect I am doing something wrong . Can you please help with this issue. I am using 1.13.1 build 41965 Platform Windows 64. Thanks for your help -- Angus McDonald amcdonald(a)boisestate.edu

2 2

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

2 1

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)

2 1

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.

3 4

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.

2 3

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

2 1