November 2019 - 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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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

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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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Electrostatic Potential
by Fernando Villa 10 Jan '20

10 Jan '20

Dear all Chimera users In UCSF ChimeraX version 0.91 (2019-08-30) I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) Then I input the commands: >surface >color electrostatic #1 map #2 palette -10,red:0,white:10,blue [image: image.png] Is it possible to calculate the red and blue area in Å2 of the molecule? Best regards, Fernando ATTE Fernando Villa Díaz

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Regarding the UNDO issue raised by Luca
by Boaz Shaanan 13 Dec '19

13 Dec '19

Hi, Is not possible to install an automatic 'save session' at intervals determined by the user just as done in an MS word session? This at least may rescue the last operations. Following my own Chimera 'disasters' of this kind, I actually save session quite frequently when it becomes heavily loaded, particularly prior to a major new operation. My 2p. Happy and warm Thanksgiving. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Wednesday, November 27, 2019 11:07 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 199, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. secondary structure restraints and crosslink restraints (Fr?nze M?ller) 2. Undo option? (Luca Pellegrini) 3. Re: Undo option? (Elaine Meng) 4. Re: secondary structure restraints and crosslink restraints (Elaine Meng) 5. Re: Auto-associate define attribute/render by attribute (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Nov 2019 13:50:32 +0100 From: Fr?nze M?ller <fraenze.mueller(a)biologie.uni-freiburg.de> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] secondary structure restraints and crosslink restraints Message-ID: <cde7ad0e-503b-b0cc-5466-006d64019f5a(a)biologie.uni-freiburg.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fr?nze M?ller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Sch?nzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

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secondary structure restraints and crosslink restraints
by Fränze Müller 27 Nov '19

27 Nov '19

Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fränze Müller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Schänzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

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Undo option?
by Luca Pellegrini 27 Nov '19

27 Nov '19

I was wondering if there are any plans for an Undo option? I just managed to wipe a detailed view of an active site with lots of side chains, by selecting one more amino acid on the ribbon drawing and then picking by mistake ’show only’ rather than ’show’ (slip of the finger). ps: I found an old post on this in 2004, explaining that there is no such option, but perhaps the Chimera authors are open to changing their mind? After all, we are using Chimera to make ever more complex drawings. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Modification of paths
by Reza Khayat 27 Nov '19

27 Nov '19

?Hi, I've installed the headless version of Chimera and have realized that it inserts the location of the headless binary into the PATH variable. Unfortunately, I can't figure out what system file has been modified. I use a tcsh shell and the .cshrc is not modified. Any help in identifying the modified system file would be greatly appreciated. Thanks. Best wishes, Rez Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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Save pdb problem
by Rui Chen 25 Nov '19

25 Nov '19

Hello, I docked a ligand into a monomer, now I want to save a new pdb file. In the new pdb file, chian A will be docked monomer, chain B will be the chain B of homodimer. I already superimposed the two PDB files and deleted chain A of homodimer. I also used change chain ID to add chain IDs to the combined PDB file. However I got the following problems: 1. In my system, there are glycans (residue name: 0YB), *I cannot add chain ID to the glycans* (residue 209-216 belongs to chain A, residue 425-432 belongs to chain B) 2. In my system, I also have a small molecule docked in chain A, I realized only *the last line of the ligand was given a chain ID "h"*, is this a problem? 3. I want to *save these two PDB files as two chains, not two models* (actually it's a homodimer except for the ligand) 4. Can I manually *delete all the connections*? Looking forward to your reply. Best regards, Rui

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Cntrl+shift + left selection makes screen go blank
by Dominique Gutierrez 25 Nov '19

25 Nov '19

Hello, Cntrl+shift + left selection makes screen go blank where I only see the green box and the pdb or map disappears until releasing the mouse. Are there any settings that prevent that in chimera or any display settings? Best, Dominique Gutierrez

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