- Chimera-users - RBVI Mailing Lists

two-letter ID of polypeptide
by Pu Qian 22 Apr '19

22 Apr '19

Hi Eric Pettersen, Thanks for your emails. I understand that current version of chimera still only use one letter ID, and column 21 is for 4-letter residues. The problem is: in current version of COOT, user can assign two-letter to a polypeptide, and the column 21 is used for it. When pdf file was output from COOT, than chimera can not use the pdb file as we expected. It could be better to use column 21 for two-letter ID. After all, very few people will use 4-letter residues. In this way, chimera still can be used for visualisation of the COOT two-letter ID pdb file, which can be convert to mmCIF format. Before conversion, we need to view it making sure there are no problems. Otherwise, it is not convince for uses who are working on bigger complex that has more than 62 polypeptides. Best regards Dr. Pu Qian --------------------------------------------------------------------------------------------- To elaborate a little on this, column 21 in an ATOM record is unassigned and Chimera conscripts that column to allow for 4-character residue names rather then 2-character chain IDs (the former were more far common a million years ago when Chimera was originally designed). So knowing that that column is part of the residue name may help you work around some things. For instance PDB residue name LIG in chain AB will be treated by Chimera as residue name LIGA in chain B (so, an atom spec of :LIGA.B rather than :LIG.AB). ?Eric Eric Pettersen UCSF Computer Graphics Lab

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color of waters using headless version
by Dhananjay 21 Apr '19

21 Apr '19

Dear users, I opened my reference pdb (ref_conf.pdb) and oriented (using ref_conf.mat) as I needed. Next, I opened another pdb (conf_1.pdb) and aligned to the reference with respect to residues 1-110. Then I deleted the reference pdb and hide all the atoms. Nest, I display waters and the atoms of residue 73 and 145 (as I wanted to show). The image is then saved. All the commands that I used are put in test.com file, as follows: open ref_conf.pdb matrixset ref_conf.mat open pdb/conf_1.pdb mm #0:1-110 #1:1-110 delet #0 ~display #1 @ display :WAT display :73@ display :145@ color magenta,r helix; color yellow,r strand; color gray,r, coil copy file temp2png.png png width 1200 height 1000 stop I run the following command: chimera test1.com When I used with GUI version 1.11 (build 41141) of Chimera, everything goes well and the saved png is exactly as I wanted. However, when I used the headless version (version 1.13.1 (build 41965) ) the waters' color changed to magenta. I don't know why the color of waters changed and does not remained as default colors (i.e. red for oxygen and white for hydrogens). Am I missing something in the above script or this is a bug with headless version? Thanks. Joshi

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Comparison of 2 structures
by Dmitry A. Semchonok 21 Apr '19

21 Apr '19

Dear colleagues, I have 2 similar structures that differs on the position of subunits. Do you know if Chimera can compare 2 structures and write a kind of report? Or is there any program that can do that? Both structures are in the pdb format Thank you. Sincerely, Dmitry

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shape sphere
by Francesco Pietra 21 Apr '19

21 Apr '19

I have read the manual about shape sphere. What I would like to do is retaining all proteic, nucleosidic, organic ligands, ions and water molecules that exist within a sphere of, say, 25A centered at a certain atom of a ligand, while discarding everything outside the sphere. Because of the content, are there special flags to be used? thanks francesco pietra (actually I am already trying with general commands but python is already working from 1 and 1/2 hr without any outcome)

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Origin of transformation matrices
by Daniel Asarnow 19 Apr '19

19 Apr '19

Hi, What's the origin for the rotation/translation output by measure rotation or fit-in-map results? If the origin index is 0, is the transformation calculated around (0, 0, 0)? I'm extending my software for transforming single-particle EM alignment parameters to accept a transformation matrix copy-pasted from Chimera and am having a slight difficulty. For most EM maps, the origin MRC header is not set, and the origin appears to be (0,0,0). Thus, if R and V are the rotation and translation from Chimera, the formula R * O + V - O where O is the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the correct translation. However, it's exactly one pixel short. Best, -da

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FW: Chimera interface displayed on a monitor - allowed?
by Williams, Joanne 18 Apr '19

18 Apr '19

From: "Bettinger, Dirk" <dirk.bettinger(a)thermofisher.com> Date: Thursday, April 18, 2019 at 7:20 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Chimera interface displayed on a monitor - allowed? Dear Mr./Ms., Your software is great. But, now for a website we are building we did a photoshoot of colleagues sitting at monitors and on one photo we would like to Photoshop a screenshot if Chimera on, in use. As if the person in the photo is working with Chimera showing a density map of a structure like apoferritin. Is there anything to object to this use, any rules to adhere to, to be allowed to show Chimera in this manner? Regards, Dirk Bettinger Content Designer Thermo Fisher Scientific Materials & Structural Analysis Achtseweg Noord 5 │5651 GG Eindhoven, The Netherlands +31 6 110 25 150 dirk.bettinger(a)thermofisher.com<mailto:dirk.bettinger@thermofisher.m>

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Using ChimeraX in no-gui mode
by James Starlight 17 Apr '19

17 Apr '19

Dear Chimera users! Would be possible to use new ChimeraX for execution of some simple scripts for structure visualisation and imaging via no-gui mode? I am using bash script to loop over pdbs and would like to 1) open each pdb which contains b-factors info in chimeraX 2) apply preset publication 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" 4) save high quality image at the selected directory using chimera render Would it be possible to do these things directly from linux terminal providing each time pdb and some script file with the list of the applied commands? chimerax-daily ${pdb} ${script} Thank you in advance!

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FW: UCSF Chimera License Inquiry
by Williams, Joanne 16 Apr '19

16 Apr '19

Hello User Help Team, Can you help address Ella’s question below regarding using Chimera with Matchmaker? I let her know that there are no trial versions of Chimera. Thank you, JoAnne From: Ella Czarina Morishita <ecm(a)vi14si.com> Date: Friday, April 12, 2019 at 6:48 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: UCSF Chimera License Inquiry Dear Sir/Madam, My name is Ella Morishita, and I am a principal investigator at a biotech in Japan. I am interested in downloading Chimera, but I was not sure if we are supposed to pay for the license for the use of Chimera at our biotech. I am currently running a case study involving structures of nucleic acids and would like to superimpose the structures using Chimera and Matchmaker. I am also not sure if Chimera and Matchmaker would work, so I was wondering if there is any trial package we can avail? Thank you. Best regards, Ella Morishita ******************************************** Principal Investigator Veritas In Silico Inc. 1-11-1 Nishi-Gotanda, Shinagawa-ku, Tokyo 141-0031 Tel: 03-6421-7537 Fax: 03-6421-7538 Email: ecm(a)vi14si.com<mailto:ecm@vi14si.com> ********************************************

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Re: [Chimera-users] Two-letter ID of polypeptide in Chimera
by Elaine Meng 16 Apr '19

16 Apr '19

Hi Pu Qian, PDB format only has one column for chain ID, so if you put in a 2-character chain ID it is no longer the correct format. Chimera only reads and understands the correct PDB format, not modified formats (except “pqr”), so I believe you would need to convert to mmCIF. See PDB format documentation, chain ID is column 22 only: <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#…> Please use the address chimera-users(a)cgl.ucsf.edu (CC’d here) for Chimera questions unless you are including private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 16, 2019, at 3:29 AM, Pu Qian <p.qian(a)sheffield.ac.uk> wrote: > > Hi Meng anf Tom, > > I used two-letter (for example, AA, AB etc.) to ID polypeptide in DPB file. The protein can be displayed using chimera, however, chains of ID, name of ligands cannot be recognised by the chimera. Is there any way I can see them in the Chimera, or I have to convert it to .cif first? > > Best regards > > Pu Qian

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Marker Link Text Label
by Carlos G. Oliver 16 Apr '19

16 Apr '19

Hello, I would like to know if it’s possible to add a text annotation to marker links (https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/volumepat…) Ideally this would be something similar to the `note` attribute in the marker objects but that would display above the link cylinders. Thanks! Best, Carlos G. Oliver McGill University

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