- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] about map spliting
by Elaine Meng 15 Apr '19

15 Apr '19

> On Apr 13, 2019, at 6:16 AM, 张雷 <leizhang(a)hsc.pku.edu.cn> wrote: > > Dear Dr. Meng, > Thanks for your previous kindly help. Now, I have tried to split a special part from a whole map with the methods of surface zone (done) and vop multiply (still trying), but I found that the effect was not satisfactory. Is there some way to split a map much more real，accurate and precise as possible. Thank your very much! > Sincerely, > Lei Hi Lei, Chimera questions should be sent to the chimera-users(a)cgl.ucsf.edu address, CC-d here. I really have no idea what you are trying to do. If you have some atoms and you want to split the map near those atoms from the rest of the map, instead use the Color Zone tool which has a Split Map button. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fw: Properly citation
by Williams, Joanne 15 Apr '19

15 Apr '19

________________________________ From: Ricardo Ferreira de Oliveira <fo.ricardo(a)gmail.com> Sent: Sunday, April 14, 2019 2:31 AM To: chimera(a)cgl.ucsf.edu Subject: Properly citation Dear sirs, I made a little academic software, that I intend to publish in GPL license, that exports LigPLot+ .drw files into two files: 1 Python file and 1 file to be read on PseudoBond reader. THis files can depict a LigPlot+ diagram in Chimera. I would like to ask your help to help me correctly cite the Chimera trademark and rights. I would also like to know if there is any impediment in building software that exports from LiPlot + to Chimera I appreciate it in advance. Best regards Ricardo Oliveira [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<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…>

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Re: [Chimera-users] Non-standard atom names
by Sid Majaha 15 Apr '19

15 Apr '19

Hi Eric Problems with atom names in adding charge to a receptor using Chimera v1.13.1 (Tools-->Surface Binding/Analysis-->Add charge) I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF. Net Charge is +0 for the residue HIS using charge method AM1_BCC Chimera warning received Correct charges are unknown for 9 non-standard atom names in otherwise standard residues. Charges of 0.0 were assigned to the unknown atoms. 1 model(s) had non-intergral total charge. Reply log is as follows, Charge model: AMBER ff14SB Assigning partial charges to residue HIS (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2 -fi mol2 -o c:\users\hp\appdata\local\temp\tmplj8p6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIS) (HIS) Welcome to antechamber 17.3: molecular input file processor. (HIS) (HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2). (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (HIS) (HIS) (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (HIS) Info: Total number of electrons: 78; net charge: 0 (HIS) (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out (HIS) (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/BCCPARM.DAT" -s 2 -j 1 (HIS) (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC (HIS) Charges for residue HIS determined Non-standard atom names: VAL HB1 (VAL 551.A HB1) VAL HB2 (VAL 551.A HB2) ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3) VAL HB3 (VAL 551.A HB3) ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2) THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1) ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1) THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3) THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2) Total charge for #0: -66.402 The following residues had non-integral charges: LYS 16.A 0.0867 LEU 27.A -0.0471 GLN 29.A 0.0392 LYS 37.A 0.0867 LYS 47.A 0.0733 ASP 52.A -0.2088 GLU 53.A -0.2103 GLU 56.A -0.1137 LYS 69.A 0.0867 ARG 77.A 0.0612 GLU 78.A -0.1137 THR 79.A 0.3128 TYR 80.A 0.0451 GLU 82.A -0.1137 GLN 90.A 0.0152 GLU 91.A -0.1137 GLU 93.A -0.1137 ARG 94.A 0.0612 PHE 98.A 0.0352 GLN 100.A 0.0392 ASN 107.A 0.0397 ARG 110.A 0.0612 LYS 132.A 0.0867 LYS 133.A 0.2148 LYS 155.A 0.0867 LYS 158.A 0.0733 GLN 166.A 0.0152 LYS 170.A 0.0733 LEU 174.A -0.0471 LYS 186.A 0.0867 GLN 200.A 0.0152 LYS 201.A 0.0733 ARG 205.A 0.153 LYS 221.A 0.0867 LYS 229.A 0.0733 LYS 236.A 0.0733 LEU 247.A -0.0471 LYS 272.A 0.0733 GLU 273.A -0.1137 GLU 276.A -0.1137 LYS 277.A 0.0733 GLU 281.A -0.1137 LYS 282.A 0.0733 GLU 293.A -0.1137 LEU 298.A -0.0471 LYS 309.A 0.0733 LYS 319.A 0.0867 ASP 320.A -0.2088 LYS 355.A 0.0867 ASP 361.A -0.2088 LYS 368.A 0.0867 LYS 374.A 0.0733 GLU 378.A -0.1137 GLU 392.A -0.1137 GLN 393.A 0.0152 LYS 398.A 0.0733 LEU 404.A -0.0471 LYS 428.A 0.0867 LYS 432.A 0.0867 LYS 462.A 0.0733 LYS 496.A 0.0867 GLU 497.A -0.2103 ASN 499.A 0.0397 ILE 509.A 0.0431 LYS 515.A 0.0733 GLU 516.A -0.1137 LYS 520.A 0.0733 LEU 528.A -0.0471 LYS 532.A 0.0733 LYS 534.A 0.0733 LYS 537.A 0.0733 LYS 541.A 0.0733 PHE 547.A 0.0352 VAL 551.A 0.1935 LYS 553.A 0.2148 LYS 556.A 0.0733 ASP 558.A -0.2088 LYS 560.A 0.0733 GLU 561.A -0.1137 GLU 566.A -0.2103 LYS 569.A 0.0733 LYS 570.A 0.0733 GLN 576.A 0.0152 LYS 586.B 0.0733 LEU 605.B -0.0471 GLN 606.B 0.0152 THR 621.B 0.3128 LYS 625.B 0.0733 ASP 630.B -0.2088 GLU 634.B -0.1137 ASN 635.B 0.0397 LYS 638.B 0.0867 GLU 656.B -0.1137 THR 657.B 0.3128 TYR 658.B 0.0451 GLU 660.B -0.1137 MET 661.B 0.0564 LYS 667.B 0.0733 GLN 668.B 0.0152 GLU 671.B -0.1137 ARG 672.B 0.0612 PHE 676.B 0.0352 GLN 678.B 0.0152 ARG 688.B 0.0612 LEU 689.B -0.0471 LYS 733.B 0.0733 GLN 744.B 0.0152 LYS 748.B 0.0733 LEU 752.B -0.0471 LYS 755.B 0.0733 ARG 760.B 0.0612 GLU 762.B -0.1137 LYS 764.B 0.2148 GLN 778.B 0.0152 LYS 779.B 0.0867 ARG 783.B 0.3792 LYS 799.B 0.0867 LYS 807.B 0.0733 LYS 814.B 0.0733 LEU 849.B -0.0471 LYS 850.B 0.0733 GLU 851.B -0.1137 GLU 854.B -0.1137 LYS 855.B 0.0867 LYS 860.B 0.0733 GLU 871.B -0.1137 ASP 875.B -0.2088 LYS 887.B 0.0733 LYS 891.B 0.0733 GLU 895.B -0.1137 LYS 897.B 0.0867 LYS 933.B 0.2148 GLU 942.B -0.1137 LYS 952.B 0.0867 GLU 956.B -0.1137 LYS 963.B 0.2148 LYS 976.B 0.0867 ARG 984.B 0.3792 LYS 1010.B 0.0867 LYS 1018.B 0.2148 LYS 1040.B 0.0733 GLU 1075.B -0.1137 ASP 1086.B -0.2088 ILE 1087.B 0.0431 LYS 1093.B 0.0733 GLU 1094.B -0.1137 GLN 1096.B 0.0152 LYS 1098.B 0.0867 LYS 1099.B 0.0867 LYS 1110.B 0.0733 LYS 1115.B 0.0733 LYS 1119.B 0.2148 ASP 1124.B -0.2088 PHE 1128.B 0.0352 LYS 1131.B 0.0733 ASP 1136.B -0.2088 LYS 1138.B 0.0733 GLU 1139.B -0.1137 GLU 1144.B -0.1137 LYS 1147.B 0.0733 LYS 1148.B 0.0733 LEU 1149.B -0.0471 GLN 1154.B 0.0152 Correct charges are unknown for 9 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log. How do I work around this? Sid

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Morphing two structures that one is mutant.
by Yehuda Halfon 14 Apr '19

14 Apr '19

Hi all, I want to do a movie with a morphing inside. One problem I have is that one structure has a deletion of 4 AA and this leads to a funky morphing. Is there a way to do so and to embed it in the movie script? Thanks, Yehuda Halfon

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Area central hole oligomer
by Roberto Marotta 13 Apr '19

13 Apr '19

Hi, I have the density map of a large oligomer resolved at 5 A. I would like to measure the area of the hole at the center of the oligomer. The five subunits that form the oligomer delimit the hole that is open and irregular in shape. My idea is to measure the area of the hole in a central slice of the map. Amy suggestions are really appreciated! Thank you, Roberto Inviato dal mio dispositivo Huawei

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Obtaining the path to a currently loaded model or volume
by Ricardo Avila 13 Apr '19

13 Apr '19

Hi, I am trying to write an extension for a tool that requires PDB files or MRC structures as input. I would like to be able to pass the model or volume that is currently loaded in Chimera to this separate executable, but for this I need to get the file path to the model's object. Is this possible to do from the Python API? Thanks in advance, Ricardo Avila

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about select and label a residul with another different from the color of the whole model
by 张雷 13 Apr '19

13 Apr '19

Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands sel #0:500 rlabel #0:500. Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China

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Problem reading Delphi .phi into Chimera
by Boaz Shaanan 12 Apr '19

12 Apr '19

I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi? Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141 Thanks, 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: Friday, April 12, 2019 9:18 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 192, Issue 19 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. Re: Obtaining the path to a currently loaded model or volume (Ricardo Avila) 2. Re: Non-standard atom names (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Fri, 12 Apr 2019 16:20:12 +0000 From: Ricardo Avila <ravila(a)protonmail.com> To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Obtaining the path to a currently loaded model or volume Message-ID: <JU71yoFqhmoWIuo0I-dYiSis0MScdk2RKaARS9mIlWZtnqimD6xWKNibmsgdhAJmtFbOVtAHUYUqZRUeGI3X0a9lL69gI9sla3pZdlFbMgA=(a)protonmail.com> Content-Type: text/plain; charset="utf-8" Thank you Eric. I was able to implement the feature I wanted for PDBs opened from a single file. I think it would be nice to be able to do it for fetched files too, so I would appreciate some help on that. I was also wondering if opened volumes have the same 'openedAs' attribute. Best, Ricardo ??????? Original Message ??????? On Thursday, April 11, 2019 2:49 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Ricardo, > Every opened model in Chimera has an ?openedAs? attribute which is either None or a 4-tuple. For models that were directly opened from a single file on the file system (rather than fetched to a file for instance), openedAs will be a tuple whose first component is the full path to that file. If you need more that that (e.g. fetched files too, which is more complicated), let me know and I can provide those details. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Apr 10, 2019, at 12:49 PM, Ricardo Avila <ravila(a)protonmail.com> wrote: >> >> Hi, >> >> I am trying to write an extension for a tool that requires PDB files or MRC structures as input. I would like to be able to pass the model or volume that is currently loaded in Chimera to this separate executable, but for this I need to get the file path to the model's object. Is this possible to do from the Python API? >> >> Thanks in advance, >> >> Ricardo Avila >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constructing biological assmebly
by Boaz Shaanan 10 Apr '19

10 Apr '19

Hi, I suppose it's a new biological assembly that has to be put together. The recommended program for doing this is Pisa which can be accessed either from one of the ccp4 gui's or directly through the PDBe/EMBL server http://www.ebi.ac.uk/pdbe/pisa/ Obviously, if it's a protein whose coordinates are in the PDB database there is an option to download the biological assembly (directly to Chimera, actually). 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, April 10, 2019 8:56 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 192, Issue 16 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. Re: Constructing a biological assembly in Chimera (Elaine Meng) 2. Origin of transformation matrices (Daniel Asarnow) 3. Re: Origin of transformation matrices (Elaine Meng) 4. New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Thomas Evangelidis) 5. Re: New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Apr 2019 08:19:32 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Ahmad Khalifa <underoath006(a)gmail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Constructing a biological assembly in Chimera Message-ID: <6A14D1BB-0771-4D5C-A894-0296321D9882(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Sorry, I don?t know of a program to do it, but maybe other users on this list will have suggestions. Elaine > On Apr 8, 2019, at 6:22 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Thank you, is there any other program that can make BIOMT? I know I can get the rotation and translation matrix of the BIOMT record if I do: measure rotation #spec1 #spec2. I wonder how I can iterate over a lot of #spec2 models and how to get the output matrices in a row text format? > > I intend to write a script that can write that information to my pdb BIOMT record. > > On Mon, Apr 8, 2019 at 5:19 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Ahmad, > The sym command does not create BIOMT matrices. It adds symmetry copies of the atomic structure based on: > > (1) BIOMT matrices that are already included in the structure file (for example, use a text-editor to view the PDB file for 1FAV) > - OR - > (2) other symmetry specified manually on the command line > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > There is no tool in Chimera for creating the BIOMT matrices or identifying symmetry from your fitted atomic copies that could be used in the ?sym? command, sorry. There is a ?measure symmetry? command for maps, but it has limitations and can only guess helical symmetries if you give it approximate rise and angle values. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> > > Elaine > > > On Apr 8, 2019, at 10:14 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > Thanks Elaine. I've been looking into this and found some info about BIOMT records and the sym command. However, I couldn't get it to work. > > > > I think what can solve my problem is if I can copy/combine and fit monomers from the "main" monomer then use the sym command to generate a BIOMT record of all these fitted structure into the main monomer. That way any modifications I make to that "main monomer" will be present in the new structures that I generate using the biological unit function in Chimera. > > > > How can I do that using the sym command? > > > > > > > > On Mon, Apr 8, 2019 at 12:12 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Ahmad, > > There is no feature to automatically apply any changes in one monomer to all the other monomers. As far as I know, you would need to first modify the monomer and then create the biological assembly of the modified monomer. > > > > If you already have the biological assembly of the unmodified monomer, another possibility is to open several copies of modified one and match them onto the unmodified ones (possibly by writing your own script to do it since I imagine it would be a lot of repetitious commands), and then close the unmodified ones. However, that might be more work than just using the modified monomer to make the assembly in the first place, and might give a slightly different result. > > > > 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 7, 2019, at 6:07 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > > > Hello, > > > I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot. > > > > > > I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins. > > > > > > Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly. > > > > > > Any other help or suggestions would be appreciated. > > > Regards. > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Tue, 9 Apr 2019 16:17:00 -0700 From: Daniel Asarnow <asarnow(a)msg.ucsf.edu> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Origin of transformation matrices Message-ID: <CALiNCbZaNphCqfBU9Hc7G7oeGCn32ZW5VY1kx6dt9VjXbgVkQQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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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