- 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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New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
by Thomas Evangelidis 10 Apr '19

10 Apr '19

Hi Chimera users, I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein. https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Glo… @Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html <https://www.cgl.ucsf.edu/chimera/tutorials.html>? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time. With best regards, Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Constructing a biological assembly in Chimera
by Ahmad Khalifa 09 Apr '19

09 Apr '19

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.

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create automatically all alternative protonation states of protein
by Thomas Evangelidis 05 Apr '19

05 Apr '19

Greetings, I want to write a script that will read a protein-ligand complex, will find all residues with alternative protonation states within a radius from the ligand, and will write to separate pdb files all combinations of alternative protonations or the protein's binding site. Is this possible in Chimera? I saw at the documentation of addh command that there is not a way to specify explicitly which residues to protonate and how (e.g. I can protonate all ASP to ASH but not ASP34 to ASH34 and keep ASP52 as it is). Thanks in advance. Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Substrate channel identification for homotrimer protein
by Chakraborty, Joydeep 05 Apr '19

05 Apr '19

Hello I was trying to generate the substrate channel including the substrate binding pocket for my enzyme using the 3V channel finder server. On setting the outer probe radius to 9 Å and inner probe almost the same as that of a water molecule, 1.5 Å, the software was able to generate very accurately the solvent accessible substrate channel, that matches the crystallography reference. The mrc file can be opened together with the pdb file in chimera to generate a similar image that I have attached for reference. However, my protein happens to be a homotrimer and theoretically it should have 3 substrate channels. Having said this, I have a general question for the community. Can anyone shed some light on the fact why 3V server does generate just one channel for the trimer instead of three? Since, very simply the server uses a rolling sphere (1.5 Å radii) to detect the cavity, I am curious as to why only one channel is shown. Also, the same thing happens with CastP that generates one substrate pocket for an entire protein irrespective of a trimer or a dimer. Since, my computational knowledge is quite limited being from a wet lab background, any feedback on this would be much appreciated. Thanks! With regards, Joydeep.

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Re: [Chimera-users] Calculting protein dipole moment
by Elaine Meng 04 Apr '19

04 Apr '19

Hi Boaz, Yes, Chimera reads PQR files and assigns the atom attributes “charge” (used by the script, I believe) and “radius" from the corresponding columns. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR> I tried an example just now. It works with either the .pqr or .pdb filename suffixes. Tested by opening the file, starting Render by Attribute, and showing the histogram for atom attribute “charge.” Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 3, 2019, at 6:31 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge? > Thanks, > Boaz

2 1

Sample 3d models of whole cells
by Fatlum Hajredini 04 Apr '19

04 Apr '19

Dear all, As part of one of my teaching assignments I am trying to make an educational video that will be projected on a planetarium dome. For this I need to make some movie scenes with whole cells (preferably bacteria) through Chimera. Does anyone have some generic sampole whole cell tomograms or something of the sort that would be suitable? Thank you, Fatlum

1 0

PDB file of D-amino acids
by Mohsen Asadbegi 04 Apr '19

04 Apr '19

Hello every one! I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file. How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way of building PDB files. Regards, Mohsen Asadbegi

3 6

Visualisation in Headless Chimera
by James Starlight 03 Apr '19

03 Apr '19

Dear Chimera users! I am using headless version of Chimera inside of my Bash script to prepare images of the pdbs. Normally I provide a pdb file with a script in loop to obrain images automatically Here are some of my questions related to the visualisation: 1) I have a problem with the "preset apply publication 1" notably Chimera is crushed when I use #set silhouette option Is it possible to make "a black border of a selected thickness" for all of the elements of secondary structure of my proteins via some another command? Actually in terms of the cartoon's style (but not a colour) I would like to obtain something like was shown here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contra… 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to colour the structure according to the B-factor information provided in the given PDB. The problem is when I provide "key" option for it to place a colour diagram on the resulted picture I ontain a crush in headless version. Do some other methods exist for the placement of the colour legend for the B-factor colouring which could be used in the headless version? Thank you for help in avance! James

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Adding color key to hydrophobicity surface (preset 3)
by Boaz Shaanan 03 Apr '19

03 Apr '19

Hi, I find preset 3 as a very convenient tool but is it possible to add a color key to the hydrophobicity surface produced in this preset (as in the options for coloring electrostatic surface) ? 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

2 4

molecular dynamics with phosphates: monobasic form unstable?
by Geoffrey Sametz 01 Apr '19

01 Apr '19

I am having my students model dipeptides where one residue is a phosphorylated serine or threonine. Molecular dynamics with the dibasic phosphate works fine. However, the student NMR data for their dipeptides is acquired at low pH, so I would like them to be able to model the monobasic form. Unfortunately, all my attempts at creating a monobasic form have resulted in the molecule "blowing up" in MD, first by crazily shaking the phosphate as if it wants to dislodge the proton, and then the entire molecule until it fragments. I have tried building these from scratch by various methods (e.g. those listed in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html ) as well as using SwissSidechain and mutating residues. I have tried exporting as a .pdb, opening in PyMOL to make sure everything looks OK, resaving as .pdb and importing PyMOL's version. I have also used a protein from PDB that had a TPO residue assigned, and snipped it down to a dipeptide.For both this manner of construction, and for building the dipeptide from scratch with SwissSidechain, Chimera interprets SwissSidechain's TPO (pThr monobasic) and SEP (pSer monobasic) as their dibasic forms (TPO2 and SEP2 respectively). PyMOL interprets these structures with the correct level of protonation, however. Is there a known issue with Chimera and treatment of [-OPO3H]-1 groups, or have I managed to make the same error across multiple build methods? -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz(a)udel.edu (302) 831-3621

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Hi good morning
by prasad ssv 30 Mar '19

30 Mar '19

How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?

2 3

rna-protein complex
by soo khim 29 Mar '19

29 Mar '19

Hi chimera, I have a RNA-protein complex pdb file. After modeled the missing loops in the protein and saved the pdb file for remodel protein structure, the RNA is missing in the new pdb file. How should i save the remodel protein model together with its RNA? Thank you Best Regards, Chan Soo Khim

2 3

Aligning (superimposing) chains form the same PDB files
by Jenaro Soto 28 Mar '19

28 Mar '19

Hi, Can Chimera superimpose all chains from one PDB file. If so how can this be accomplished? I have tried using the MatchMaker tool but it ask me to select at least one different reference model. I have also tried Match -> Align but it also asked me to only choose one chain per model. Any help would be appreciated. Best, Jenaro -- Jenaro Soto PhD Student UC Irvine | Department of Pharmaceutical Sciences

2 1

New script: CREATE ALL ALTERNATIVE RECEPTOR PROTONATIONS
by Thomas Evangelidis 28 Mar '19

28 Mar '19

New script and tutorial: CREATE ALL ALTERNATIVE RECEPTOR PROTONATION STATE COMBINATIONS. Useful for those that do MD, docking, or any other structure-based drug design method. https://github.com/tevang/tutorials/tree/master/create_alternative_protonat… <https://github.com/tevang/tutorials/tree/master/create_alternative_protonat…> -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

2 1

electron density map superimposed on protein model
by Jenaro Soto 27 Mar '19

27 Mar '19

Hi Everyone, I am new to Chimera and am still getting to know the program. So far I have found the tutorials helpful, but they don't seem to have the answer to this very specific question. I want to know how I can overlay a protein structure and electron density map correctly. I am currently analyzing a published structure and would like to look at the the electron density map superimposed on the protein model. I was able to fetch the electron density map by using the 'open edsID:PDB_ID' command. However, it doesn't seem like my structure and the electron density are overlaid correctly. This might be because I moved the structure a lot before calling in the electron density map. How can I have the electron density map overlaid to the structure correctly (like the author intended it to be). Any tips will be appreciated. Best, Jenaro

2 1

focus over N frames
by Elena Zehr 27 Mar '19

27 Mar '19

Hello, I wish to use "focus" command in a movie script. I focus on an atom range as following focus :4-6@CA I wish to bring the atoms in focus over N frames. How do I do this? Many thanks, Elena

2 1

drawing stereographic projections for point groups in Chimera
by Arvind SHARMA 27 Mar '19

27 Mar '19

Hi, Is there a way to draw stereographic projections in chimera or chimeraX for the point groups? I want to draw these projections for icosahedral point groups (of T=3 virus), keeping the outer shell from chimera Multi-scale Models. Idea is to make something as in attached file. Would be great if someone has ideas how to do it or a script is available. Thanks a lot. Best, Arvind.

2 2

Save multiscale model as PDB?
by Divjak Maja 26 Mar '19

26 Mar '19

Hi Elaine, Hope you're well! I'm working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I've tried looking in the Help documentation, but can't find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> 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 2

Change map gridding for better display
by Ahmad Khalifa 25 Mar '19

25 Mar '19

How can I change the gridding of my cryo-EM map to make it look better? I know I can resample a map in chimera on the grid of another, but I'm not sure which absolute gridding is better to view the map and how to change the gridding without a reference.

2 1

creating a new color palette - viridis
by Saladi, Shyam M. 22 Mar '19

22 Mar '19

Hello -- I see that a number of color palettes were added to chimera a little more than a year ago now: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013872.html I would like to try using viridis (https://bids.github.io/colormap/) instead of standard rainbow/spectrum for coloring a protein from its N to C termini. Would someone be able to give me direction on how to create a new a color palette to do this? The RGB values making up viridis can directly be found here: here: https://github.com/BIDS/colormap/blob/master/colormaps.py Thanks, Shyam

2 1

Using Chimera _ Query
by Hina Khan 22 Mar '19

22 Mar '19

Dear team, I would like to know if I can use images generated and modified using Chimera 1.13.1 in my master's thesis. I look forward to having your response. Sincerely, Hina

2 2

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

4 6

(no subject)
by JOHN FLANAGAN 21 Mar '19

21 Mar '19

Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something? CheersJohn John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033

3 3

Structure is not fitted and map has multiple duplicates in Coot
by Ahmad Khalifa 20 Mar '19

20 Mar '19

I have a cryo-EM map that I want to segment. I have structures surrounding the density of interest from all sides. I did a molmap in chimera and subtracted everything the molmap. I then cleaned the excess density around my protein using volume eraser. Now the map that I get opens fine in Chimera. But I tried to open a model and my density in Coot, the screenshot is what I got: 1) the structure is not fitted 2) the density appears to have multiple copies of my proteins, it's supposed to be only one unit there What is wrong here exactly, I'm suspecting it's the volume eraser! Is there a better way to segment the density given how I have atomic models for all the surrounding densities, but not the density of interest? Regards.

3 2

color key in chimera X
by Pranav Shah 18 Mar '19

18 Mar '19

Hi, I have a isosurface rendering that I have colored by radius as well as local resolution. I want to now place a colour key in the image to indicate the relevance of the colors. Is there a way to achieve this in ChimeraX? If not, is there a way to easily port the commands to Chimera? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

3 2

could not find binaries for addh and addcharge programs
by Zafer AYDIN 18 Mar '19

18 Mar '19

Hi, I installed chimera software to my Ubuntu workstation. I want to add hydrogen bonds and charges to ligand molecules. I could not find the addh and addcharge executables under the chimera directory. I would readlly appreciate if you can provide me basic guidelines for how to add hydrogen bonds and charges to ligand molecules using chimera from command-line (not from GUI). Many thanks, Zafer Aydin AGÜ Computer Engineering Department Kayseri, Turkey

2 5

drawing axes of rotational symmetry
by Arvind SHARMA 15 Mar '19

15 Mar '19

Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share. Have a lovely weekend, arvind.

2 4

32-bit release
by Marwa Elnaiem 14 Mar '19

14 Mar '19

Dear UCSF Chimera team, I highly need to use the software Chimera, but unfortunately, my operating system is 32-bit which is no longer supported. I would like to ask if any old release of chimera that I could download on my 32-bit operating system. Could you please help? Regards, Marwa

2 1

Re: [Chimera-users] CASTp to Chimera
by Elaine Meng 13 Mar '19

13 Mar '19

> On Mar 13, 2019, at 9:57 AM, Chakraborty, Joydeep <jc323(a)njit.edu> wrote: > > Hi Elaine > I am trying to show the active site space fill model as depicted by the CASTp. However I am having difficulty to generate the same file using chimera. I was wondering if there is any special way we could depict a ribbon diagram of the protein with a space filled active site pocket. > Thanks, > Joydeep. Hi Joydeep, A picture would have been helpful, but I’m guessing you mean how it looks at the CASTp website. I looked at the website and see it shows some transparent spheres filling the pocket. However, these spheres are not described in any of the files Chimera gets from CASTp (which are the same as the files you get if you choose “Download” on their website), so we don’t have any way of showing them, sorry. I didn’t see any way to get the spheres from the website… I agree it would be useful! Just to help explain it to everybody else, I attached an image showing left to right: the Chimera CASTp dialog, Chimera window showing PDB structure 3TRG ribbon with molecular surface of biggest pocket from CASTp, and image of the same structure and pocket at the CASTp website <http://sts.bioe.uic.edu/castp/index.html?3trg>, including the transparent spheres: For future reference, it is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d on this message) to ensure you get an answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 1

MD simulation fails with barostat
by Simon Wheeler 13 Mar '19

13 Mar '19

Hi everyone. I'm trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I've applied periodic boundary conditions and specified the box size. Does anyone know what I'm doing wrong? Thanks, Simon

2 1

CHIMERA ISSUES
by Acco . 13 Mar '19

13 Mar '19

Hello, I am a beginner with Chimera and I am looking for how to "bring to front" the residues that I have selected displaying the remaining structure of the protein in kind of blurred view. Is it possible to do this? Thank you in advance for your help Sincerely, Andrea

3 3

how to load pseudobonds from command line?
by Michał Kadlof 12 Mar '19

12 Mar '19

Hello, I'd like to display my psudobond in chimera script. How can I do it? -- regards Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

membrane boundaries
by Anaswara Ashok 12 Mar '19

12 Mar '19

Hi I would like to know if we could add membrane boundaries of proteins with chimera? -- Regards Anaswara Ashok

3 2

OS differences in Chimera
by Marco J. Müller 11 Mar '19

11 Mar '19

Dear Chimera team, I do have a question regarding differences between OSes. Our group recently encountered a problem in the surface creation of proteins, which might be related to the OS. Recently, for some structures, directly obtained from the PDB (e.g. 6GB5, 1H97, 4YLJ) or prepared single-chain structures for docking runs, the surface creation of the proteins resulted in error 5 from mscalc.exe. This, however, seems to be an isolated problem of the Windows versions of ucsf chimera 1.12-1.13.1, as the same versions of chimera on macOS or Linux (Lubuntu) could successfully create these surfaces. Even more strangely, we are pretty sure that we could show surfaces of the very same files about half a year ago with these versions (1.12 and 1.13rc1). Did a recent update of Windows change the behavior of chimera? ChimeraX could actually show these surfaces on Windows, but gave us some other troubles. We did have a look at http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012874.html which did solve our problem for now, but we would like to know whether we can improve the reliability of chimera's functions, aside from tips mentioned in http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. An older post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005805.html) indicates that it is a numerical problem, is this still the case and means that it is indeed OS-dependent? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

2 1

font problem
by 管泓翔 11 Mar '19

11 Mar '19

When I started chimera, it showed "Cannot find a usable font Aborted (core dumped)". How to fix the problem? Thank you HH

2 3

Deterministic traversal of a chemical graph
by Jaime Rodríguez-Guerra Pedregal 08 Mar '19

08 Mar '19

Dear Chimera team, I have two questions regarding the same idea. I am trying to develop a script to find topologically equivalent residues in a structure (e.g. MOF, cages, and so on). To do this, I am using SplitMolecule.split.split_connected and then comparing the resulting pieces by number of atoms, empirical formula and, ultimately, I would like to compare the chemical graph (i.e. test for graph isomorphism). Is there any built-in function/object for that in Chimera? Since I didn't want to overcomplicate the algorithm, for now I am trusting that there won't be isomers in the structure and the empirical formula (actually a collections.Counter applied to atom.element.name<http://atom.element.name>) is enough of a test.This is working ok but, in some cases, the resulting pieces have totally different atom names because they come from a unified generic residue that encompasses all the pieces. As a result, I want to rename them in the same way consistently. My first attempt at this consists of finding the chimera.Root atom of each piece and then using chimera.Molecule.traverseAtoms to iterate over the piece. However, I've found that the Root is not always the same (topologically speaking) atom, so the naming scheme differs from piece to piece. Is there anyway to guarantee topologically equivalent traversals? I guess that both questions would lead to the same result, because it seems that I will need a chemical graph anyway. Thank you in advance, Jaime.

2 3

Saving files from MD Movie
by Divjak Maja 05 Mar '19

05 Mar '19

Hello! I have been using Chimera for analysis of H-Ras morphing from its GDP-bound inactive state to the GTP-bound active state. It works very nicely and a lovely movie is produced. What I am having difficulty with however, is saving the output of the morph as a series of PDB files that I can import to Autodesk Maya with the molecular Maya plugin. When I try to save from the movie window ie using file >save PDB, all I get is one PDB file containing a single structure. I also tried to save using the main window file > save PDB > save all frames and the same thing happens. I then tried selecting each frame individually and saving with unique numbered file names, but again, when trying to import into Maya, all I get is one structure, not a changing structure. Even the first and last frame PDBs are the same. Could you please advise as to how to save the morph output as a useful PDB series, I must be missing something? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> 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 2

Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The OpenGL graphics library is an operating system library. If you install it then Chimera should find it. There is nothing more you would have to do. Tom > On Mar 4, 2019, at 1:00 PM, Rosenberg, Mark F <mark.rosenberg(a)imperial.ac.uk> wrote: > > Hi Tom > Sorry to bother you again. > I have found installed/ the library. How do I tell Chimera where to look for it please when building ? > Thank you again. > Mark > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, March 4, 2019 6:54:44 PM > To: Rosenberg, Mark F > Cc: Rosenberg, Mark F; chimera-users(a)cgl.ucsf.edu BB > Subject: Re: Chimera installation on Windows Sub System Ubuntu > > The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. > > Tom > > >> On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: >> >> >> Dear Tom >> Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. >> >> I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. >> >> I have got so far but I keep on getting the below error. >> >> I have tried to see if I am missing any libraries to no avail. >> >> Do you have any suggestions please ? >> >> Thank you very much. >> >> Kind Regards >> >> Mark >> >> Traceback (most recent call last): >> File "/opt/Chimera/share/__main__.py", line 73, in <module> >> value = chimeraInit.init(sys.argv) >> File "/opt/Chimera/share/chimeraInit.py", line 666, in init >> import chimera >> File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> >> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >> ImportError: libGL.so.1: cannot open shared object file: No such file or directory >> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

1 0

Re: [Chimera-users] Chimera installation on Windows Sub System Ubuntu
by Tom Goddard 04 Mar '19

04 Mar '19

The error installing on the Ubuntu virtual machine means that the opengl graphics library libGL.so.1 was not found. Probably you need to install a graphics driver for the Ubuntu virtual machine in order for Chimera to start. Tom > On Mar 4, 2019, at 9:40 AM, Rosenberg, Mark F wrote: > > > Dear Tom > Hope you are well. I think I have been at this for days. I am trying to install Chimera on a Windows installation but I have had a few bugs which I have submitted to Bugs. > > I thought in the meantime , I could try and install Chimera in the Windows Subsystem with Ubuntu. > > I have got so far but I keep on getting the below error. > > I have tried to see if I am missing any libraries to no avail. > > Do you have any suggestions please ? > > Thank you very much. > > Kind Regards > > Mark > > Traceback (most recent call last): > File "/opt/Chimera/share/__main__.py", line 73, in <module> > value = chimeraInit.init(sys.argv) > File "/opt/Chimera/share/chimeraInit.py", line 666, in init > import chimera > File "/opt/Chimera/share/chimera/__init__.py", line 16, in <module> > from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform > ImportError: libGL.so.1: cannot open shared object file: No such file or directory > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

1 0

How to setup appropriate parameters during auto dock vina
by temban billyhp 02 Mar '19

02 Mar '19

Hi, How should I vary docking parameters when carrying out ligand/receptor docking in order to obtain correct results. Is there any logical trend to follow. I have always used the default mode. Best regards Sent from Yahoo Mail on Android

2 1

Re: [Chimera-users] Morph Help
by Elaine Meng 01 Mar '19

01 Mar '19

Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however). ChimeraX also allows changing hinge spacing. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users(a)cgl.ucsf.edu or chimerax-users(a)cgl.ucsf.edu (depending on which program you’re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul(a)baylor.edu> wrote: > > Hi, > > I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up. > > Thanks > Debamita

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Chimera using question
by Khải Trần Gia 28 Feb '19

28 Feb '19

Dear Mr/Mrs, I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? I am looking forward for your replying. Thank you. Best regards, Khai.

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Chimera Help
by Debamita Paul 28 Feb '19

28 Feb '19

morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1t0Up4tsMWqLe7ipmUEfRzth0OFNN…> morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1C_cQTG9d5k10rKOQnW_XayfDGZt1…> Hi Dr. Meng, I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph

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Can Chimera read electron density difference map files from RIDL?
by Murpholino Peligro 28 Feb '19

28 Feb '19

Here is what RIDL is https://github.com/GarmanGroup/RIDL I can open the map in coot specifying is a difference map and it opens nicely over the protein. In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P ... Thanks

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Seeking for help
by temban billyhp 27 Feb '19

27 Feb '19

SirI prepared the DNA molecule using the dock prep with its default options but when I lunched auto dock vina alongside with my ligand, I received a message that auto dock vina cannot prepare the receptor due to an error. How can I solve this problem. I will be greatful listening from you. Best wishes. Sent from Yahoo Mail on Android

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Installation problem on Fedora 29
by Murpholino Peligro 26 Feb '19

26 Feb '19

[murphy@eva02 Downloads]$ ./chimera.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/murphy/Downloads' inflating: chimera_install_6JK7q6/installer inflating: chimera_install_6JK7q6/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-1.13.1 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/murphy/.local/UCSF-Chimera64-1.13.1' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yes Traceback (most recent call last): File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimeraInit.py", line 666, in init import chimera File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/murphy/.local/UCSF-Chimera64-1.13.1/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/murphy/.local/UCSF-Chimera64-1.13.1/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_6JK7q6' Installation is done; press return. Help please.

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how to hide just H-bonds between water molecules with themselves?
by masoud aliyar 22 Feb '19

22 Feb '19

Hello I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don’t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279 ********************* The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame. second, if I set selection mode on append and write this script: ********************* ~display :SOL zonesel :279 3 :SOL select up display sel select :38:53:147:279 findhbond linewidth 3 color blue selRestrict both ********************* The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don’t want it. How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain? Thank you, everyone,

2 1

Defining CMYK color scheme for color actions
by Boaz Shaanan 21 Feb '19

21 Feb '19

Hi, Some journals require usage of CMYK color scheme. I see that the CMYK option exists in the color editor but is it possible to define CMYK for all the color actions (actions --> color) without having to go through the color editor for each color? Or am I missing something altogether? Thanks for you advice, 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

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Measure angle and effect length
by Shishir Adhikari 21 Feb '19

21 Feb '19

Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks

2 2

ViewDock tool not showing PDBQT vina output file
by Walker, Kevin 21 Feb '19

21 Feb '19

The subject line summarizes the challenge. I can open all other file types of interest (pdb, pyc, py) for viewing. However, I am unable to open a pdbqt vinaout file within Chimera 1.13. The result: Chimera session freezes and can only be shut down through the Windows 10 task manager. Have uninstall and reinstalled Chimera, cycled computer off and back on, and updated graphic driver and rolled by graphic driver to previous version, all to no avail. Windows 10 64-bit Chimera 1.13 Graphics Card: AMD Radeon 480 Memory: 11 GB

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Chimera PDB2PQR
by Sowmya Indrakumar 21 Feb '19

21 Feb '19

Dear Developers, I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice. Thanks a lot for your help! Regards Sowmya [cid:cdf013bd-01d5-4d3d-9dd2-554c27674417]

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Chimera
by Giovanny Rincon S 21 Feb '19

21 Feb '19

Hello, I am a graduate student in Balearic Islands, I am doing a protein study with Chimera, I wanted to ask if it is possible to change the background color to White. Thank you so Much

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Broad selection with command
by masoud aliyar 21 Feb '19

21 Feb '19

I use "zonesel" command to select SOL residues around ligand. but this command did not select entire residue and just select atoms that are the given zone.how can I use command-line to broaden residue selection and select entire residue atoms?. I know I can use the keyboard to broaden selection, but I want to use the command-line

2 2

STL/OBJ 3D models exported by Chimera cannot be read in Office 2019
by Jaime Rodríguez-Guerra Pedregal 20 Feb '19

20 Feb '19

Hi, Chimera team! I have recently discovered that Office 2019 has support for 3D objects that can be rotated, animated, zoomed... So I was curious about the possibilities for our molecular presentations. I knew Chimera allows to export molecules to several 3D formats and crossed my fingers so there was at least one format supported by Office. - Good news: there are two! STL and OBJ are both exported by Chimera and supported by Office. - Bad news: while the files can be correctly "loaded" in Office, they are not displayed at all! "Image could not be shown". Is this something that must be addressed in Chimera or is Microsoft's fault? The error message is very succinct and does not provide more details. I have attached the files I created with Chimera just in case. Thank you very much! Jaime.

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Chimera laptop features required
by p.tapi＠alice.it 20 Feb '19

20 Feb '19

Sir, I'm going to use USFC Chimera program working for La Sapienza University in Rome Italy ... before to get the program, I would like to understand the best recommended laptop features to easy run the program under Microsoft Windows WIN 10 platform .. May you answer me regarding the main laptop features ( CPU type, speed, RAM, SSD, screen resolution, etc ) you recommended ? What you suggestions ? Thanks in advance Regards Silvia Taglieri Rome Italy

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linking plane slider among between volume models
by Michael Elbaum 19 Feb '19

19 Feb '19

Hi. I'm looking at volume and surface data simultaneously. I'd like to select a range of planes, and then when I change the selection to have it apply to both datasets. For example I'm looking at density in "solid" mode together with a smoothed isosurface. To keep them in step I should change the setting manually (in the gui) for each dataset individually. It's surprisingly easy to lose the precise overlap. It would be helpful to choose the datasets to which the planes parameters apply. Perhaps there's a non-gui way to do this? If not possible in Classic Chimera, then please just consider as a suggestion for ChimeraX. thanks, Michael

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Re: [Chimera-users] [chimerax-users] Can ChimeraX morph between two surfaces?
by Steve Chou 19 Feb '19

19 Feb '19

Hi Elaine, Thanks for your detailed explanation! What's the format of the pseudobond file? Should it look like this? =============================== #1/A:13@NE2 #1/A:502@MG =============================== All the best, Steve On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Steve, > Actually I’m surprised the Mg and water were included (even if present at > both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under “Atoms in Common”: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > For the case where composition changes, you could add in a fake Mg ion and > water to the structure that’s missing them, but you’d have to decide where > to put them. Also it was my understanding that they had to be tethered to > the biopolymer chain (e.g. add distance measurement, which can then be > hidden), but maybe that requirement has changed, or the Mg does already > have a metal-coordination pseudobond to the biopolymer. > > Or if you don’t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > Thanks, Elaine! > > You command "rainbow structures" works beautifully. > > There is "a Mg ion" and "a water molecule" in the two conformations. > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > Is there a way to morph the specific components properly? > > Steve > > > >

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Error while doing autodock vina via chimera
by Sourav Mondal 19 Feb '19

19 Feb '19

I was tring to dock the phytochemical (cid-3114) with protein (pdb id -5YFN) , this is the error I am getting. What is the reason for the error? How to overcome this error? Model 0 (human isocitrate dehydrogenase.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No SEQRES records for human isocitrate dehydrogenase.pdb (#0) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: #0 LYS 1.C Chain-final residues that are actual C terminii: #0 MG 410.C Chain-final residues that are not actual C terminii: 396 hydrogen bonds Hydrogens added Wrote E:\Sem 1\BIOINFO\human_isd_3114.receptor.pdb Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2B Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:NAP409:O2D Unable to assign MAP type to atom Mg Sorry, there are no Gasteiger parameters available for atom human_isd_3114.receptor:C:MG 410:MG Wrote E:\Sem 1\BIOINFO\human_isd_3114.ligand.pdb Autodock Vina ligand docking initiated for human isocitrate dehydrogenase.pdb Status file contents: 1 1550389354.82 1550389354.92 Running AutoDock Vina for human isocitrate dehydrogenase.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 4016 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# WARNING: The search space volume > 27000 Angstrom^3 (See FAQ) Detected 8 CPUs WARNING: at low exhaustiveness, it may be impossible to utilize all CPUs Reading input ... ----- Sent from Mail for Windows 10

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rmf3 control in Chimera
by Daniel Ziemianowicz 15 Feb '19

15 Feb '19

Hello, I can't find anything about this online, but I was told that there should be some control on the components of rmf3 files. Specifically, I would like to map my data onto an rmf structure from IMP. Normally I would use render/define attribute for some types of data and xlinkanalyzer plugin for crosslink data. However, I can't quite figure out how to control rmf structures in this same manner. I am hoping I could do something like this: given a bead with residue x and another bead containing residue y, I can map a crosslink to those beads. Likewise, with render by attribute, I can color the beads containing the relevant residues. The farthest I was able to get was reading the rmfalias documentation but that is also a bit confusing and I was not able to perform the aliasing - specifically it says rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ] as the command but then it gives an example filename/nodename1/nodename2/nodename3 which seems to contradict the "usage" format. Either way I was not able to select or alias-name the beads I would like. Below I attached an example of the hierarchy in my file, how can I select e.g. "13-22_bead" of "EED"? I hope this was not a confusing question, let me know if I need to clarify. I can also email Ben Webb from the Sali lab if this is more relevant for them. Thank you, Dan [cid:image001.png@01D4C486.CABA8470]

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Question about AutoDock
by Cassidy Terrell 13 Feb '19

13 Feb '19

Hello, I am using the AutoDock feature in UCSF Chimera and after clicking "Apply" everything appears to work normally and then program says: E*xecution complete - check outputs to verify successful execution* In the past a ViewDock window with the results would automatically pop-up after the execution completed - however this is no longer happening and I do not know how to access the output files. The program did not write a *name.pdbqt *file - all other files are there though. Any suggestions for accessing the output file would be much appreciated!! -- Cassidy R. Terrell, Ph.D. Assistant Professor, Biochemistry University of Minnesota, Rochester 111 South Broadway Rochester, MN 55904 *Always believe something wonderful is about to happen*

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Troubleshooting Docking Problem
by Alexandru Buhimschi 13 Feb '19

13 Feb '19

Hello- I have been trying to perform a docking search for small molecule binding to a B-DNA double helix (e.g. 1ZFH). Unfortunately, when I set up the ligand and receptor, I receive the following error: IndexError: list index out of range Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages. cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. I am not sure what I can do to address this, but I have tried multiple DNA structures and the result appears to be the same. I have also encountered this error which I could not resolve either: ValueError: Could not find atomic number for Ha Ha > failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. Please let me know if there is anything I should do to address this issue. Best, Alex

2 1

Measure unmodeled density
by Chen Sun 13 Feb '19

13 Feb '19

Dear Chimera users, I have a map with extra density in it and I'd like to know the volume of the extra density. So is there an existing command in Chimera that can measure the volume of unmodeled density? Best regards, Chen Chen Sun Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S.Martin Jischke Dr. West Lafayette, IN 47907 "The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts. --Bertrand Russell"

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Volume Viewer Planes
by Michael Elbaum 12 Feb '19

12 Feb '19

Hi. Here's an issue regarding the use of "Planes" in the Volume Viewer, not really a proper bug but often an inconvenience. When I choose a subset of Planes there is obviously some calculation, and the calculation has to be redone when I move the slider. For a large volume this can be very slow, especially for Surface rendering. If I use the number box to save time, the calculation updates for each change "instantaneously", meaning slowly. For example if I want to move from 110 to 85, the calculation updates for 11, 1, 8, and 85. I think it would be more efficient to wait for an Enter, or even just to add a delay of 2-3 seconds. I hope you can consider this in future versions. thanks, Michael

2 2

Linking structure to Multialign viewer
by Ahmad Khalifa 12 Feb '19

12 Feb '19

I have multiple copies of the same structure open. How to link specific chains of model IDs to Multialign viewer, to be able to highlight sequence of the residues I select? Thanks.

2 1

using a surface as a mask for a volume
by Michael Elbaum 11 Feb '19

11 Feb '19

Hi. I have a volume (EM tomography data) which I display together with a surface. I'd like to use that surface to mask away the volume elements that lie outside the surface boundary. Is it possible to define and display a restricted region this way? It's similar to Segment Map but without the segmentation step. thanks, Michael

2 2

Does UCSF Chimera support RTX 2080 Ti?
by Jun Ha Song 11 Feb '19

11 Feb '19

Dear RBVI, I am currently deciding which graphic card to upgrade to, and I wonder if UCSF Chimera support RTX2080Ti. Would there be any bugs due to graphic cards being RTX? Best, Junha.

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Hello chimera my name is Alberto, I would like to know if there is any way to see the double bonds in the structures.
by Alberto garcia lopez 11 Feb '19

11 Feb '19

Enviado desde Correo<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

2 1

Strange and inconsistent Chimera behavior recently on W7/Nvidia OS
by Boaz Shaanan 08 Feb '19

08 Feb '19

Hi, I started to have strange and inconsistent behavior of chimera when I open PDB's. My system is W7 with Nvidia 840M graphics card (which has been functioning fine for nearly 3 years). I am running the latest daily build but noticed this strange behavior with previous versions as well as the production one. I attach 3 snip pictures, the first two are of pdb files opened, one OK (as usual) and the other distorted. The 3rd snip pictures is of the Nvidia debug when I start Chimera in command file as chimera.exe --debug-opengl. It became quite a lottery for me as for how pdb file will open. The .py files open OK so far as I recall. Please help me with this recent mystery. 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

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Question
by Vito Calderone 07 Feb '19

07 Feb '19

I have superposed two structures and printed the attached figure with sequence superposition and Ca RMSD. Is there a list of residue by residue RMSD as well? I can’t find it anywhere apparently. Thanks Vito

2 1

Running vina locally
by Sam Freeman-Fox 06 Feb '19

06 Feb '19

Hi, I am looking at running docking simulations locally, and see that with the vina command line execution (*vina* *docking* *receptor* *recmodel* <frameatom_spec.html> *ligand* *ligmodel* <frameatom_spec.html> *options <#options>) *one of the available options is to change the backend from using the Opal web service to a local executable. Could you advise on where I would be able to download such a local executable in order to get this to run. Many Thanks, Sam Freeman

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How to color density maps using markers?
by Ahmad Khalifa 05 Feb '19

05 Feb '19

I know I can use volume tracer to place markers in the density. There was a tutorial explaining the use of these markers to color certain areas of my density map, however I lost track of it. Best regards.

2 5

Help: 'broken pipe' error
by Mungo Carstairs (Staff) 04 Feb '19

04 Feb '19

Hi there, I'm experimenting with Jalview as Javascript talking to Chimera over the latter's REST server. The first few 'list models' commands work fine, but when I send a command 'open cifID:4zhp' I (usually but not always) get an error '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces below as to the reason for this? Thanks. Chimera 1.12 (build 41481) on OSX Sierra 10.12.6. REST server on host 127.0.0.1 port 53135 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 163, in _run replyobj.error(str(v) + '\n') File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 637, in error _replyStack[-1].error(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) See reply log for Python traceback. ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53326) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 159, in _run chimera.runCommand(cmd) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2750, in runCommand makeCommand(*args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", line 20, in command self.module("cmdline").process(cmdName, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 12, in process doList(args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 543, in doList doExtensionFunc(func, otherArgs, **kwargs) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 192, in listr replyobj.info(info) File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 625, in info _replyStack[-1].info(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 202, in message self.writeLine(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) See reply log for Python traceback. ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53329) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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Slicing/Subdividing Models in Chimera
by Mauser, Jonathon 04 Feb '19

04 Feb '19

Hello, I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of “anatomical” cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. I have tried simply clipping into the model, which does essentially what I would like to do, but I don’t know how to delete everything that I’ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished? Thank you! Jon Jonathon Mauser, Ph.D. Assistant Professor Department of Chemistry Winona State University Office: Pasteur Hall 330 P: 507-457-5874 E: jmauser(a)winona.edu <mailto:jmauser@winona.edu>

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Display showing a gap in my chain
by Ahmad Khalifa 04 Feb '19

04 Feb '19

After merging two structures in Coot, chimera is showing a chain break at one end where I merged my molecule. The other end is displayed correctly. How can I fix that?

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Combine atom-spec non-alphanumeric no-nunderscore character error
by Ahmad Khalifa 01 Feb '19

01 Feb '19

I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working! Regards.

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question
by Craig Scoville 31 Jan '19

31 Jan '19

Dear Staff -- I am interested in using Chimera but have a question regarding its use. I am interested in looking at the shape of small polypeptides --usually ranging from 5-20 amino acids -- does this program allow me to input amino acid sequences and then look at confirmational shapes? make substitutions and then compare confirmational shapes? Does the proprietary nature of my work prohibit me from using Chimera? Sincerely, Dr Scoville

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rmsd graph
by SEFA ÇELİK 31 Jan '19

31 Jan '19

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph(using the plotting in the MD Movie trajectory viewer). And I got the result. But, graph's x-axis "frame" and y-axis "rmsd" value. I want the x axis to be the "time". Briefly, I want to see how the value of rmsd changes with time. *I added files to the e-mail. Can you explain what "1001 frames" mean? And how do I convert "1001 frames" to time. I want to see the RMSD change by time.* Can you help with this? Could you explain in detail? Best regard Assoc Prof. Dr. Sefa Celik

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Morph conformation - side chains
by arrafzaher＠campus.technion.ac.il 28 Jan '19

28 Jan '19

Hi, I noticed Morph conformation only compares backbone Is it possible to compare side chains conformation change Lets say enzyme vs. phosphorylated same enzyme on a tyrosine residue (TPO) Thanks Zaher

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babel-type not found
by Ryan Cairns 25 Jan '19

25 Jan '19

Hi, When using AutoDock vina, I keep getting the message 'AttributeError: member babel_type not found'. I have uninstalled and reinstalled to try and fix it with no luck. Any suggestions on how to fix this? Thanks, Ryan Ryan Cairns PhD student School of Chemistry University of Nottingham pcxrc5(a)nottingham.ac.uk O'Reilly Research Group http://www.oreillyresearchgroup.com/ This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Select multiple chains
by Racaniello, Vincent R. 25 Jan '19

25 Jan '19

In pdb 4CTF there are multiple identical chains, e.g. A0, A1, A2, A3, A4 etc. I can select one with select :.A0 How do I select multiple chains, e.g. A0-A4? ______________________________ Vincent Racaniello, Ph.D. | Higgins Professor Department of Microbiology & Immunology Columbia University, New York virology.ws | microbe.tv "Tanto sa ciascuno quanto opera"

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Chimera Issue: Surface Calculation Failed - MSCalc returned code 5
by Megan Yung 25 Jan '19

25 Jan '19

Hello, I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached. Thank you very much, Meg

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Re: [Chimera-users] Update VDW Dots During Torsion Rotation
by Eric Pettersen 24 Jan '19

24 Jan '19

Glad it did what you needed! —Eric > On Jan 24, 2019, at 11:29 AM, Brian E Coggins <bec2(a)duke.edu> wrote: > > Eric, > > Hack or not, this does the job perfectly! Many thanks. > > Brian > > >> On Jan 23, 2019, at 6:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Brian, >> It seems the vdw command caches the computed surface points and that therefore various tricks with ~vdw/vdw don’t update the surface. However changing the dot density does clear the cache and cause a recomputation, so you can use this awful hack to get the vdw surface to update as you adjust torsions: >> >> perframe “vdwdens 5.1; vdwdens 5” >> >> Every frame, the density will be changed to 5.1 and then back to the (default) 5. You might want to use different numbers. I prefer not to be “credited” with this idea. :-) >> >> >> not Eric Pettersen >> not from the UCSF Computer Graphics Lab >> >> >>> On Jan 23, 2019, at 3:14 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>> >>> Hi Brian, >>> This is not a direct answer to your question, but alternatives to showing VDW dots are: >>> >>> (A) show sphere representation (VDW spheres) instead of stick representation of atoms >>> >>> (B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands: >>> >>> surftrans 75 >>> surftrans 0 >>> surfrep mesh >>> >>> There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass icon), inspect: MSMS surface, increase “vertex density” and maybe dot size. >>> >>> Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds. >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Jan 23, 2019, at 1:29 PM, Brian E Coggins <bec2(a)duke.edu <mailto:bec2@duke.edu>> wrote: >>>> >>>> Hello, >>>> >>>> If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes? >>>> >>>> Thanks, >>>> Brian >>>> >>>> --- >>>> Brian E. Coggins, Ph.D. >>>> Assistant Research Professor of Biochemistry >>>> Duke University, Durham, NC >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…> >>> >> > > --- > Brian E. Coggins, Ph.D. > Assistant Research Professor of Biochemistry > Duke University, Durham, NC > > > >

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Update VDW Dots During Torsion Rotation
by Brian E Coggins 23 Jan '19

23 Jan '19

Hello, If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes? Thanks, Brian --- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC

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Visualize dot_surface dat file in chimera
by Ashok Nayak 23 Jan '19

23 Jan '19

Hi, I have a HOLE dot surface fie exported from coot in the .DAT format. Unfortunately I cant display it in chimera. Could you suggest me the compatible format in chimera to visualize the dot surface files Its in X Y Z r g b Hexcol format 234.17638 238.94343 268.17244 0.44800 0.47168 0.80000 #7278cc 234.33047 238.06957 268.17244 0.44800 0.47168 0.80000 #7278cc 234.63396 237.23575 268.17244 0.44800 0.47168 0.80000 #7278cc 235.29419 242.56321 267.72878 0.44800 0.47168 0.80000 #7278cc Any suggestion will be appreciated

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Serine 371 in a protein (ATR)
by leifepeterson＠sbcglobal.net 22 Jan '19

22 Jan '19

Hi Elaine, A particular protein binds with e.g. Serine-371 of another protein (ATR). In order to find that pocket in a PDBQT image of ATR, can I simply look for AA=371? Thanks, Leif Peterson

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how to get chimera to use the auth_seq_id in .cif format files
by Carmen San Martin 21 Jan '19

21 Jan '19

Hi all, I am using chimera to display a structure with a 10-residue gap. When I use a pdb format file, the gap appears as a dashed line and everything is fine. However, when I convert the coordinate file to cif format, chimera draws a very long bond across the gap. Further, the residue numbering seems to have changed, so that now instead of skipping the 10 figures in the gap, the residues at both sides are consecutively numbered, and therefore the numbering in the rest of the protein is wrong. I understand this happens because chimera is using the cif column "label_seq_id" instead of "auth_seq_id" to identify the residue number. Is there a way to make chimera use the auth_seq_id column instead? Sorry if this has already been answered, I googled it and saw similar questions but not the actual answer to this one. Best, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://tinyurl.com/carmensanmartinlab https://sites.google.com/site/adenonet/ ------------------------------------------------------------

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I-TASSER secondary structure
by nadineh.1991＠web.de 21 Jan '19

21 Jan '19

2 2

match command
by Hernando J Sosa 20 Jan '19

20 Jan '19

Dear Chimera, Can somebody clarify the syntax of the match command. I am specifically trying to move several atoms (residues or ligands) to match their location in another model *without* moving the rest of the model. e.g. match #0:ADP.A #1:ADP.A works fine but moves the whole model #0 But match #0:ADP.A #1:ADP.A atoms Or using any other option after the atom specifications generate the following error: "an even number of space-separated atom specs are required" According to the user-guide website the syntax is: match atom-spec1 atom-spec2 options Not sure what the problem is. Thanks H.

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question
by Willenbring, Holger 18 Jan '19

18 Jan '19

Hello, Can UCSF Chimera be used to model the structure of an AAV capsid starting from the DNA sequence? Best, Holger Willenbring

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Volume blob and sum internal map value(s)
by Esser, Lothar (NIH/NCI) [E] 17 Jan '19

17 Jan '19

Hi, I seem to remember that the following is possible but I cannot figure it out anymore: One can read, say, an electron density map, contour it at desired level and in "Measure and Color Blobs" one can individually select blobs that are of interest and determine their volume and surface area. That works well. What I don't remember is how to integrate the map values inside the blob. I think it was implemented once but it currently escapes me. Any advice welcome. Thanks, Lothar

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