April 2019 - Chimera-users - RBVI Mailing Lists

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

17 Apr '19

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

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

16 Apr '19

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

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

16 Apr '19

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

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

16 Apr '19

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

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Error in starting Chimera (Return code: -1073741819)
by 박지민(Park, Jimin) 15 Apr '19

15 Apr '19

Hello. I've used Chimera for a year, but I can't start Chimera suddenly.I deleted the old version, and installed the latest version, chimera-1.13.1-win64.But it showed the same error.When I start chimera, I got this message.--------------------------------------------------Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit----------------------------------------------------I found the similar error reported previously. (http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html)So I ran the dxdiag program on my computer and attached the file including all information from dxdiag.I will be grateful for any help you can provide. Best wishes,Jimin Park.

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Helical Parameter estimate using Chimera
by Rejaul Hoq Nayem 15 Apr '19

15 Apr '19

Hi All, I want to estimate Helical parameter ( Helical Rise, Twist, asymmetric sub unit, per turn ) of Tau filament for Reference Module generation using Chimera. Is it possible to estimate from raw micrographs or 2D Class Average by Chimera? I was wondering if any of you can provide me procedure if any, will be a great help. Eagerly waiting for your reply. Thanks in Advance, Reja [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/14/19, 8:11:49 PM

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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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Chimera-users April 2019