- Chimera-users - RBVI Mailing Lists

Volume Step default
by Rebecca Swett 10 May '19

10 May '19

HI all, I was wondering if it was possible to set the Volume Viewer step to 1 as default instead of 4. Is this something I could add to my .chimera/preferences file? Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 1

to hide atoms using command lines
by C.J. 08 May '19

08 May '19

Dear specialist, I know how to use hide selected atoms (Menu: Actions => Atoms/Bonds => Hide), but I would like to use command lines instead. Anyone could help me with that? Thank you! Best regards! C.J.

2 2

FW: Association info
by Hernando J Sosa 08 May '19

08 May '19

Thanks Eric, it works. To summarize: #---------------------------------------------------------------------- def findMAV(): from chimera.extension import manager from MultAlignViewer.MAViewer import MAViewer mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)] if not mavs: raise AssertionError("No MAV instances") return mavs[-1] #---------------------------------------------------------------------- mav = findMAV() mav.saveAssocInfo('myfile.asc') #---------------------------------------------------------------------- Best Hernando

2 1

Re: [Chimera-users] Non-standard atom names
by Sid Majaha 08 May '19

08 May '19

Hi Eric So I have been only using dock6 for docking and now want to venture in using dock3. I tried checking online for tutorials that I could look at but there are just a couple of them. On the UCSF website, there is a tutorial but requires the use of dock blaster. I just have a few questions; Is there another way of using dock3.6 without using dock blaster? Is there another simpler tutorial for dock3.6 that you could recommend me to use? Are the dock 3.6 steps similar to the steps of dock6? Sid Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Tuesday, April 16, 2019 6:46:31 AM To: Sid Majaha Cc: Elaine Meng Subject: Re: [Chimera-users] Non-standard atom names You’re welcome. AM1-BCC does take considerably longer than Gasteiger, but in this case the great majority of the time is spent adding the missing side chains. —Eric > On Apr 15, 2019, at 1:18 AM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: > > Hi Eric > > Thank you so much for your help. I was able to see as well that my protein might have been too large for the calculations of the charges to take place efficiently because after following the procedure you gave me, it took a much longer time than using Gasteiger. Thank you so much for your help. > > Sid > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> > Sent: Saturday, April 13, 2019 2:18:39 AM > To: Sid Majaha > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Non-standard atom names > > Hi Sid, > The 2BXF structure has many, many missing heavy side-chain atoms. I recommend using the Dock Prep tool (Tools→Structure Editing→Dock Prep), which will use a rotamer library to fill out missing/incomplete side chains before adding hydrogens and assigning charges. Use the dialog check boxes to turn off any Dock Prep steps you don’t want (e.g. Write Mol2 file). Applying a lot of rotamers takes a few minutes, so you might want to bring up the Reply Log first (Favorites→Reply Log) so you can keep an eye on the Dock Prep progress while you possibly do something else. > > ―Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: >> >> >> Hi Eric >> >> Problems with atom names in adding charge to a receptor using Chimera v1.13.1 >> (ToolsàSurface Binding/AnalysisàAdd 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 >> >> >> _______________________________________________ >> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > _______________________________________________ > 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

2 3

RR distance map, scale normalization
by Arvind SHARMA 07 May '19

07 May '19

Hi, I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white. Thanks. Best wishes, Arvind.

4 10

Handling electrostatic potential in cube format
by Boaz Shaanan 06 May '19

06 May '19

Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues. Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version. Thanks for your help. 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

3 4

Re: [Chimera-users] [chimera-dev] Loop refinement in chain A and Chain B
by Elaine Meng 06 May '19

06 May '19

Hi Aashish, The address for questions about using Chimera is chimera-users(a)cgl.ucsf.edu (CC’d here). Chimera-dev is for programming questions. It sounds like you did find the “model/refine loops” dialog for using the Modeller web service. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> In that dialog, you would need to choose either “non-terminal missing structure” (if the missing residues are in the middle) or “all missing structure” (if some of the missing residues are in the termini), and also enter a license key for running Modeller. However, I have no idea what you mean by “not running,” so I can’t give any more help than that. Also, be aware that in Chimera using this dialog, you can only model one chain at a time. I.e. when it is adding the residues to chain A it does not care if they are in a bad place relative to chain B, and vice versa. Our newer program ChimeraX has the advantage that you can sensibly model the dimer using the Modeller web service, with the two chains “seeing” each other. However, to use that you would have to download and learn a different program. <http://www.rbvi.ucsf.edu/chimerax/index.html> <http://www.rbvi.ucsf.edu/chimerax/download.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html#comparative> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2019, at 5:39 AM, Aashish Bhatt <aashish.ph16221(a)inst.ac.in> wrote: > > Dear Sir/ Ma'am > > I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. > Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. > > Can you please give me an idea of how to build the complete structure? > > Best regards > > Aashish > INST-Mohali > India

1 0

How do I find the active site?
by Abryn Jeuness Luna 06 May '19

06 May '19

Good day! I am currently using UCSF Chimera for my protein structure analysis. However, I cannot find the active site of my protein structure. How do I find the active site, including the amino acids in it using UCSF Chimera? Thank you. Regards, Abryn

2 1

regarding to minimization and preparation of sdf files for docking.
by prasad ssv 05 May '19

05 May '19

hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,

3 4

Re: [Chimera-users] Chimera-users Digest, Vol 193, Issue 5
by Boaz Shaanan 05 May '19

05 May '19

Hi Again, Following my complaint on the cube format I started to play with .dx format of APBS which so far seems more promising in how it projects on the protein surface. Cheers, 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: Sunday, May 5, 2019 8:18 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 193, Issue 5 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. save sequence alignment (Hernando J Sosa) 2. Re: save sequence alignment (Eric Pettersen) 3. Re: RR distance map, scale normalization (Arvind SHARMA) 4. Handling electrostatic potential in cube format (Boaz Shaanan) 5. How to select residues/atoms only those within my cryo-EM map region (Kim, Doo Nam) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 May 2019 21:03:33 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] save sequence alignment Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154B87577(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Dear Chimera, Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? Thanks H. ------------------------------ Message: 2 Date: Fri, 3 May 2019 15:19:36 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save sequence alignment Message-ID: <EFACEFC8-FD06-4C10-AE7B-704CD8925BCF(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Hernando, This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can?t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course. Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> wrote: > > Dear Chimera, > > Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? > > Thanks > > H. > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0