April 2019 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

5 6

Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 14 Jan '20

14 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 5

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

Re: [Chimera-users] Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

1 0

Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

Hi, Does Chimera accept electrostatic potential in cube format (apparently that's what the new Delphi version 8.4 produces). I noticed a cube input under gaussian cube grid, is that the one I should use? Apparently the source of my recent problem with reading an electrostatic potential map had to do with this change of format. I'd appreciate your input. 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 1

Deleting data contained in a session
by David Sáez 30 Apr '19

30 Apr '19

Dear Chimera experts: I have saved multiple sessions of molecular dynamics trajectories. Each session is about 5MB. Nevertheless, one of those files is huge, about 120MB. Checking the differences, I noticed that one of the files contained in the session, which normally is a one-frame .pdb, in the large case corresponds to a .nc file, a whole trajectory containing a large number of frames. I did not notice this before because when I opened the .py file, the MD movie box is not shown. As I am only interested in the currently displayed frame of this .nc file, is there a way to delete the additional frames? Some command line trick that would allow me to get rid of the uninteresting frames, and decrease the file size, without having to re-make the whole session again? My most immediate concern is that the file size is too large to be uploaded to a journal online platform. Any help is appreciated, Regards.

2 2

How to join two modelled chain of protein using chimera
by Bhanu Sharma 29 Apr '19

29 Apr '19

I have modelled two chains of protein(A,B) sepratrely. now i want to join these two chains as like of original protein and want to save it as a pdb file format . Can anyone please help me? Best regards, Bhanu sharma

2 2

A query
by Bhanu Sharma 27 Apr '19

27 Apr '19

Dear sir/mam I have done homology modelling for a protein having two chains (A,B). I have modelled them seprately one after another. Now i want to join these two chains to make complete protein. And i want to do it using chimera. Can you please help me how to do this. Best regards, Bhanu sharma

1 0

Changing the default temp folder for chimera
by Yehuda Halfon 25 Apr '19

25 Apr '19

Hi all, I try to make a movie in chimera and it fills my C drive. Can I change the temp folder, in which the pics are stored, to another empty drive? Thanks, Yehuda Halfon

2 1

Surface representation
by MARIA CLARA BLANES MIRA 25 Apr '19

25 Apr '19

Hello, I would like to know if Chimera could show the surfaces like VMD does with the command QuickSurf (I attach the image with the protein in yellow and the lipids in green). I have been trying with a lot of different variations of the surface command but I can not find the way to make the surface ’softer'…. I have also been trying with spheres representation but the image shows too much information. I need a simplest view, similar to the image because this way it is easier see them move in the .dcd file. It not so important for the protein, just for the lipids. Could you help me with this, please? Thank you very much, clara

2 7

Chimera-users April 2019