[Chimera-users] Problem reading Delphi .phi into Chimera
Boaz Shaanan
bshaanan at bgu.ac.il
Fri Apr 12 13:15:01 PDT 2019
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 at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
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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)
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Message: 1
Date: Fri, 12 Apr 2019 16:20:12 +0000
From: Ricardo Avila <ravila at protonmail.com>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Obtaining the path to a currently loaded
model or volume
Message-ID:
<JU71yoFqhmoWIuo0I-dYiSis0MScdk2RKaARS9mIlWZtnqimD6xWKNibmsgdhAJmtFbOVtAHUYUqZRUeGI3X0a9lL69gI9sla3pZdlFbMgA=@protonmail.com>
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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 at 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 at 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 at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 2
Date: Fri, 12 Apr 2019 11:18:39 -0700
From: Eric Pettersen <pett at cgl.ucsf.edu>
To: Sid Majaha <sidumomajaha at live.com>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Non-standard atom names
Message-ID: <BF6AB17E-A217-4BA2-853C-07FA4BF4F2C3 at cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
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 at live.com> wrote:
>
>
> 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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