[chimerax-users] Ignored bad PDB record found

[Maurício Menegatti Rigo]

Hi,

sorry bothering again. But I think I try every way possible.I've installed
both versions, ChimeraX 0.5 release (Dec 20, 2017) and also the current
daily build. Same error. I tried to install as root, also gives me the same
error. I've updated my NVIDIA driver and also some Linux packages. Still,
the same error.

Don't know what to do. I'm working on Ubuntu 14.04 LTS (Graphics GeForce
GTX970/PCIe/SSE2)


Maurício Menegatti Rigo, *Ph.D.*
Pós-doutorando
Programa de Pós-graduação em Pediatria e Saúde da Criança
Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
Porto Alegre, RS, Brasil
Tel: +55 51 3320-3000 (Ramal 6037)
Cel: +55 51 98180-4574
http://lattes.cnpq.br/4948877541502725


*"Fire and Blood"*

2018-01-25 16:40 GMT-02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> I was able to open your file on an Ubuntu 16.04 system and ChimeraX 0.5
> with the exact same behavior that Elaine got on her Mac.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On Jan 25, 2018, at 10:33 AM, Maurício Menegatti Rigo <
> mauriciomr1985 at gmail.com> wrote:
>
> Hi Elaine,
>
> Thank you for your help. I'll verify my system then.
>
> Sincerely,
> Mauricio Menegatti Rigo
>
> Em 25/01/2018 16:20, "Elaine Meng" <meng at cgl.ucsf.edu> escreveu:
>
>> Hi Maurício,
>> I don’t have this problem opening your PDB file with ChimeraX 0.5 release
>> (Dec 20, 2017) and also the current daily build.  I only get one warning
>> message that can be ignored, that it does not like the END on line 2615,
>> and the structure looks fine.  I’m testing on Mac.
>>
>> I’m not sure what’s happening for you.  I guess you could make sure you
>> are using a fairly recent version; otherwise, maybe it is something
>> specific to your system or platform.
>> Elaine
>>
>> > On Jan 25, 2018, at 10:05 AM, Maurício Menegatti Rigo <
>> mauriciomr1985 at gmail.com> wrote:
>> >
>> > Sure, this is my file.
>> >
>> >
>> > 2018-01-25 16:01 GMT-02:00 Elaine Meng <meng at cgl.ucsf.edu>:
>> > Dear Mauricio,
>> > It’s hard to tell without having the file, or at least part of it that
>> gives these messages.  Could send as attachment to the list, or if private,
>> just to me.
>> > Best,
>> > Elaine
>> > -----
>> > Elaine C. Meng, Ph.D.
>> > UCSF Chimera(X) team
>> > Department of Pharmaceutical Chemistry
>> > University of California, San Francisco
>> >
>> > > On Jan 25, 2018, at 8:55 AM, Maurício Menegatti Rigo <
>> mauriciomr1985 at gmail.com> wrote:
>> > >
>> > > I don't understand, my .pdb file seems perfectly fine, but I keep
>> getting this error:
>> > >
>> > > Ignored bad PDB record found on line 1
>> > > ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N
>> > >
>> > > Ignored bad PDB record found on line 2
>> > > ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C
>> > >
>> > > Ignored bad PDB record found on line 3
>> > > ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C
>> > >
>> > > Ignored bad PDB record found on line 4
>> > > ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O
>> > >
>> > > Ignored bad PDB record found on line 5
>> > > ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C
>> > >
>> > > 2610 messages similar to the above omitted
>> > >
>> > > I can open it in Chimera, PyMol, VMD, among others. But in ChimeraX
>> is always the same error. I'm working on Linux (Ubuntu 14.04) with ChimeraX
>> version 0.5 (2018-01-24).
>> > >
>> > > Any help?
>> > >
>> > > Thanks in advance,
>> > > Mauricio M Rigo, Ph.D
>> >
>> > <BEST_SiglecE_murine-BL00230001-chainA.pdb>
>>
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