[chimerax-users] Ignored bad PDB record found

Wed Jan 31 10:16:45 PST 2018

Not sure what the problem could be.  It’s possible that sending the file via email “sanitized” some non-standard characters (particularly end-of-line characters) and therefore the file I received worked when the original file didn’t.  Therefore I an sending the file back to you as an attachment.  See if it works.  I am also attaching a Chimera session with the file already opened so you can at least also get some work done with it.

In a terminal window, what output do you get from the “locale” command?

—Eric

> On Jan 31, 2018, at 3:53 AM, Maurício Menegatti Rigo <mauriciomr1985 at gmail.com> wrote:
> 
> 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 <http://lattes.cnpq.br/4948877541502725>
> 
> "Fire and Blood"
> 
> 2018-01-25 16:40 GMT-02:00 Eric Pettersen <pett at cgl.ucsf.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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