<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 31, 2018, at 3:53 AM, Maurício Menegatti Rigo <<a href="mailto:mauriciomr1985@gmail.com" class="">mauriciomr1985@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Hi, <br class=""><br class=""></div>sorry bothering again. But I think I try every way possible.I've installed both versions, <span class="m_5375515592069386787gmail-m_-4368635605611157519gmail-il">ChimeraX</span> 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.<br class=""><br class=""></div><div class="">Don't know what to do. I'm working on Ubuntu 14.04 LTS (Graphics GeForce GTX970/PCIe/SSE2)<br class=""></div><br class=""></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><font color="#999999" class="">Maurício Menegatti Rigo, <i class="">Ph.D.</i></font></div><div class=""><span style="color:rgb(153,153,153);font-size:12.8px" class="">Pós-doutorando</span></div><div class=""><span style="color:rgb(153,153,153);font-size:12.8px" class="">Programa de Pós-graduação em Pediatria e Saúde da Criança</span></div><div class=""></div><div class=""><span style="color:rgb(153,153,153);font-size:12.8px" class="">Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)</span><span style="color:rgb(153,153,153);font-size:12.8px" class=""><br class=""></span></div><div class=""><font color="#999999" class="">Porto Alegre, RS, Brasil<br class="">Tel: +55 51 3320-3000 (Ramal 6037)</font></div><div class=""><font color="#999999" class="">Cel: +55 51 98180-4574</font></div><div class=""><font color="#999999" class=""><a href="http://lattes.cnpq.br/4948877541502725" target="_blank" class="">http://lattes.cnpq.br/4948877541502725</a></font></div><div class=""><font color="#999999" class=""><br class=""></font></div><div class=""><font color="#999999" class=""><i class="">"Fire and Blood"<br class=""></i></font></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">2018-01-25 16:40 GMT-02:00 Eric Pettersen <span dir="ltr" class=""><<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">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.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class=""><span class="m_-1989792545949820394Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div class=""><span class="m_-1989792545949820394Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div></div>
</div>
<div class=""><br class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On Jan 25, 2018, at 10:33 AM, Maurício Menegatti Rigo <<a href="mailto:mauriciomr1985@gmail.com" target="_blank" class="">mauriciomr1985@gmail.com</a>> wrote:</div><br class="m_-1989792545949820394Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><div dir="auto" class="">Hi Elaine,<div dir="auto" class=""><br class=""></div><div dir="auto" class="">Thank you for your help. I'll verify my system then. </div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Sincerely,</div><div dir="auto" class="">Mauricio Menegatti Rigo</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">Em 25/01/2018 16:20, "Elaine Meng" <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> escreveu:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Maurício,<br class="">
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.<br class="">
<br class="">
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.<br class="">
Elaine<br class="">
<br class="">
> On Jan 25, 2018, at 10:05 AM, Maurício Menegatti Rigo <<a href="mailto:mauriciomr1985@gmail.com" target="_blank" class="">mauriciomr1985@gmail.com</a>> wrote:<br class="">
><br class="">
> Sure, this is my file.<br class="">
><br class="">
><br class="">
> 2018-01-25 16:01 GMT-02:00 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>>:<br class="">
> Dear Mauricio,<br class="">
> 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.<br class="">
> Best,<br class="">
> Elaine<br class="">
> -----<br class="">
> Elaine C. Meng, Ph.D.<br class="">
> UCSF Chimera(X) team<br class="">
> Department of Pharmaceutical Chemistry<br class="">
> University of California, San Francisco<br class="">
><br class="">
> > On Jan 25, 2018, at 8:55 AM, Maurício Menegatti Rigo <<a href="mailto:mauriciomr1985@gmail.com" target="_blank" class="">mauriciomr1985@gmail.com</a>> wrote:<br class="">
> ><br class="">
> > I don't understand, my .pdb file seems perfectly fine, but I keep getting this error:<br class="">
> ><br class="">
> > Ignored bad PDB record found on line 1<br class="">
> > ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N<br class="">
> ><br class="">
> > Ignored bad PDB record found on line 2<br class="">
> > ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C<br class="">
> ><br class="">
> > Ignored bad PDB record found on line 3<br class="">
> > ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C<br class="">
> ><br class="">
> > Ignored bad PDB record found on line 4<br class="">
> > ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O<br class="">
> ><br class="">
> > Ignored bad PDB record found on line 5<br class="">
> > ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C<br class="">
> ><br class="">
> > 2610 messages similar to the above omitted<br class="">
> ><br class="">
> > 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).<br class="">
> ><br class="">
> > Any help?<br class="">
> ><br class="">
> > Thanks in advance,<br class="">
> > Mauricio M Rigo, Ph.D<br class="">
><br class="">
> <BEST_SiglecE_murine-BL0023000<wbr class="">1-chainA.pdb><br class="">
</blockquote></div></div></div></div>
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