I don't understand, my .pdb file seems perfectly fine, but I keep getting this error: *Ignored bad PDB record found on line 1ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N Ignored bad PDB record found on line 2ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C Ignored bad PDB record found on line 3ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C Ignored bad PDB record found on line 4ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O Ignored bad PDB record found on line 5ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C2610 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
I don't understand, my .pdb file seems perfectly fine, but I keep getting this error: *Ignored bad PDB record found on line 1ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N Ignored bad PDB record found on line 2ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C Ignored bad PDB record found on line 3ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C Ignored bad PDB record found on line 4ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O Ignored bad PDB record found on line 5ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C2610 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
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@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
Sure, this is my file. 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 16:01 GMT-02:00 Elaine Meng <meng@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@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
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@gmail.com> wrote:
Sure, this is my file.
2018-01-25 16:01 GMT-02:00 Elaine Meng <meng@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@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>
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@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@gmail.com> wrote:
Sure, this is my file.
2018-01-25 16:01 GMT-02:00 Elaine Meng <meng@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@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>
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@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@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:mauriciomr1985@gmail.com>> wrote:
Sure, this is my file.
2018-01-25 16:01 GMT-02:00 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:mauriciomr1985@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>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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@gmail.com> wrote:
Sure, this is my file.
2018-01-25 16:01 GMT-02:00 Elaine Meng <meng@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@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>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu <mailto:pett@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@gmail.com <mailto:mauriciomr1985@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@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:mauriciomr1985@gmail.com>> wrote:
Sure, this is my file.
2018-01-25 16:01 GMT-02:00 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@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@gmail.com <mailto:mauriciomr1985@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>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Maurício Menegatti Rigo