warning: Ignored bad PDB record found on line
Hello, This morning I kept getting this error "warning: Ignored bad PDB record found on line nnn" whenever I use the python script to try to open a pdb file. The python script I'm using is the usual "chimera.openModels.open(pdbID, type='PDB')[0]". This function call is how I've always been using Chimera, and this morning is the first time I'm getting this issue. I dont see a problem with my internet connection, and I can open the PDB file using File->Fetch by ID, so it doesn't seem like the pdb file has any problems. Only the python script gives me problems. Is anyone else experiencing this problem? Best, XBL
Also, I am using Chimera v1.9. This is a new version I downloaded just a couple of days ago. Hadn't had a problem before using older versions. XBL -------- ???? -------- ??: warning: Ignored bad PDB record found on line ??: Thu, 05 Jun 2014 08:30:49 -0400 ???: Xiao-Bo Li <x22li@uwaterloo.ca> ???: chimera-users@cgl.ucsf.edu Hello, This morning I kept getting this error "warning: Ignored bad PDB record found on line nnn" whenever I use the python script to try to open a pdb file. The python script I'm using is the usual "chimera.openModels.open(pdbID, type='PDB')[0]". This function call is how I've always been using Chimera, and this morning is the first time I'm getting this issue. I dont see a problem with my internet connection, and I can open the PDB file using File->Fetch by ID, so it doesn't seem like the pdb file has any problems. Only the python script gives me problems. Is anyone else experiencing this problem? Best, XBL
Hi, Are you actually getting these messages with PDB files from the RCSB? Normally, you get these messages when using files with a lot of non-standard PDB records in them -- i.e. from PDB files generated by programs or scripts. If you are getting them from a standard PDB entry please let me know which ID it is. That said, you are probably also getting these messages when opening the file with Fetch, but the messages are going to the reply log so you aren't noticing them unless you have the reply log open, whereas if you are running a script from IDLE or the from a Unix command line, they are going to IDLE or standard error respectively, so you are seeing them all immediately. You options are: (1) Fix the PDB file to remove the non-standard records, or (2) Use the '--silent' flag if you are running the script from the command line, to suppress the messages, or (3) Set chimera.silent to True before running the script in IDLE to achieve the same result as (2) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 5, 2014, at 5:33 AM, Xiao-Bo Li <x22li@uwaterloo.ca> wrote:
Also, I am using Chimera v1.9. This is a new version I downloaded just a couple of days ago. Hadn't had a problem before using older versions.
XBL
-------- 原始消息 -------- 主题: warning: Ignored bad PDB record found on line 日期: Thu, 05 Jun 2014 08:30:49 -0400 发件人: Xiao-Bo Li <x22li@uwaterloo.ca> 收件人: chimera-users@cgl.ucsf.edu
Hello,
This morning I kept getting this error
"warning: Ignored bad PDB record found on line nnn"
whenever I use the python script to try to open a pdb file. The python script I'm using is the usual "chimera.openModels.open(pdbID, type='PDB')[0]". This function call is how I've always been using Chimera, and this morning is the first time I'm getting this issue.
I dont see a problem with my internet connection, and I can open the PDB file using File->Fetch by ID, so it doesn't seem like the pdb file has any problems. Only the python script gives me problems. Is anyone else experiencing this problem?
Best,
XBL
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Eric Pettersen -
Xiao-Bo Li