Problem reading Delphi .phi into Chimera
I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi? Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141 Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu> Sent: Friday, April 12, 2019 9:18 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 192, Issue 19 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Obtaining the path to a currently loaded model or volume (Ricardo Avila) 2. Re: Non-standard atom names (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Fri, 12 Apr 2019 16:20:12 +0000 From: Ricardo Avila <ravila@protonmail.com> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Obtaining the path to a currently loaded model or volume Message-ID: <JU71yoFqhmoWIuo0I-dYiSis0MScdk2RKaARS9mIlWZtnqimD6xWKNibmsgdhAJmtFbOVtAHUYUqZRUeGI3X0a9lL69gI9sla3pZdlFbMgA=@protonmail.com> Content-Type: text/plain; charset="utf-8" Thank you Eric. I was able to implement the feature I wanted for PDBs opened from a single file. I think it would be nice to be able to do it for fetched files too, so I would appreciate some help on that. I was also wondering if opened volumes have the same 'openedAs' attribute. Best, Ricardo ??????? Original Message ??????? On Thursday, April 11, 2019 2:49 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Ricardo, Every opened model in Chimera has an ?openedAs? attribute which is either None or a 4-tuple. For models that were directly opened from a single file on the file system (rather than fetched to a file for instance), openedAs will be a tuple whose first component is the full path to that file. If you need more that that (e.g. fetched files too, which is more complicated), let me know and I can provide those details.
?Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 10, 2019, at 12:49 PM, Ricardo Avila <ravila@protonmail.com> wrote:
Hi,
I am trying to write an extension for a tool that requires PDB files or MRC structures as input. I would like to be able to pass the model or volume that is currently loaded in Chimera to this separate executable, but for this I need to get the file path to the model's object. Is this possible to do from the Python API?
Thanks in advance,
Ricardo Avila _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Boaz, I may be wrong, but the error message sounds like there could be an inconsistency between record size and file size, rather than some specific size limit having been reached. I.e., the file might be corrupted or truncated, or the values written at unexpected precision. Do you use any other programs that read phi files, and if so, can they read this file? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2019, at 1:15 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi?
Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141
Thanks, Boaz
Hi Elaine, I read the Delphi .phi files only to Chimera. I'll check again the Delphi output to see what the difference between this and other files that I read successfully into Chimera. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, April 12, 2019 11:46 PM To: ��� ���� Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem reading Delphi .phi into Chimera Hi Boaz, I may be wrong, but the error message sounds like there could be an inconsistency between record size and file size, rather than some specific size limit having been reached. I.e., the file might be corrupted or truncated, or the values written at unexpected precision. Do you use any other programs that read phi files, and if so, can they read this file? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2019, at 1:15 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi?
Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141
Thanks, Boaz
Hi Boaz, Elaine is right that the message means that the file looks either truncated or corrupted to Chimera. A delphi file contains records with sizes of each record specified in the file and Chimera read the size of a record as 2 Gbytes, when the file itself was only 2 Mbytes long, so it said something is wrong with this file. Tom
On Apr 12, 2019, at 1:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Boaz, I may be wrong, but the error message sounds like there could be an inconsistency between record size and file size, rather than some specific size limit having been reached. I.e., the file might be corrupted or truncated, or the values written at unexpected precision. Do you use any other programs that read phi files, and if so, can they read this file? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2019, at 1:15 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi?
Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141
Thanks, Boaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, I'll look for the source of the problem that you and Elaine pointed out. It may have to do with a newer Delphi version that I used to generate the file whereas previously I used an older version. Thanks a lot for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Saturday, April 13, 2019 1:23 AM To: UCSF Chimera Mailing List Cc: ��� ���� Subject: Re: [Chimera-users] Problem reading Delphi .phi into Chimera Hi Boaz, Elaine is right that the message means that the file looks either truncated or corrupted to Chimera. A delphi file contains records with sizes of each record specified in the file and Chimera read the size of a record as 2 Gbytes, when the file itself was only 2 Mbytes long, so it said something is wrong with this file. Tom
On Apr 12, 2019, at 1:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Boaz, I may be wrong, but the error message sounds like there could be an inconsistency between record size and file size, rather than some specific size limit having been reached. I.e., the file might be corrupted or truncated, or the values written at unexpected precision. Do you use any other programs that read phi files, and if so, can they read this file? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2019, at 1:15 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
I get the message below in the reply log while reading in a Delphi .phi file. I understand that it has to do with record size or something. I've been reading other .phi files with no problem. What are the limits on record size in Chimera and how do I set them in Delphi?
Error reading file S1_6QIL_AB_EF_dimer_isoB_salt_2.0.phi, format delphi Record size 1852798752 > file size 2197141
Thanks, Boaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Boaz Shaanan -
Elaine Meng -
Tom Goddard