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