[Chimera-users] Problem reading Delphi .phi into Chimera

Boaz Shaanan bshaanan at bgu.ac.il
Fri Apr 12 16:02:30 PDT 2019

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 Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

From: Tom Goddard <goddard at sonic.net>
Sent: Saturday, April 13, 2019 1:23 AM
To: UCSF Chimera Mailing List
Cc: בעז שאנן
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.


> On Apr 12, 2019, at 1:46 PM, Elaine Meng <meng at 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 at 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
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