Hi Yong, Why make an ensemble when you don't want to search with and ensemble? You could run separate phaser jobs, one after the other, with your search models. I guess that this is what is meant by "SERIAL". Maybe Phaser has an option to do this, but it is also not difficult to write a small script to do this.
Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Yong Wang Gesendet: Donnerstag, 9. Dezember 2021 22:28 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser Hi Randy, I did not use the ensemble as I am not doing the typical jobs: I don't want an ensemble as a template, instead I would like to test each individual model separately. I re-formatted a multi-model pdb file (the original file did not have the MODEL line) on my own. Changing to "MODEL 0" did not change the error message. By the way, Phaser output suggested " SYNTAX ERROR: Use SERIAL". What is the usage of "SERIAL"? I can't find that keyword in the manual. Thanks, Yong -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Randy John Read Sent: Thursday, December 9, 2021 4:18 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Hi Yong, If you make an ensemble with ensembler, the models are numbered from 1 to n, so there's no requirement to start from 0. Did you use ensembler to make your ensemble model file? If you did and Phaser is failing, could you send me the file so we can figure out the problem? Otherwise, the easiest solution might be to use ensembler to generate the ensemble! Best wishes, Randy Read > On 9 Dec 2021, at 21:00, Yong Wang > <00003c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk<mailto:00003c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk>> > wrote: > > Hi, > > > > The first model number in the pdb file is 1. In the script it is "MODEL 1". I > will try "MODEL 0" in the script to see how it goes. > > > > Thanks, > > > > Yong > > > > From: Boaz Shaanan <bshaa...@bgu.ac.il<mailto:bshaa...@bgu.ac.il>> > Sent: Wednesday, December 8, 2021 7:37 AM > To: Yong Wang <wang_yon...@lilly.com<mailto:wang_yon...@lilly.com>> > Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model > PDB file using Phaser > > > > EXTERNAL EMAIL: Use caution before replying, clicking links, and opening > attachments. > > > Hi, > > Did you try to edit 'Model 1' to 'Model 0'? > > I seem to recall that it was reported on this bb as the solution to this > problem. > > Cheers, > > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > > > On 7 Dec 2021 22:56, Yong Wang > <00003c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk<mailto:00003c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk>> > wrote: > > Hi All, > > > > I am interested in using individual models from a PDB file containing > multiple models with MODEL/ENDMDL records as a template for use in Phaser. > The usage in the manual "ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS>1 | > ID <ID>2 | CARD ON3] CHAIN "<CHAIN>"4 MODEL <NUM>5 " seems to support this. > However, I am getting an error shown below: > > > > ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 > > > > $$ > > <B><FONT COLOR="#FF8800"> > > $TEXT:Warning: $$ Baubles Markup $$ > > ------------------------------------------------------------------------------------------ > > SYNTAX ERROR: Use SERIAL > > ------------------------------------------------------------------------------------------ > > $$ > > > > I am assuming that the error is from using the "MODEL 1" and not due to > something else. Does anyone have any suggestion on this problem? > > > > Thanks, > > > > Yong > > > > > > > > Yong Wang, Ph.D. > > > > Senior Research Advisor > > Global Structural Biology > > Lilly Research Laboratories > > Lilly Corporate Center > > Indianapolis, IN 46285 > > U.S.A. > > > > Tel: +1 (317) 655 9145 > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk<mailto:rj...@cam.ac.uk> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity/> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
