Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser
Hi Randy, Thanks for the trouble shoot and update to the documentation. Now the keyword "MODEL SERIAL" is doing what it intends to do. My problem is fixed. Regards, Yong -Original Message- From: Randy John Read Sent: Friday, December 10, 2021 6:22 AM To: Yong Wang Cc: 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, Sorry, this is a scripting feature I haven’t actually used before! It turns out there was an error in the documentation, and where you select one MODEL from a multimodel PDB file (including an ensemble from ensembler or even one model from an NMR ensemble), you have to put “MODEL SERIAL”. It takes the model that is named in the PDB file with the specified model number. I’ve just fixed the documentation on our website. Best wishes, Randy Read > On 9 Dec 2021, at 21:27, Yong Wang wrote: > > 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 On Behalf Of Randy John Read > Sent: Thursday, December 9, 2021 4:18 PM > To: 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 >> <3c4fc05cc53b-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 >> Sent: Wednesday, December 8, 2021 7:37 AM >> To: Yong Wang >> Cc: 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 >> <3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | >> ID 2 | CARD ON3] CHAIN ""4 MODEL 5 ” seems to support this. >> However, I am getting an error shown below: >> >> >> >> ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 >> >> >> >> $$ >> >> >> >> $TEXT:Warning: $$ 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? >> >> >> >>
[ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser
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 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 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 > <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk<mailto:3c4fc05cc53b-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 mailto:bshaa...@bgu.ac.il>> > Sent: Wednesday, December 8, 2021 7:37 AM > To: Yong Wang 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 > <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk<mailto:3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | > ID 2 | CARD ON3] CHAIN ""4 MODEL 5 " seems to support this. > However, I am getting an error shown below: > > > > ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 > > > > $$ > > > > $TEXT:Warning: $$ 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
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 On Behalf Of Randy John Read Sent: Thursday, December 9, 2021 4:18 PM To: 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 > <3c4fc05cc53b-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 > Sent: Wednesday, December 8, 2021 7:37 AM > To: Yong Wang > Cc: 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 > <3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | > ID 2 | CARD ON3] CHAIN ""4 MODEL 5 ” seems to support this. > However, I am getting an error shown below: > > > > ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 > > > > $$ > > > > $TEXT:Warning: $$ 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 > > > To unsubscribe from the CCP4BB list, click the following link: > 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 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 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/ 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/
Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser
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 > <3c4fc05cc53b-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 > Sent: Wednesday, December 8, 2021 7:37 AM > To: Yong Wang > Cc: 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 > <3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | > ID 2 | CARD ON3] CHAIN ""4 MODEL 5 ” seems to support this. > However, I am getting an error shown below: > > > > ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 > > > > $$ > > > > $TEXT:Warning: $$ 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 > > > To unsubscribe from the CCP4BB list, click the following link: > 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 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 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/
Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser
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 Sent: Wednesday, December 8, 2021 7:37 AM To: Yong Wang Cc: 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 <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk<mailto:3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | ID 2 | CARD ON3] CHAIN ""4 MODEL 5 " seems to support this. However, I am getting an error shown below: ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 $$ $TEXT:Warning: $$ 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 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/
Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser
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 <3c4fc05cc53b-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 [PDB|CIF] [RMS 1 | ID 2 | CARD ON3] CHAIN ""4 MODEL 5 ” seems to support this. However, I am getting an error shown below: ENSEmble mol PDB out.pdb RMS 1.5 MODEL 1 $$ $TEXT:Warning: $$ 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 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/
