[ccp4bb] Fwd: [ccp4bb] phaser issue MR
Dear all, thank you for your suggestions, I finally fix the problem as follows. I'll write a summary here for future reference. 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED - I provide the .sol file - The program gives the error I sent yesterday 3) Phaser run 3# it works again Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed... - I provided again all the ensembles I gave in run 1# - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#) - It runs So, this was my fix :-) I hear many times the sentence fix a solution, but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end. Best wishes, Have a nice day. Almudena -- Forwarded message -- From: Almudena Ponce Salvatierra maps.fa...@gmail.com Date: 2014-06-03 9:49 GMT+02:00 Subject: Re: [ccp4bb] phaser issue MR To: Airlie McCoy ajm...@cam.ac.uk Dear Airlie, don't worry, actually it was you who gave me the clue when you told me what the error was standing for. I will try to be a clear as possible: 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED - I provide the .sol file - The program gives the error I sent yesterday 3) Phaser run 3# it works again Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed... - I provided again all the ensembles I gave in run 1# - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#) - It runs So, this was my fix :-) I hear many times the sentence fix a solution, but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end. I have another question, if you don't mind. How good does the TFZ score get in one of this iterative Molecular replacement routines? I am now above 5 (5.4) which I know is unlikely but I need to take into account that I start with fragments that maybe are not exactly as they are in the structure (I mean in reality) and also that the model is incomplete, meaning that even though I have now most of it places there are still some regions that are not connected, some others with empty electron density... What would you recommend in this case? I also have the following warinings: - Best model and data are insufficient to reach half expected LLG target: placement of one/first ensemble will be very difficult. - Search request requires more scattering than defined in composition. Composition increased to accomodate search components. Thank you very much for your time and consideration. Best wishes, Almudena. 2014-06-02 22:33 GMT+02:00 Airlie McCoy ajm...@cam.ac.uk: Hi Almundena, Apologies, I had not had a chance to look at it... what was your fix? Airlie On Jun 2 2014, Almudena Ponce Salvatierra wrote: Dear Airlie, I already solved the problem. Thank you very much anyway. Best wishes, Almudena 2014-06-02 15:43 GMT+02:00 Almudena Ponce Salvatierra maps.fa...@gmail.com : Sorry, Airlie, the input is this one, ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT $TEXT:Script: $$ Baubles Markup $$ #---PHASER COMMAND SCRIPT GENERATED BY CCP4I--- TITLE start MODE MR_AUTO ROOT /data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_24 #---DEFINE DATA--- HKLIN /data/almudena/ccp4/iterativeMR/epmr/forccp4_itMR.mtz LABIN F=FP SIGF=SIGFP SGALTERNATIVE SELECT HAND #---DEFINE ENSEMBLES--- ENSEMBLE loop PDB /data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/4ntloop-coot-0.pdb IDENT 99.0 ENSEMBLE 6bp PDB /data/almudena/ccp4/iterativeMR/epmr
Re: [ccp4bb] [ccp4bb] phaser issue MR
Dear Almudena, We actually have a tutorial that goes through the process of defining a solution step by step: http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input. The .sol file is a small text file that just contains the description of how a defined ensemble should be rotated and translated. If you look at that file, you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still have to be provided in the script that refers to the .sol file. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 3 Jun 2014, at 09:55, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, thank you for your suggestions, I finally fix the problem as follows. I'll write a summary here for future reference. 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED - I provide the .sol file - The program gives the error I sent yesterday 3) Phaser run 3# it works again Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed... - I provided again all the ensembles I gave in run 1# - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#) - It runs So, this was my fix :-) I hear many times the sentence fix a solution, but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end. Best wishes, Have a nice day. Almudena -- Forwarded message -- From: Almudena Ponce Salvatierra maps.fa...@gmail.com Date: 2014-06-03 9:49 GMT+02:00 Subject: Re: [ccp4bb] phaser issue MR To: Airlie McCoy ajm...@cam.ac.uk Dear Airlie, don't worry, actually it was you who gave me the clue when you told me what the error was standing for. I will try to be a clear as possible: 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were not placed in the previous run and REMOVE THE ONES THAT HAD BEEN PLACED - I provide the .sol file - The program gives the error I sent yesterday 3) Phaser run 3# it works again Since you said what happened was that Phaser was not finding something and the .sol file contained information about the ensembles that I removed... - I provided again all the ensembles I gave in run 1# - I provide de .sol file (I understand it will fix the solution of the ensembles from run 1#) - It runs So, this was my fix :-) I hear many times the sentence fix a solution, but then whenever I asked someone (before yesterday), each person refers to it in an ambiguous way! some say you need to provide phaser with the pdb from the solution you want to fix, some say that you need to provide the .sol file from what you want to fix and then provide only one new ensemble at the time... maybe it would be useful to have some script/example online of the command line itself, so that one knows what to input exactly. Maybe each one's way of explaining the same thing can lead to misunderstandings at the end. I have another question, if you don't mind. How good does the TFZ score get in one of this iterative Molecular replacement routines? I am now above 5 (5.4) which I know is unlikely but I need to take into account that I start with fragments that maybe are not exactly as they are in the structure (I mean in reality) and also that the model is incomplete, meaning that even though I have now most of it places there are still some regions that are not connected, some others with empty electron density... What would you recommend in this case? I also have the following warinings: - Best model and data are insufficient to reach half expected LLG target: placement of one/first ensemble will be very difficult. - Search request requires more scattering than defined in composition. Composition increased
[ccp4bb] phaser issue MR
Dear all, I am using Phaser for Molecular replacement. After Phaser places part of the structure, I would like to run it again, giving this time as search ensembles new pieces of structure. I thought what I had to do was simply to put in know solution the .sol file coming out from the previous Phaser run. However when I do so I get the following message: UNHANDLED ERROR: Program internal error in source file data_pdb.cc (line 144) *** Consistency check (M MOLECULE.size()) failed. *** Please email this log file with some supporting information and/or data to cimr-pha...@lists.cam.ac.uk Could anybody please tell me how to proceed? Maybe there is some option I am not using or some addtional data I need to provide the program... I don't know. Any suggestions are welcome! Thanks a lot in advance! Best wishes, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
