[ccp4bb] Heavy-atom derivatives
Dear all, I'm looking for a method to solve the phase problem. Thus, I would like some help about heavy-atom derivatives. What is the best heavy-atom to make soaking? I tried Iodine (because my protein have a lot of tyrosines), but no results... I read some papers about quick-soak, its a good method? Using platine, Hg, Br... Any suggestions? Thank you so much. Best wishes, -- Giulliana Rangel M.S. Biotechnology Program - UNIFESP Structural Biology Laboratory Phone: +55 (12) 3309-9698 330 Talim St ZIP CODE 12231-280 São José dos Campos - SP/ BR
Re: [ccp4bb] Heavy-atom derivatives
Hi Giulliana, here is a nice and simple method on how to select heavy atoms for phasing using native PAGE (please see Fig. 1): http://www.ncbi.nlm.nih.gov/pubmed/10903954 Structure. 2000 Jul 15;8(7):R143-9. Screening for phasing atoms in protein crystallography. Boggon TJ, Shapiro L. Hope that helps, Tomas On Mon, Jun 29, 2015 at 8:47 AM, Giulliana Rangel giulliana.ran...@gmail.com wrote: Dear all, I'm looking for a method to solve the phase problem. Thus, I would like some help about heavy-atom derivatives. What is the best heavy-atom to make soaking? I tried Iodine (because my protein have a lot of tyrosines), but no results... I read some papers about quick-soak, its a good method? Using platine, Hg, Br... Any suggestions? Thank you so much. Best wishes, -- Giulliana Rangel M.S. Biotechnology Program - UNIFESP Structural Biology Laboratory Phone: +55 (12) 3309-9698 330 Talim St ZIP CODE 12231-280 São José dos Campos - SP/ BR
Re: [ccp4bb] imosflm errors
All of the above started to work On Mon, Jun 29, 2015 at 2:27 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Hi Ivan When you say it started to work do you mean xia2, imosflm ccp4i, or just one of these?? :-) On 29 Jun 2015, at 08:38, xaravich ivan wrote: Thanks Graeme, I just uninstalled CCP4 and ccp4i Tcl, then re installed ccp4i tcl+tk first and then CCP4+arpwARP and then it started to work finally. I don't know why this would be the case, but for the timing it seems to work. Thanks, Ivan On Mon, Jun 29, 2015 at 12:07 AM, Graeme Winter graeme.win...@gmail.com wrote: Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more information: http://xia2.sourceforge.net/using_xia2.html However this will not resolve your original iMosflm problem, which is the subject of the post (just responding to your ccp4i problem) Best wishes Graeme On Mon, Jun 29, 2015 at 12:26 AM xaravich ivan xaravich.i...@gmail.com wrote: Thanks for your suggestion, Jurgen I tried xia2 and tried it several times, turning the machine off, rebooting, using different data sets, exiting ccp4i but every time it gives this error msg.(attached) On Sun, Jun 28, 2015 at 2:16 PM, Jurgen Bosch jbos...@jhu.edu wrote: Try xia2 from ccp4i and see if it also chokes. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 13:51, xaravich ivan xaravich.i...@gmail.com wrote: Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] imosflm errors
Hi Ivan When you say it started to work do you mean xia2, imosflm ccp4i, or just one of these?? :-) On 29 Jun 2015, at 08:38, xaravich ivan wrote: Thanks Graeme, I just uninstalled CCP4 and ccp4i Tcl, then re installed ccp4i tcl+tk first and then CCP4+arpwARP and then it started to work finally. I don't know why this would be the case, but for the timing it seems to work. Thanks, Ivan On Mon, Jun 29, 2015 at 12:07 AM, Graeme Winter graeme.win...@gmail.com wrote: Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more information: http://xia2.sourceforge.net/using_xia2.html However this will not resolve your original iMosflm problem, which is the subject of the post (just responding to your ccp4i problem) Best wishes Graeme On Mon, Jun 29, 2015 at 12:26 AM xaravich ivan xaravich.i...@gmail.com wrote: Thanks for your suggestion, Jurgen I tried xia2 and tried it several times, turning the machine off, rebooting, using different data sets, exiting ccp4i but every time it gives this error msg.(attached) On Sun, Jun 28, 2015 at 2:16 PM, Jurgen Bosch jbos...@jhu.edu wrote: Try xia2 from ccp4i and see if it also chokes. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 13:51, xaravich ivan xaravich.i...@gmail.com wrote: Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
You’ve got to put values in for “search parameters,” tell it how many ensembles to look for. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 11:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!! Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the error that is poping up indicating I have not set an ensamble. How can I set an ensamble if I have only one PDB? Or do I have to make some changes in the input. (I just put an arbitrary name for ensmale that sounds similar to the single PDB input (search model) file Thanks, Ivan On Mon, Jun 29, 2015 at 1:01 AM, herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote: Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von xaravich ivan Gesendet: Montag, 29. Juni 2015 09:43 An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
Hi Ivan, I always run phaser via my own script, but I checked the ccp4i gui: the error message indicates that you did not set a search option. In the tab “Search parameters” I found an item “Perform search using” followed by a box. When nothing is clicked here, the box is empty so Phaser does not know what to do. I am pretty sure that defining your ensemble in this box will solve your problem. Best, Herman Von: xaravich ivan [mailto:xaravich.i...@gmail.com] Gesendet: Montag, 29. Juni 2015 17:49 An: Schreuder, Herman RD/DE Cc: ccp4bb Betreff: Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!! Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the error that is poping up indicating I have not set an ensamble. How can I set an ensamble if I have only one PDB? Or do I have to make some changes in the input. (I just put an arbitrary name for ensmale that sounds similar to the single PDB input (search model) file Thanks, Ivan On Mon, Jun 29, 2015 at 1:01 AM, herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote: Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von xaravich ivan Gesendet: Montag, 29. Juni 2015 09:43 An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan
Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
Thanks everyone, It works now. cheers, Ivan On Mon, Jun 29, 2015 at 8:59 AM, Gabor Bunkoczi gb...@cam.ac.uk wrote: Hi Ivan, you need to tell Phaser which ensemble to use for searching. Open the Search parameters tab, and select the ensemble you defined. HTH, Gabor On 2015-06-29 16:48, xaravich ivan wrote: Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the error that is poping up indicating I have not set an ensamble. How can I set an ensamble if I have only one PDB? Or do I have to make some changes in the input. (I just put an arbitrary name for ensmale that sounds similar to the single PDB input (search model) file Thanks, Ivan On Mon, Jun 29, 2015 at 1:01 AM, herman.schreu...@sanofi.com wrote: Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON xaravich ivan GESENDET: Montag, 29. Juni 2015 09:43 AN: CCP4BB@JISCMAIL.AC.UK BETREFF: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan -- ## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##
Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
Hi Ivan, you need to tell Phaser which ensemble to use for searching. Open the Search parameters tab, and select the ensemble you defined. HTH, Gabor On 2015-06-29 16:48, xaravich ivan wrote: Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the error that is poping up indicating I have not set an ensamble. How can I set an ensamble if I have only one PDB? Or do I have to make some changes in the input. (I just put an arbitrary name for ensmale that sounds similar to the single PDB input (search model) file Thanks, Ivan On Mon, Jun 29, 2015 at 1:01 AM, herman.schreu...@sanofi.com wrote: Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON xaravich ivan GESENDET: Montag, 29. Juni 2015 09:43 AN: CCP4BB@JISCMAIL.AC.UK BETREFF: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan -- ## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##
[ccp4bb] Phaser solution and solvent content for arp warp
Hi everyone, I think I have finally got a solution in Phaser (screen shot attached) as the TFZ is 10. However the solution PDB has 30 molecules in it as the search model was an NMR solution. As I have 0.944 Angs resolution data pretty complete, I thought of building the initial model in ArpWarp. I prepared a new PDB file form the Phaser solution output with only one molecule instead of 30. Prepared the sequence file in pir format for the target. Now the wilson plot says B-factor of 3.66 and solvent content 0.98 even if I cut off the low resolution data to 8.0 from 20.0 and increase the high resolution to 1.0. Initially when I calculated the mathews coefficient it showed the best estimate to be 2 molecules in the assymmetric unit. Am I missing something again? Thanks in advance, Ivan
Re: [ccp4bb] Phaser solution and solvent content for arp warp
Just throw your phaser-placed model into Buccaneer JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 3:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phaser solution and solvent content for arp warp Hi everyone, I think I have finally got a solution in Phaser (screen shot attached) as the TFZ is 10. However the solution PDB has 30 molecules in it as the search model was an NMR solution. As I have 0.944 Angs resolution data pretty complete, I thought of building the initial model in ArpWarp. I prepared a new PDB file form the Phaser solution output with only one molecule instead of 30. Prepared the sequence file in pir format for the target. Now the wilson plot says B-factor of 3.66 and solvent content 0.98 even if I cut off the low resolution data to 8.0 from 20.0 and increase the high resolution to 1.0. Initially when I calculated the mathews coefficient it showed the best estimate to be 2 molecules in the assymmetric unit. Am I missing something again? Thanks in advance, Ivan
Re: [ccp4bb] Phaser solution and solvent content for arp warp
I think I would be tempted to chainsaw one of the ensemble chains of 2IT8 (they look very similar except for side-chain disposition) and use 1 or 2 of these as search models in a Phaser run. If this works, you should see good Z-values and the final result inspected in Coot should show good molecular packing with clear solvent channels and no isolated molecules. Electron density should look reasonable, and if there are any known non-protein features (like metal ions) they should clearly show up in difference density. If the initial Phaser solution looks OK in terms of packing, I would be tempted to take the phased generated and, using the sequence of your protein, subject it to auto-building with Parrot and Buccanner, using 2-fold NCS (if you do in fact have 2 molecules in the ASU). With any luck, you should be able to auto-build 90% of your model. This approach worked for us for a medium resolution problem with 8-fold symmetry for a really marginal search model. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 6/29/2015 3:10 PM, xaravich ivan wrote: Hi everyone, I think I have finally got a solution in Phaser (screen shot attached) as the TFZ is 10. However the solution PDB has 30 molecules in it as the search model was an NMR solution. As I have 0.944 Angs resolution data pretty complete, I thought of building the initial model in ArpWarp. I prepared a new PDB file form the Phaser solution output with only one molecule instead of 30. Prepared the sequence file in pir format for the target. Now the wilson plot says B-factor of 3.66 and solvent content 0.98 even if I cut off the low resolution data to 8.0 from 20.0 and increase the high resolution to 1.0. Initially when I calculated the mathews coefficient it showed the best estimate to be 2 molecules in the assymmetric unit. Am I missing something again? Thanks in advance, Ivan
Re: [ccp4bb] imosflm errors
Thanks Graeme, I just uninstalled CCP4 and ccp4i Tcl, then re installed ccp4i tcl+tk first and then CCP4+arpwARP and then it started to work finally. I don't know why this would be the case, but for the timing it seems to work. Thanks, Ivan On Mon, Jun 29, 2015 at 12:07 AM, Graeme Winter graeme.win...@gmail.com wrote: Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more information: http://xia2.sourceforge.net/using_xia2.html However this will not resolve your original iMosflm problem, which is the subject of the post (just responding to your ccp4i problem) Best wishes Graeme On Mon, Jun 29, 2015 at 12:26 AM xaravich ivan xaravich.i...@gmail.com wrote: Thanks for your suggestion, Jurgen I tried xia2 and tried it several times, turning the machine off, rebooting, using different data sets, exiting ccp4i but every time it gives this error msg.(attached) On Sun, Jun 28, 2015 at 2:16 PM, Jurgen Bosch jbos...@jhu.edu wrote: Try xia2 from ccp4i and see if it also chokes. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 13:51, xaravich ivan xaravich.i...@gmail.com wrote: Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png
[ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!
Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von xaravich ivan Gesendet: Montag, 29. Juni 2015 09:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Single search Model input in Phaser!!! Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan
[ccp4bb] Single search Model input in Phaser!!!
Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. Am I missing something or am I only able to use Molrep or programs other than Phaser with one search model as input. Everytime I put my search model in ensamble mode it fails (which is expected I guess) but how can I use only one chainsaw generated search model in Phaser, or can I? Thanks, Ivan
Re: [ccp4bb] imosflm errors
Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more information: http://xia2.sourceforge.net/using_xia2.html However this will not resolve your original iMosflm problem, which is the subject of the post (just responding to your ccp4i problem) Best wishes Graeme On Mon, Jun 29, 2015 at 12:26 AM xaravich ivan xaravich.i...@gmail.com wrote: Thanks for your suggestion, Jurgen I tried xia2 and tried it several times, turning the machine off, rebooting, using different data sets, exiting ccp4i but every time it gives this error msg.(attached) On Sun, Jun 28, 2015 at 2:16 PM, Jurgen Bosch jbos...@jhu.edu wrote: Try xia2 from ccp4i and see if it also chokes. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 13:51, xaravich ivan xaravich.i...@gmail.com wrote: Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png
