an error in the operation of SF-Tool
Dear All, By the RCSB SF-Tool I have tried to convert my PDB file and the corresponding mtz file into mmCIF for the purpose of RCSB depositation, by the Automatic (default) mode. I got the following message: "Converting structure factor to mmCIF format.... Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file" Obviously there is an error message, although the conversion is succesful. As for I intend to deposit the structure including the mmCIF file into RCSB, I am afraid I have lost some message in the MTZ file and mmCIF file. Will you please tell me how can I add the labels, which have been lost I think, to the mtz file, so that the labels message will also be included into the mmCIF file if it was necessary? Cheers, Dialing
On Tue, Jan 3, 2012 at 9:33 PM, Dialing Pretty
By the RCSB SF-Tool I have tried to convert my PDB file and the corresponding mtz file into mmCIF for the purpose of RCSB depositation, by the Automatic (default) mode. I got the following message:
"Converting structure factor to mmCIF format.... Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file"
Obviously there is an error message, although the conversion is succesful.
As for I intend to deposit the structure including the mmCIF file into RCSB, I am afraid I have lost some message in the MTZ file and mmCIF file.
Will you please tell me how can I add the labels, which have been lost I think, to the mtz file, so that the labels message will also be included into the mmCIF file if it was necessary?
I don't think it's possible to have an MTZ file without labels. This sounds like something you need to contact the RCSB about - we don't know anything about how SF-tool works. However, for future reference, could you please send me the output of this command? phenix.mtz.dump data.mtz (where data.mtz is replaced with the file you're trying to convert) thanks, Nat
Dear All, Today I have tried to use phenix autobuild, I find in the built model, some residues in the PDB has been changed to simple residues. Will you please introduce to me the theory behind this? In addition, what will be the difference between Rebuild-in-place "auto", "true"and "false"? Especially the difference between Rebuild-in-place "true"and "false"? Cheers, Dialing
Dear All, Will you please tell me the difference between phenix. reduce and phnix.ready_set? Cheers, Dialing
Dear All, By the Graphics of phenix refine, I want to select all the atoms of the first 2 residues, will you please what I should to input in the "Selection" item? If I want to select all the atoms of both the first 2 residues and the last 2 residues, what should I input? Suppose I have a chain with 20 amino acids, and as expected the density of the first 2 residues and the last 2 residues are low, by occupancy refinement can I make the conformation of the first 2 residues and the last 2 residues reliable? Cheers, Dialing
Hi, compare http://phenix-online.org/documentation/hydrogens.htm and http://phenix-online.org/documentation/ready_set.htm which should answer your question. Pavel On 1/6/12 3:21 AM, Dialing Pretty wrote:
__Dear All,__
Will you please tell me the difference between phenix. reduce and phnix.ready_set?
Cheers,
Dialing
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Hi Dialing, you will find the answers here: http://phenix-online.org/documentation/autobuild.htm Pavel On 1/5/12 4:21 PM, Dialing Pretty wrote:
Dear All,
Today I have tried to use phenix autobuild, I find in the built model, some residues in the PDB has been changed to simple residues. Will you please introduce to me the theory behind this?
In addition, what will be the difference between Rebuild-in-place "auto", "true"and "false"? Especially the difference between Rebuild-in-place "true"and "false"?
Cheers,
Dialing
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Dear All, I just run a Phenix Autobuid without input pdb model. But After I got the final result, I find the final Rfree is 0.27 and final Rwork is 0.20. I think the difference is too large. What is your opinion on it? Cheers, Fenghui
The result seems very good, I think you need just several rounds of manual
model adjustment......What's your resolution?
On Fri, Jan 6, 2012 at 12:41 PM, Dialing Pretty
Dear All,
I just run a Phenix Autobuid without input pdb model. But After I got the final result, I find the final Rfree is 0.27 and final Rwork is 0.20. I think the difference is too large.
What is your opinion on it?
Cheers,
Fenghui
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Dear All, I just did a water picking using the following parameter file. However the MolProbity analysis demonstarted that the clash of some added water with the protein atom can be as high as 0.9 A. Will you please tell me how to modify the following parameter file so that all the water with clash higher than 0.4 A will be not selected? In addition, do you think "primary_map_cutoff = 3.0" is practical? I think in somw situation this value can be as low as lower than 1.0. I am looking forward to getting a reply from you. Cheers, Dialing refinement { ordered_solvent { low_resolution = 3.0 b_iso_min = 1.0 b_iso_max = 50.0 b_iso = 25.0 primary_map_type = mFobs-DFmodel primary_map_cutoff = 3.0 secondary_map_and_map_cc_filter { cc_map_2_type = 2mFobs-DFmodel } } peak_search { map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 } } }
Dear All, Several days ago I have run several Phenix autobuild, all successful. But today I have tried several Phenix autobuild, all failed, with the typical error message as following. I am looking forward to getting your reply on how to solve the problem I met. Cheers, Dialing UN_FILE_3.log Calling method: autobuild 3 Collecting models.... Solution for try : 1 cycle_best_1.pdb No model from try 1 Solution for try : 2 cycle_best_1.pdb No model from try 2 Solution for try : 3 cycle_best_1.pdb No model from try 3 Removing directories where subprocesses were run... *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: NOTE: no model built...quitting ******************************************************************************** *************ERROR ENDING *******************
Dear All, Can the Phenix software get mixed with the PHE and ARG? I use the Coot to build a peptide. 2 fragments of peptides are suitable for one specific part of electronic density map, and there is only one residue can distinguish which fragment of peptide is the real peptide fragment for that part of electronic density map, i.e., in one fragment of peptide it contains ARG, and in the other fragment of peptide it contains PHE. As for after Coot rebuild I still need the refinemnt, I am afraid whether the PHENIX can distinguish the PHE and ARG if I cannot distinguish it so nicely in the Coot when I rebuild the peptide. I am looking forward to getting your reply. Dialing
Dear Dialing, If you use phenix.refine on the model that you have rebuilt by hand, then it will not change the sequence from what you have specified. If you use phenix.autobuild and specify "rebuild_in_place=False" then autobuild will reinterpret the sequence and could change it from what you have chosen. All the best, Tom T
Dear All,
Can the Phenix software get mixed with the PHE and ARG?
I use the Coot to build a peptide. 2 fragments of peptides are suitable for one specific part of electronic density map, and there is only one residue can distinguish which fragment of peptide is the real peptide fragment for that part of electronic density map, i.e., in one fragment of peptide it contains ARG, and in the other fragment of peptide it contains PHE.
As for after Coot rebuild I still need the refinemnt, I am afraid whether the PHENIX can distinguish the PHE and ARG if I cannot distinguish it so nicely in the Coot when I rebuild the peptide.
I am looking forward to getting your reply.
Dialing_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear Dialing, This error message, "NOTE: no model built...quitting" usually means that the starting map was so terrible that it could not be interpreted at all. You might want to check the inputs and also have a look at the starting maps to see if they are in fact what you expect. All the best, Tom T
Dear All,
Several days ago I have run several Phenix autobuild, all successful. But today I have tried several Phenix autobuild, all failed, with the typical error message as following.
I am looking forward to getting your reply on how to solve the problem I met.
Cheers,
Dialing
UN_FILE_3.log Calling method: autobuild 3 Collecting models....
Solution for try : 1 cycle_best_1.pdb No model from try 1
Solution for try : 2 cycle_best_1.pdb No model from try 2
Solution for try : 3 cycle_best_1.pdb No model from try 3
Removing directories where subprocesses were run...
*************ERROR ENDING *******************
******************************************************************************** Failed to carry out AutoBuild_build_cycle:
NOTE: no model built...quitting
********************************************************************************
*************ERROR ENDING *******************_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear All, I just did a Phenix refine, but it gave the following sorry message: Number of atoms with unknown nonbounded energy type symbol: 3. I remember when I process the peptide with Coot, several H atoms were separated from the atoms they were attached to. I do not know whether this is the reason why the Phenix gives symbol 3. I am looking forward to getting your reply. Cheers, Dialing
The list of atoms should appear next to the line you sent. Could you send
that list to me (or simply the whole log file)?
On Fri, Jan 13, 2012 at 1:00 AM, Dialing Pretty
Dear All,
I just did a Phenix refine, but it gave the following sorry message:
Number of atoms with unknown nonbounded energy type symbol: 3.
I remember when I process the peptide with Coot, several H atoms were separated from the atoms they were attached to. I do not know whether this is the reason why the Phenix gives symbol 3.
I am looking forward to getting your reply.
Cheers,
Dialing
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Dear All, For the Phenix loop build, does it mean a loop will be built for the flexible part without electronic density? Cheers, Dialing
Hi Dialing, No, normally loops are not built for any part of the model for which there is no density. -Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Dialing Pretty [[email protected]] Sent: Wednesday, January 18, 2012 10:11 PM To: PHENIX user mailing list Subject: [phenixbb] For phenix loop build Dear All, For the Phenix loop build, does it mean a loop will be built for the flexible part without electronic density? Cheers, Dialing
participants (7)
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Dialing Pretty -
Nathaniel Echols -
Pavel Afonine -
Ralf Grosse-Kunstleve -
Terwilliger, Thomas C -
Thomas C. Terwilliger
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