Hi, Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? I have another question. In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID? As for example:- pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log ROTATE [INVERT] [MATRIX] values CHAIN A end eof This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate. Thank you in advance and have a nice THANKS GIVING WEEKEND Hena
Hi Hena,
In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID?
phenix.pdbtools is the tool to do such manipulations: http://www.phenix-online.org/documentation/pdbtools.htm Examples: - remove chain A: phenix.pdbtools model.pdb remove="chain A" or equivalently: phenix.pdbtools model.pdb keep="not chain A" - remove SEGID: phenix.pdbtools model.pdb remove="segid A" Pavel
On Tue, Nov 22, 2011 at 7:50 AM, Hena Dutta
Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this?
This was the first hit on Google: http://www.pymolwiki.org/index.php/AngleBetweenHelices -Nat
Dear All, I am new to Phenix. I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile.If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. This structure was solved by molecular replacement using a bacterial protein with 38% identity.I am wondering if there is an model bias? I have not identified particular region in model for bias. My questions are: Am I right in thinking if there is model bias based on above info?I added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before.I have couple of classical papers next to me but I need help. I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB. Happy Thanksgiving.. Rajesh Date: Tue, 22 Nov 2011 10:50:53 -0500 From: [email protected] To: [email protected] Subject: [phenixbb] measuring angle Hi, Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? I have another question. In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID? As for example:- pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log ROTATE [INVERT] [MATRIX] values CHAIN A end eof This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate. Thank you in advance and have a nice THANKS GIVING WEEKEND Hena _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Tue, Nov 22, 2011 at 7:35 PM, Rajesh kumar
I am new to Phenix. I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile. If I fix the outliers they wouldn't go away and molprobity score remains same or get worst.
Which version of Phenix are you using, and what are your current RMS(bonds) and RMS(angles)? Do you have NCS, and have you optimized the weights?
I added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned?
Yes. If you have a system with multiple processor cores, or a queueing system, I'd recommend taking advantage of these when running AutoBuild - although the SA omit maps are very slow, the composite omit map procedure parallelizes very nicely. -Nat
Hi Rajesh, model bias, in a nutshell, is when you see something in the map that is conveyed by the model (that may not be correct) and not by the data. I am not sure how one can get an idea about model bias looking at triplet of numbers: Rwork, Rfree and Molprobity percentile. By the way, your Rwork/Rfree look pretty good (given the 2.7A resolution). Anyway, if everything else: bunch of model and data statistics, local and global model-to-data quality fit all look well (*), and you are still suspecting something isn't right, then you can invest from a few days to a week or so into computing an "Iterative Build OMIT map" as described here: Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008) This map is supposed to be bias free. Pavel (*) For more details see here: http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile. If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. This structure was solved by molecular replacement using a bacterial protein with 38% identity. I am wondering if there is an model bias? I have not identified particular region in model for bias.
My questions are: Am I right in thinking if there is model bias based on above info? I added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before. I have couple of classical papers next to me but I need help. I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB.
Hi,
I am also a bit confused about your suspicion. If your Rwork/Rfree
22.7/27.9 for a 2.7 angstrom data, you have probably reached the so called
endpoint of your refinement, unless Molprobity shows serious deviation.
What is the basis of your skepticism? Were you expecting this structure to
be different from the bacterial model to fit your hypothesis? I would be a
bit careful in such situations!
On Tue, Nov 22, 2011 at 10:01 PM, Pavel Afonine
** Hi Rajesh,
model bias, in a nutshell, is when you see something in the map that is conveyed by the model (that may not be correct) and not by the data.
I am not sure how one can get an idea about model bias looking at triplet of numbers: Rwork, Rfree and Molprobity percentile. By the way, your Rwork/Rfree look pretty good (given the 2.7A resolution).
Anyway, if everything else: bunch of model and data statistics, local and global model-to-data quality fit all look well (*), and you are still suspecting something isn't right, then you can invest from a few days to a week or so into computing an "Iterative Build OMIT map" as described here:
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008)
This map is supposed to be bias free.
Pavel
(*) For more details see here: http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile. If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. This structure was solved by molecular replacement using a bacterial protein with 38% identity. I am wondering if there is an model bias? I have not identified particular region in model for bias.
My questions are: Am I right in thinking if there is model bias based on above info? I added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before. I have couple of classical papers next to me but I need help. I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear All, I have run 100 rounds of Phenix refine, and it took long time to reach round 100. But at round 100 it has been for several hours without indication to complete, although the working light is still flashing. I am looking forward to getting your reply on how to solve this problem. Best regards. Dialing
Hi Dialing, is there a particular reason why you wanted run more macro-cycles (100) than the default (3)? Try running phenix.refine with "--show-process-info" and see if its memory requirements match what you have on your computer. Do it with a fewer number of macro-cycles, like 1 or even zero. Make sure you are using the latest version of PHENIX, since I guess the problem is related to the memory intake, and it was improved recently. Pavel.
Dear All, I have run 100 rounds of Phenix refine, and it took long time to reach round 100. But at round 100it has been for several hours without indication to complete, although the working light is still flashing. I am looking forward to getting your reply on how to solve this problem. Best regards. Dialing
participants (6)
-
Dialing Pretty -
Hena Dutta -
Nathaniel Echols -
Pavel Afonine -
Rajesh kumar -
xaravich ivan