Iridium hexamine problems with eLBOW
I experience problems generating a correct CIF file for iridium hexamine (IRI in the eLBOW database). The geometry is supposed to be octahedral and eLBOW outputs a prism regardless of the options checked in the GUI. eLBOW actually does the same for the octahedral Mg(OH2)6. Does someone know how to rule this out? Thanks to everybody. Ben -- Benoît Masquida Chargé de Recherche CNRS IBMC Strasbourg UPR 9002 ARN [email protected] +33 (0)3 88 41 70 45 +33 (0)6 70 23 79 50 +33(0)3 88 60 22 18 (fax)
Ben
There are some problems with metal complexes that I'm working to
solve. However, you can also use the geometry in the Chemical
Components thus
phenix.elbow --chemical-component=IRI --final-geometry=IRI
or if you use the GUI the image is attached.
Please note that the geometry in the Chemical Components is not
perfect for the hydrogens. I'll put this issue high on my to-do list
and will send you better restraints file soon and fix the algorithm
for future users.
Cheers
Nigel
On Wed, Jul 4, 2012 at 1:53 AM, Benoît Masquida
I experience problems generating a correct CIF file for iridium hexamine (IRI in the eLBOW database).
The geometry is supposed to be octahedral and eLBOW outputs a prism regardless of the options checked in the GUI. eLBOW actually does the same for the octahedral Mg(OH2)6.
Does someone know how to rule this out?
Thanks to everybody.
Ben
-- Benoît Masquida Chargé de Recherche CNRS IBMC Strasbourg UPR 9002 ARN [email protected] +33 (0)3 88 41 70 45 +33 (0)6 70 23 79 50 +33(0)3 88 60 22 18 (fax)
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
Hi all, I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness? Thanks in advance! Fengyun
Hi Fengyun, I have trouble understanding the statement "The output from SCALA give the completeness of about 97 to 99%". Overall completeness is just one number. Completeness in bins is a bunch of numbers, which are completeness per resolution bin. Completeness may be in range (eg. from d_min to d_max) or from d_min to inf. Sometimes they may be very different numbers. Anyway, when it comes to refinement, phenix.refine log file reports initial reflection statistics somewhere at the very beginning of log file: this is what actually in your input reflection file. Later on phenix.refine may (or may not) remove a few reflections as outliers, which is also reported in the log file. I guess same information is obvious in the GUI as well. So what exactly is your question? Pavel On 7/6/12 9:24 PM, [email protected] wrote:
Hi all,
I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness?
Thanks in advance! Fengyun
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Hi Pavel,
Sorry that i didn't state clearly. When I say 97 to 99%, they are the
numbers for different resolution shells.
I read from the truncate output file that many reflections are
rejected because,
( having EITHER Iobs .LT. -3.7*SDobs OR Iobs .LT.
(SDobs)**2/MeanI - 4.0*SDobs )
this might be the reason completeness drops.
Thanks!
Fengyun
Quoting Pavel Afonine
Hi Fengyun,
I have trouble understanding the statement "The output from SCALA give the completeness of about 97 to 99%". Overall completeness is just one number. Completeness in bins is a bunch of numbers, which are completeness per resolution bin. Completeness may be in range (eg. from d_min to d_max) or from d_min to inf. Sometimes they may be very different numbers.
Anyway, when it comes to refinement, phenix.refine log file reports initial reflection statistics somewhere at the very beginning of log file: this is what actually in your input reflection file. Later on phenix.refine may (or may not) remove a few reflections as outliers, which is also reported in the log file. I guess same information is obvious in the GUI as well.
So what exactly is your question?
Pavel
On 7/6/12 9:24 PM, [email protected] wrote:
Hi all,
I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness?
Thanks in advance! Fengyun
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Try looking at the differences in completeness when you run CCP4's Truncate with TRUNCATE YES and TRUNCATE NO. The former option alters the intensity distribution such that most of the weak data are set to small positive values. Depending on phenix.refine's current policies this may alter how many reflections are included in refinement. Another way to see this is to look at the range of values for Imean data in the MTZ file using something like Mtzdump - if the completeness reported by Mtzdump is what you expect, but the range of values includes negative intensities that might be the source of your problem. Negative intensities can be a significant proportion of data for anisotropic diffraction. BTW: you're posting on Phenixbb for CCP4 programs. Better to ask this question in CCP4bb if the above doesn't answer it. Phil Jeffrey Princeton ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Saturday, July 07, 2012 12:24 AM To: PHENIX user mailing list Subject: [phenixbb] a question on completeness Hi all, I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness? Thanks in advance! Fengyun _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thank you for your advices!
Fengyun
Quoting "Jeffrey, Philip D."
Try looking at the differences in completeness when you run CCP4's Truncate with TRUNCATE YES and TRUNCATE NO. The former option alters the intensity distribution such that most of the weak data are set to small positive values. Depending on phenix.refine's current policies this may alter how many reflections are included in refinement.
Another way to see this is to look at the range of values for Imean data in the MTZ file using something like Mtzdump - if the completeness reported by Mtzdump is what you expect, but the range of values includes negative intensities that might be the source of your problem. Negative intensities can be a significant proportion of data for anisotropic diffraction.
BTW: you're posting on Phenixbb for CCP4 programs. Better to ask this question in CCP4bb if the above doesn't answer it.
Phil Jeffrey Princeton
________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Saturday, July 07, 2012 12:24 AM To: PHENIX user mailing list Subject: [phenixbb] a question on completeness
Hi all,
I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness?
Thanks in advance! Fengyun
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participants (5)
-
Benoît Masquida -
fn1＠rice.edu -
Jeffrey, Philip D. -
Nigel Moriarty -
Pavel Afonine