Dear Colleagues,
With good start shim set, the topshim with flag of convcomp works now on CDCl3 solvent. I appreciate all the helps offered by the colleagues in this community.
Best regards,
Weidong
From: Hu, Weidong
Sent: Tuesday, July 05, 2011 11:07 AM
To: ammrl_at_ammrl.org
Subject: response summary for " topshim trouble shooting"
Dear Colleagues:
Thank you very much for your useful information for the trouble shooting of topshim error message "too many points lost during fit". I received a lot of responses, and many of them should be very helpful. (I need to check them out on instruments). I guess it is not an unusual error happens to users, I would like to put the responses together so that all community can share some tricks to avoid or solve this problem.
I should add some more information to my earlier email to response some questions from colleagues. We use Topspin 2.1 with patchlevel 6. We have one 500 with regular TXI probe, and 600 with cryoprobe. The error message typically happens with 1d topshim on solvent of CDCl3 and D2O. As a routine, I usually generate 3D shim file from sucrose 10% D2O sample for a shim template for users from time to time. But, when this error message happens, I usually did not generate another 3D in situ as trouble shooting. I usually just try load a different shim file to see the problem goes away or not. Occationally, I use topshim convcomp try to solve this problem. If I can't, I use auto shim.
From the responses, I think I may need to generate another 3D in situ as one way for trouble shooting. Another thing I learned from the response is that when we see the statement "echo time must be reduced", the topshim already adjusted the echo time automatically, I don't need to mess around and adjust the parameter.
Short summary is this error may be caused by something not quite right with hardware, sample position, diffusion related problem, bad starting shim set and sample conditions. I learned a great deal from all the responses. And the following are the summary of the responses. I hope that I did not offend anyone by posting their responses.
Thank you again for those who take your precious time and provide helps for me.
Weidong
*********** responses from great colleagues**********
Clemens Anklin [clemens.anklin_at_bruker-biospin.com]:
this looks like problems with convection or similar. What is the solvent when you get this error.
it could also be that your initial shims are not good enough. Have you trieed running a topshim 3d to improve the shims?
When the program says "echo time must be reduced" it does it right there, you do not need to change any parameters.
It looks like you are running Topspin2.0, a convection compensated routine for topshim is available with Topspin 2.1 pl 6. We can send you the DVD with the new version.
Clemens Anklin [clemens.anklin_at_bruker-biospin.com]:
for the CDCl3 samples I would expect that the convcomp option might help. In D2O sample that will not help as the viscosity of D2O is too high to allow convection to happen.
When this happens again can you please execute the command topshim plot and then send us the files that are in /opt/topspin/data/TopShimData/nmr
thanks
John Decatur [jdd13_at_columbia.edu]:
I have seen this on our systems, too. A bruker engineer was here installing a probe and we saw the message of too many points lost and "echo time must be reduced" and in our case, topshim failed when these messages appeared. We reran the calibration (in service section of Topshim) and we found the number of coefficients given after calibration were less than four and their values were not close to one, such as 0.6 or so. The engineer was not sure why this was happening but he felt sure this was a probe problem such as cracked insert or misalignment or something. so the probe is back in billerica now. Sorry I have no solution for you but I thought I'd share our experience. I would delete the calibration and then redo it. You must already have a pretty good 3D shim before doing so.
g-sukenick_at_ski.mskcc.org<mailto:g-sukenick_at_ski.mskcc.org>:
Couple of data points:
If it happens with any solvent, then maybe it's time to update CDCl3 edlock parameters.
If it happens with specific solvents then the offset in the edlock table might need adjustment.
If it is happening only with some samples and not others, might be salt content in the samples.
What I do to keep things running with a variety of users is have them run AU that calls topshim and if it fails it goes on to do regular auto shim.
Josh Kurutz [jkurutz_at_northwestern.edu]:
Have you upgraded to patch level 6 (Topspin 2.1.6)? I was sorting through an upgrade from 2.1.4 to 2.1.6 with a Bruker engineer, and he mentioned some changes to Topspin that were implemented in later versions. Perhaps upgrading software (and updating firmware) might help.
Jerry [jerryldallas_at_gmail.com]:
In my experience with topshim this error message goes away if you spin the sample.
Adrienne Davis [Adrienne.Davis_at_nottingham.ac.uk]:
I'm not sure about the answer to your topshim query but it is possible that you are suffering from bad convection in your samples - if you have a cryoprobe is your air flow rate sufficiently high? We did have this problem sometime ago (we worked round it by using the 'topshim convcomp' option, i.e. we used the convection compensated topshim).
When, during the next warmup, we took the cryoprobe airline off we found that there were a few titchy specs of dust blocking the little hole into the probe, we don't know how they got through the filters (we suspect they may have come from our refurbished BCU05) but anyway removing this blockage sorted the problem.
Matthias Findeisen [findeis_at_rz.uni-leipzig.de]:
You are running into a diffusion problem.
You have to avoid diffiusion by short samples oder lower temperatures (if possible).
A good trick is to spin the sample (rotation about 20 Hz)
Genevieve Seabrook [gseabroo_at_uhnresearch.ca]:
About a month and a half ago I also got the message "echo time must be reduced" in Topspin gui. Then we totally lost the shims for some odd reason. After I re-shimmed the magnet this error message disappeared. I think it was the result of terrible shims in our case (so many users). I would suggest to put your sucrose sample in your magnet and shim you sample nicely. Then see if you still get this error message.
Please let me know what others say about it.
Thank you and good luck.
Mike Lumsden [mike.lumsden_at_dal.ca]:
Hi Weidong, my understanding is that when you get this message, it means the starting shims for your sample are quite bad. I don't think it is a topshim problem in any way.
Assuming you are getting this message on a nicely prepared sample, you should just do some manual shimming first and then rerun topshim. Another thing we do in our facility is read in a standard shim file for every new sample, which helps to minimize this issue.
Hope this helps,
Ilangovan, Udayar [Ilangovan_at_uthscsa.edu]:
We had the same problem last week when a user wanted to do the "topshim 2h 1d". So, while troubleshooting, I found out that he did not position the sample properly using the depth gauge. When the sample was positioned properly, topshim ran successfully without any error.
Hope this helps.
Craig Grimmer [grimmerc_at_ukzn.ac.za]:
I see this problem occasionally on my automation system, particularly with solvents with a relatively weak lock signal (CDCl3 most of the time). I queried this with Bruker recently and it was suggested that I increase the gas flow rate through the probe. I haven't seen the error since but it is an intermittent problem so that may be coincidental. Perhaps you might try this also.
Please post a follow-up on this topic.
**********end***********
From: Hu, Weidong
Sent: Friday, July 01, 2011 1:21 PM
To: ammrl_at_ammrl.org
Subject: topshim trouble shooting
Dear Colleagues,
We have an intermittent problem with topshim. It often complains like following:
"Performshimming-too many points lost during fit"
Checking the shim report through "topshim gui", it says "echo time must be reduced". I assumed this must be the second echo time is too long, and not enough signal left. I checked the default.par under /opt/topspin2.0/conf/instr/topshim/parameters, and found something like ##$DELAY= (0..7) with values of 0 0.13 0.64 300 900 0.5 5 3e-05 and ##DURMAX= (0..1) with values of 15 60. The other related one is ##$DE= 100. I am not sure which parameter I should change (reduce). After I change it, and save to a new file name say myshim.par. Should I just run "topshim myshim"?
Thank you very much for your input.
Dr. Weidong Hu, NMR Manager
Immunology Division, City of Hope National Medical Center
Tel: 626 256 4673, Ext. 63416, Fax: 626 301 8186
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Received on Wed Jul 13 2011 - 12:42:26 MST