[ccp4bb] Configuring remote servers with qsub
I'm having issues getting ccp4i2 to submit jobs to remote servers. I
would like to use qsub, but I have also tried ssh with no luck.
CCP4 is fully updated. Regardless of the method I try I get the
following error:
Traceback (most recent call last):
File "/share/apps/ccp4-7.0/share/ccp4i2/qtgui/CCP4ProjectViewer.py",
line 419, in runTask
self.taskFrame.inputFrame.runTask(mode)
File "/share/apps/ccp4-7.0/share/ccp4i2/qtgui/CCP4ProjectViewer.py",
line 2424, in runTask
self.runRemotely(jobId,projectId)
File "/share/apps/ccp4-7.0/share/ccp4i2/qtgui/CCP4ProjectViewer.py",
line 2561, in runRemotely
dialog.setInfo(message)
File "/share/apps/ccp4-7.0/share/ccp4i2/qtgui/CCP4JobControlGui.py",
line 286, in setInfo
if not self.widgets.has_key('info'):
AttributeError: 'CServerParamsDialog' object has no attribute 'widgets'
Seems like something is fundamentally wrong here. Maybe with qt version?
[ccp4bb] How to search 2 models (ensembles) in Molrep
Dear Crystallographers, How to search 2 models (ensembles) in Molrep for molecular replacement? It seems there is just one model input place in Molrep GUI. In Phaser MR, this can be done with clicking the "add ensemble" button to add another ensemble, but I am not sure how to do it in Molrep.
Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?
Something that could perhaps be of use here is what I like to call the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of mercury. According to the Food and Drug Administration website here in the USA the average mercury content of anchovies is 0.34 ppm, which is about 1 microgram per ounce of fish. Tuna can be higher, but varies a lot from fish to fish. My point here is that most institutions regard the amount of mercury you bring onsite for purposes of eating for lunch, be it sushi or pizza, as small enough to be negligible. I tend to agree. So, one could argue that 1 microgram of Hg per day is a "safe amount". Especially if you don't eat it. In terms of protein crystals, a 100 micron wide cube has a volume of 1 nanoliter, and if it were soaked to a final concentration of 50 mM Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng. So, 100 protein crystals soaked with Hg add up to roughly 1 APE. Please note that I am in no way encouraging you to eat your protein crystals, and especially not the solutions you soak them in. You should do your own APE calculations for those. But I do think it important to note just how tiny the amount of metal in our crystals really is. Now, mercury is purportedly the second-most-toxic metal after Plutonium. But Pu derivatives are uncommon. In fact, until recently (4zhd) Pu derivatives were unheard of. The authors I'm sure will tell you 4zhd involved no small amount of paperwork. But as long as you are not working with Pu, you can regard every other metal as less toxic than Hg. Another good example is selenium; by far the most common metal derivative. Although toxic, Se is also a dietary requirement. I suppose this is an excellent demonstration of what "moderation" really means. The Recommended Daily Allowance (RDA) of selenium in the USA for adult men and pregnant women is 55-60 micrograms per day. In crystals, one Se atom per 100 amino acids at 50% solvent comes to an overall concentration of 50 mM. So, a 100 micron crystal contains about 4 ng of Se. It would take 15,000 such crystals to add up to the US RDA. The synchrotrons I work at don't go thought that many crystals every day. But even if they did, I'd stick to my commercially available multivitamin to get my dietary selenium. So, although it is never a good idea to be sloppy with chemicals in the lab, I think it is also important to do the math and think about not just the toxicity of the things we work with on the bench, but the everyday items all around us. It is never a good idea to be antagonistic with regulators about such things. They are only trying to do their job, and all they are trained to know about are LD50s and how to stay as far below them as possible. A little gently-pointed-out insight into non-lethal applications of heavy metals can be helpful all around. The over-the-counter drug Pepto Bismol (bismuth subsalicylate) is almost 50% bismuth by weight, a metal that is right next to mercury on the periodic table. Brominated vegetable oil contains no bromine, by the way. And dandruff shampoos such as Selsun Blue make an excellent and surprisingly radiation-hard reference for the selenium edge. -James Holton MAD Scientist On 9/4/2017 3:13 AM, Dr Stephen Graham wrote: Hi all, (This email is aimed primarily at my UK colleagues, but feel free to read on and gloat that you don't have to write safety forms in your lab/country!). I need to sort out written risk assessments for heavy atom soaking of crystals in my lab. I wondered whether anyone would be willing to share the risk assessments they have in their institute/company so that I can seek inspiration and make sure I'm keeping up with best practice. Many thanks, Stephen
[ccp4bb] SOLVED: configuring remote servers with qsub. SSH port option
Of course, almost immediately after posting I described that I simply need to add "localhost" to the server section to get qsub to work. However, I think it would be useful if developers would add a port option for anything that requires ssh/scp. Many people avoid keeping ssh on port 22. Currently this is hardcoded in share/ccp4i2/core/CCP4JobServer.py.
Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?
James, What you wrote doesn't look like official risk assessment document. However, your essay is very informative and entertaining. Thank you. Regards, Vaheh Oganesyan www.medimmune.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton Sent: Wednesday, September 06, 2017 2:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Risk assessment for heavy atom soaking - examples? Something that could perhaps be of use here is what I like to call the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of mercury. According to the Food and Drug Administration website here in the USA the average mercury content of anchovies is 0.34 ppm, which is about 1 microgram per ounce of fish. Tuna can be higher, but varies a lot from fish to fish. My point here is that most institutions regard the amount of mercury you bring onsite for purposes of eating for lunch, be it sushi or pizza, as small enough to be negligible. I tend to agree. So, one could argue that 1 microgram of Hg per day is a "safe amount". Especially if you don't eat it. In terms of protein crystals, a 100 micron wide cube has a volume of 1 nanoliter, and if it were soaked to a final concentration of 50 mM Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng. So, 100 protein crystals soaked with Hg add up to roughly 1 APE. Please note that I am in no way encouraging you to eat your protein crystals, and especially not the solutions you soak them in. You should do your own APE calculations for those. But I do think it important to note just how tiny the amount of metal in our crystals really is. Now, mercury is purportedly the second-most-toxic metal after Plutonium. But Pu derivatives are uncommon. In fact, until recently (4zhd) Pu derivatives were unheard of. The authors I'm sure will tell you 4zhd involved no small amount of paperwork. But as long as you are not working with Pu, you can regard every other metal as less toxic than Hg. Another good example is selenium; by far the most common metal derivative. Although toxic, Se is also a dietary requirement. I suppose this is an excellent demonstration of what "moderation" really means. The Recommended Daily Allowance (RDA) of selenium in the USA for adult men and pregnant women is 55-60 micrograms per day. In crystals, one Se atom per 100 amino acids at 50% solvent comes to an overall concentration of 50 mM. So, a 100 micron crystal contains about 4 ng of Se. It would take 15,000 such crystals to add up to the US RDA. The synchrotrons I work at don't go thought that many crystals every day. But even if they did, I'd stick to my commercially available multivitamin to get my dietary selenium. So, although it is never a good idea to be sloppy with chemicals in the lab, I think it is also important to do the math and think about not just the toxicity of the things we work with on the bench, but the everyday items all around us. It is never a good idea to be antagonistic with regulators about such things. They are only trying to do their job, and all they are trained to know about are LD50s and how to stay as far below them as possible. A little gently-pointed-out insight into non-lethal applications of heavy metals can be helpful all around. The over-the-counter drug Pepto Bismol (bismuth subsalicylate) is almost 50% bismuth by weight, a metal that is right next to mercury on the periodic table. Brominated vegetable oil contains no bromine, by the way. And dandruff shampoos such as Selsun Blue make an excellent and surprisingly radiation-hard reference for the selenium edge. -James Holton MAD Scientist On 9/4/2017 3:13 AM, Dr Stephen Graham wrote: > Hi all, > > (This email is aimed primarily at my UK colleagues, but feel free to > read on and gloat that you don't have to write safety forms in your > lab/country!). > > I need to sort out written risk assessments for heavy atom soaking of > crystals in my lab. I wondered whether anyone would be willing to > share the risk assessments they have in their institute/company so > that I can seek inspiration and make sure I'm keeping up with best > practice. > > Many thanks, > > Stephen > To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?
Was just pointed out to me off-list that my anchovy data was off, so I just double-checked the FDA website: https://www.fda.gov/food/foodborneillnesscontaminants/metals/ucm115644.htm Turns out the latest number for anchovies is 0.016 ppm, or 0.5 ug per ounce (28g). So, if you use a whole 2 oz can, that's still ~ 1 microgram Hg as the Anchovie Pizza Equivalent. And it looks like one piece of bigeye tuna sushi could be as much as ~14g*1.816ppm = 25 APEs -James Holton MAD Scientist On 9/6/2017 11:44 AM, James Holton wrote: Something that could perhaps be of use here is what I like to call the "Anchovie Pizza Equivalent" (APE), which is about 1 microgram of mercury. According to the Food and Drug Administration website here in the USA the average mercury content of anchovies is 0.34 ppm, which is about 1 microgram per ounce of fish. Tuna can be higher, but varies a lot from fish to fish. My point here is that most institutions regard the amount of mercury you bring onsite for purposes of eating for lunch, be it sushi or pizza, as small enough to be negligible. I tend to agree. So, one could argue that 1 microgram of Hg per day is a "safe amount". Especially if you don't eat it. In terms of protein crystals, a 100 micron wide cube has a volume of 1 nanoliter, and if it were soaked to a final concentration of 50 mM Hg that is 1e-9 L * 50e-3 mol/L *200 g/mol = 10 ng. So, 100 protein crystals soaked with Hg add up to roughly 1 APE. Please note that I am in no way encouraging you to eat your protein crystals, and especially not the solutions you soak them in. You should do your own APE calculations for those. But I do think it important to note just how tiny the amount of metal in our crystals really is. Now, mercury is purportedly the second-most-toxic metal after Plutonium. But Pu derivatives are uncommon. In fact, until recently (4zhd) Pu derivatives were unheard of. The authors I'm sure will tell you 4zhd involved no small amount of paperwork. But as long as you are not working with Pu, you can regard every other metal as less toxic than Hg. Another good example is selenium; by far the most common metal derivative. Although toxic, Se is also a dietary requirement. I suppose this is an excellent demonstration of what "moderation" really means. The Recommended Daily Allowance (RDA) of selenium in the USA for adult men and pregnant women is 55-60 micrograms per day. In crystals, one Se atom per 100 amino acids at 50% solvent comes to an overall concentration of 50 mM. So, a 100 micron crystal contains about 4 ng of Se. It would take 15,000 such crystals to add up to the US RDA. The synchrotrons I work at don't go thought that many crystals every day. But even if they did, I'd stick to my commercially available multivitamin to get my dietary selenium. So, although it is never a good idea to be sloppy with chemicals in the lab, I think it is also important to do the math and think about not just the toxicity of the things we work with on the bench, but the everyday items all around us. It is never a good idea to be antagonistic with regulators about such things. They are only trying to do their job, and all they are trained to know about are LD50s and how to stay as far below them as possible. A little gently-pointed-out insight into non-lethal applications of heavy metals can be helpful all around. The over-the-counter drug Pepto Bismol (bismuth subsalicylate) is almost 50% bismuth by weight, a metal that is right next to mercury on the periodic table. Brominated vegetable oil contains no bromine, by the way. And dandruff shampoos such as Selsun Blue make an excellent and surprisingly radiation-hard reference for the selenium edge. -James Holton MAD Scientist On 9/4/2017 3:13 AM, Dr Stephen Graham wrote: Hi all, (This email is aimed primarily at my UK colleagues, but feel free to read on and gloat that you don't have to write safety forms in your lab/country!). I need to sort out written risk assessments for heavy atom soaking of crystals in my lab. I wondered whether anyone would be willing to share the risk assessments they have in their institute/company so that I can seek inspiration and make sure I'm keeping up with best practice. Many thanks, Stephen
[ccp4bb] Postdoc position to study membrane protein structure
The position A NIH-funded postdoctoral position is immediately available in the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School at Houston (https://med.uth.edu/bmb/research-centers/center-for-membrane-biology/). In collaboration with the group of Dr. John Spudich, the fellow will work in the lab of Dr. Lei Zheng to study the structure of channelrhodopsin proteins using X-ray crystallography and cryo-EM approaches. Channelrhodopsin proteins have become extremely powerful tools in optogenetic studies. The candidate will have an opportunity to work with new channelrhodopsin proteins recently identified in Dr. Spudich’s lab to study the molecular mechanisms of their novel ion conductivity and light-induced channel gating. See below link for project info: https://www.ncbi.nlm.nih.gov/pubmed/26113638 . The lab is located in the Texas Medical Center, the largest medical campus in the world, with great resources and environment for biomedical research. Houston is the 4th populous city in the United States and is highly international and dynamic. The candidate Qualified candidates should have a recent Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein is a big advantage. A successful candidate is expected to be highly skilled and self-motivated and is willing to work in a collaborative environment. Interested candidates should send a CV, one page research experience summary and contact information for three references to lei.zh...@uth.tmc.edu. Salary will compensate based on NIH standard and candidate’s experience. Starting date is negotiable. Lei Zheng, Ph.D. Associate Professor Center for Membrane Biology Department of Biochemistry and Molecular Biology University of Texas McGovern Medical School 6431 Fannin Street, MSB 6.218 (office), 6.408 (lab) Houston, TX 77030 Tel: 713-500-6083 (office), -7451 (lab)
Re: [ccp4bb] How to search 2 models (ensembles) in Molrep
Hmm - I will think tomorrow. MOLREP certainly can read NMR ensembles but there you have several models in one file each heading MODEL 1 ... MODEL 2 ... etc. Eleanor On 6 September 2017 at 19:32, Xiao Lei wrote: > Dear Crystallographers, > > How to search 2 models (ensembles) in Molrep for molecular replacement? > It seems there is just one model input place in Molrep GUI. In Phaser MR, > this can be done with clicking the "add ensemble" button to add another > ensemble, but I am not sure how to do it in Molrep. > > >
