[ccp4bb] chirality problem
Dear Users, I am facing difficulties to validate my structure according to PDB server. I have solved my structure and now want to submit in PDB but during validation process i have some chirality problem specially VAL and LEU amino acids there are total 18 amino acids which deviated from the chirality so how can i solve this problem. Any suggestion would be highly appreciated. Best Regards AFSHAN
Re: [ccp4bb] chirality problem
Hi Afshan, Just swap the (names of) the CD and CG atoms, no need for refinement. The CCP4 dictionary allows both chiralities for LEU and VAL, so Refmac won't detect the problem. The problem is still very real to many programs so it should be fixed. Cheers, Robbie Joosten Date: Thu, 5 Jan 2012 02:46:30 -0800 From: afshan...@yahoo.com Subject: [ccp4bb] chirality problem To: CCP4BB@JISCMAIL.AC.UK Dear Users, I am facing difficulties to validate my structure according to PDB server. I have solved my structure and now want to submit in PDB but during validation process i have some chirality problem specially VAL and LEU amino acids there are total 18 amino acids which deviated from the chirality so how can i solve this problem. Any suggestion would be highly appreciated. Best Regards AFSHAN
Re: [ccp4bb] From non-twinned to twinned?
Thanks. Your suggestion remind me that I forgot to mention one more information. Actually, I did try to shot different regions of crystal to reduce radiation damage. Say, the sca1 set used one region and the sca2 set used another. Is it possible that this two regions has different crystal domain arrangement (one is normal and another is twinned)? The crystal looks like a nice single crystal. Zhiyi On 1/5/12, Carlos Frazao fra...@itqb.unl.pt wrote: Hi If the beam cross section is significantly smaller then the crystal dimensions, when you rotate the crystal you will be constantly illuminating new volumes of the crystal. If the crystal contains differently oriented single crystal domains (that is indeed a twinned crystal) then you may have orientations where only one of those single crystal domains are being measured, and other orientations where multiple single crystal domains are collected. The same applies if you apply translations at the crystal (to collect data from fresh crystal regions to decrease the radiation damage effect). Hope it helps, cheers, Carlos Zhiyi Wei wrote: Thank you for all the quick reply. Here are the additional information about the crystal. The crystal was frozen and shot in synchrotron. The collection was 1degree/frame. The space group and unit cell are P21 and a=70 b=165 c=170 alpha=90 beta=90.1 gamma=90. I processed the data in P1 first (I did not see any abnormal changes during integration), and then merge them using P21 or P2221. P21 gives reasonable Rmerge of ~10% while P2221 has much higher Rmerge of ~30%. I reprocessed the data with mosflm using P1. And Pointless also suggested the space group of P21. Zhiyi On 1/5/12, Jens Kaiser kai...@caltech.edu wrote: What are your cell constants and space group? It sounds to me you misindexed and then artificially twinned your structure by integrating/merging in too high of a symmetry. I've seen that happen for primitive hexagonal which was actually C-centered monoclinic. Also, in my experience this is more likely to happen with denzo/scalepack as it refines every image and does postrefinement in scalepack. XDS will decide for you on a symmetry after integration, and in MOSFLM you should see earlier that something is wrong. HTH Jens On Wed, 2012-01-04 at 21:42 +0800, Zhiyi Wei wrote: Dear all, I recently collected a dataset (~2000 frames) from a single crystal. If merge first 600 frames (sca1) or last 600 frames (sca2), Rmerge values from scalepack seem to be ok (~10%) though rejection ratios are high (~5%). But if I merge all frames together, Rmerge value goes up to ~20% and rejection is extremely high (~20%). Then, I checked sca1 and sca2 by xtriage in phenix. Surprisingly, the logfiles told me that sca1 is no twining while sca2 is very likely to be twinned. I never met this case before. So, I am wondering if it is possible from a non-twinned structure to a twinned structure just due to radiation damage. If the answer is yes, does it mean that I should not collect a large number of frames to amplify anomalous signals by using this crystal? Thanks a lot! Best, Zhiyi -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt www.itqb.unl.pt
Re: [ccp4bb] live streaming of ccp4 study weekend
How is everyone finding the stream? It was extremely flaky this morning here, cutting out every 15-20 seconds. The afternoon session doesn't seem to be faring any different at this end, sadly. Just wondering if it is a problem at our end or theirs. cheers charlie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of charles.ball...@stfc.ac.uk Sent: 04 January 2012 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] live streaming of ccp4 study weekend Dear All for all those not lucky enough to attend the CCP4 Study Weekend on Data collection and processing in Warwick there will be live streaming. This is at the link http://extrplay.dl.ac.uk/ kicking off with the what's new session at 9:00am GMT. The main event starts at 11:00am GMT. The full program is at http://www.cse.scitech.ac.uk/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4
Re: [ccp4bb] live streaming of ccp4 study weekend
I can't get it to work on Firefox, Safari, or Chrome using a Mac with OS 10.6.8. David Mueller On 1/5/12 8:31 AM, Charles Allerston charles.allers...@sgc.ox.ac.uk wrote: How is everyone finding the stream? It was extremely flaky this morning here, cutting out every 15-20 seconds. The afternoon session doesn't seem to be faring any different at this end, sadly. Just wondering if it is a problem at our end or theirs. cheers charlie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of charles.ball...@stfc.ac.uk Sent: 04 January 2012 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] live streaming of ccp4 study weekend Dear All for all those not lucky enough to attend the CCP4 Study Weekend on Data collection and processing in Warwick there will be live streaming. This is at the link http://extrplay.dl.ac.uk/ kicking off with the what's new session at 9:00am GMT. The main event starts at 11:00am GMT. The full program is at http://www.cse.scitech.ac.uk/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4
Re: [ccp4bb] live streaming of ccp4 study weekend
Hi Charles, For both the morning (after I got up) and afternoon session slides have been fine - no video or audio though. A connection to the server could not be established :( Had to update my RealPlayer to a Nov 2011 release before seeing anything. Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Senior Scientist, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here! -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Charles Allerston Sent: Thursday, January 05, 2012 9:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] live streaming of ccp4 study weekend How is everyone finding the stream? It was extremely flaky this morning here, cutting out every 15-20 seconds. The afternoon session doesn't seem to be faring any different at this end, sadly. Just wondering if it is a problem at our end or theirs. cheers charlie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of charles.ball...@stfc.ac.uk Sent: 04 January 2012 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] live streaming of ccp4 study weekend Dear All for all those not lucky enough to attend the CCP4 Study Weekend on Data collection and processing in Warwick there will be live streaming. This is at the link http://extrplay.dl.ac.uk/ kicking off with the what's new session at 9:00am GMT. The main event starts at 11:00am GMT. The full program is at http://www.cse.scitech.ac.uk/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4
Re: [ccp4bb] live streaming of ccp4 study weekend
I also had the same problem, I could only get between 2-30secs at a time, whichever browser I used. I thought it might be my connection but maybe not if you're having the same problem. Will the videos be available for download afterwards? Hazel On Thu, 5 Jan 2012, Charles Allerston wrote: How is everyone finding the stream? It was extremely flaky this morning here, cutting out every 15-20 seconds. The afternoon session doesn't seem to be faring any different at this end, sadly. Just wondering if it is a problem at our end or theirs. cheers charlie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of charles.ball...@stfc.ac.uk Sent: 04 January 2012 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] live streaming of ccp4 study weekend Dear All for all those not lucky enough to attend the CCP4 Study Weekend on Data collection and processing in Warwick there will be live streaming. This is at the link http://extrplay.dl.ac.uk/ kicking off with the what's new session at 9:00am GMT. The main event starts at 11:00am GMT. The full program is at http://www.cse.scitech.ac.uk/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4 -- pi =3.14159265358979323846264338327950288419716939937510582097494459230781640628 62089986280348253421170679821480865132
Re: [ccp4bb] live streaming of ccp4 study weekend
The video works fine if you load http://extrplay.dl.ac.uk/CCP4/20120105-2/rnh.ram as a network stream into VLC (www.videolan.org) . Trying to play it with real player just didn't work. And VLC doesn't require your admin password to spew garbage all over your system. You don't get the jpg preview of the slides but at least the audio/video works on OS X 10.6.8. F On Jan 5, 2012, at 7:38 AM, David Mueller wrote: I can't get it to work on Firefox, Safari, or Chrome using a Mac with OS 10.6.8. David Mueller On 1/5/12 8:31 AM, Charles Allerston charles.allers...@sgc.ox.ac.uk wrote: How is everyone finding the stream? It was extremely flaky this morning here, cutting out every 15-20 seconds. The afternoon session doesn't seem to be faring any different at this end, sadly. Just wondering if it is a problem at our end or theirs. cheers charlie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of charles.ball...@stfc.ac.uk Sent: 04 January 2012 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] live streaming of ccp4 study weekend Dear All for all those not lucky enough to attend the CCP4 Study Weekend on Data collection and processing in Warwick there will be live streaming. This is at the link http://extrplay.dl.ac.uk/ kicking off with the what's new session at 9:00am GMT. The main event starts at 11:00am GMT. The full program is at http://www.cse.scitech.ac.uk/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4 - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] live streaming of ccp4 study weekend
For what it's worth, I get it on Firefox and Safari using a Mac with OS 10.6.8. The sound is fine but the slides don't update automatically. I have to hit reload at every slide. Keeps me awake. Andreas On 05/01/2012 2:38, David Mueller wrote: I can't get it to work on Firefox, Safari, or Chrome using a Mac with OS 10.6.8. David Mueller -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] From non-twinned to twinned?
On Thu, 2012-01-05 at 20:40 +0800, Zhiyi Wei wrote: Is it possible that this two regions has different crystal domain arrangement (one is normal and another is twinned)? Absolutely. This will, of course, vary for different crystal systems, but from what I have seen it appears that a different crystal section removed by ~50 micron behaves statistically as if it is a different crystal. This is with high quality crystals, so for more regular situation this can be even shorter. As far as nice single crystals go, looks may be deceiving. Twinned crystals often look great. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
