Re: [ccp4bb] Coot 0.9 curlew has no entry
Dear Paul, Thank you for your response and your time! In this case I will just try it again sometime later. Best, Chen On Mon, Jul 15, 2019 at 7:05 PM Paul Emsley wrote: > On 15/07/2019 12:37, Chen Zhao wrote: > > > > I am sorry to bother you, but I was trying to install the long range > refine, sphere refine, tandem refine, > > etc. utilities in coot 0.9 for cryo EM map. I was following the > instructions on the youtube video, however, > > when I typed in curlew() in python scripting interface, I got a > completely empty list. Does anyone know why > > this is happening? > > The Curlew function connects to the Coot web site to find the latest list > of extensions. However, I have > been unable to rebuild the web site since it was restored from backup > several days ago. I will try to get it > done this week. > > Regards, > > Paul. > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Coot 0.9 curlew has no entry
Dear all, I am sorry to bother you, but I was trying to install the long range refine, sphere refine, tandem refine, etc. utilities in coot 0.9 for cryo EM map. I was following the instructions on the youtube video, however, when I typed in curlew() in python scripting interface, I got a completely empty list. Does anyone know why this is happening? I appreciate all the inputs! Best, Chen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] COOT over SSH
Dear all, I have not been able to open COOT through SSH, in cases where COOT is version 0.8.9.2-pre-revision-7884 packaged with SBGrid mounted on a server running scientific linux. The error message is: Gtk-Message: Failed to load module "canberra-gtk-module" INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/data/monomers/ INFO:: Reading coordinate file: /programs/x86_64-linux/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb PDB file /programs/x86_64-linux/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 The program 'coot-bin' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue (integer parameter out of range for operation)'. (Details: serial 309 error_code 2 request_code 154 minor_code 3) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: Gtk-Message: Failed to load module "canberra-gtk-module" coot-exe: "/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/libexec/coot-bin" /usr/bin/ls coot-version: /programs/x86_64-linux/ccp4/7.0/ccp4-7.0/libexec/coot-bin platform: /usr/bin/uname core: #f No core file found. No debugging However, when I tried to locate canberra-gtk-module, I got the following output: locate libcanberra-gtk-module.so /usr/lib64/gtk-2.0/modules/libcanberra-gtk-module.so /usr/lib64/gtk-3.0/modules/libcanberra-gtk-module.so I tried to create a soft link of these files to /usr/lib but it did not solve the problem. Does anyone have any idea? Thanks a lot in advance, Chen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?
Thanks for everybody's suggestions! I finally fixed coot following Zhijie's suggestion, where I set "one window" mode in Xlaunch. For pymol, I just gave up... I am not sure whether the NVIDIA graphic card is making things more complicated... Best, Chen On Thu, Jul 2, 2015 at 1:29 AM, Zhijie Li wrote: > Hi Chen, > > I followed instructions on this page and it seems to be working: > > http://www.geo.mtu.edu/geoschem/docs/putty_install.html > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.geo.mtu.edu_geoschem_docs_putty-5Finstall.html&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=xfQGepyCVehabnXteqeg61Xem6P7gGu-1ba56BOC5wc&s=cgZAn_6jKDjQ-qmii2I1r5svq0nA403oEVm7Mite95I&e=> > > One thing I think is worth mentioning is that in Putty-connection-SSH-X11, > I put localhost:0.0 instead of 10.0, as for putty itself, it is requesting > from Xming for the use of display 0.0. > > For COOT, it seems that I have to set Xlaunch in “one window” mode or > simply run Xming.exe. But still there is some issue with refreshing the > screen when choosing menu items. > > My systems are CentOS 6.6 and Windows 7/Putty0.60/Xming6.9.0.31. > > Zhijie > > > > *From:* Chen Zhao > *Sent:* Wednesday, July 01, 2015 7:05 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a > windows client? > > Thank you Dale, but when I added " localhost:10.0" to X display > location, the problem still exist, just without the phrase "localhost:10.0" > in the warning. My X11 forwarding is enabled all the time and all other > GUIs work just fine. > > And thank you for your clarification on the concept of server and client > "in the X11 word". It makes a lot of sense and I just didn't give it a > second thought! > > Best, > Chen > > On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud > wrote: > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> >>Both the ssh client and server must be set up with "X11Forwarding >> yes". The message sounds like your local computer is not set up to >> accept X11 tunneling. (By the way, in the X11 world the remote system >> is the "client" and your local system the "server".) >> >> Dale Tronrud >> >> On 7/1/2015 3:40 PM, Chen Zhao wrote: >> > Hi all, >> > >> > Sorry to bother you, but I am trying to fix a long-standing problem >> > that I cannot run Coot and Pymol through Xming/PUTTY by SSH >> > connection on a windows client. The error messages are pretty >> > similar for both: Coot: PuTTY X11 proxy: unable to connect to >> > forwarded X server: Network error: Connection refused >> > (coot-real:23113): Gtk-WARNING **: cannot open display: >> > localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to >> > forwarded X server: Network error: Connection refused freeglut >> > (pymol): failed to open display 'localhost:10.0' >> > >> > Does anybody have some ideas? >> > >> > Thank you so much, Chen >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v2.0.22 (MingW32) >> >> iEYEARECAAYFAlWUbgYACgkQU5C0gGfAG10hVgCeLmuE4pHFrapu9biY9nHO/Bpi >> 5O8An17UN+hgpr7/6A+mny+XOBfJV/T5 >> =iTfz >> -END PGP SIGNATURE- >> > >
Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?
Thank you Dale, but when I added " localhost:10.0" to X display location, the problem still exist, just without the phrase "localhost:10.0" in the warning. My X11 forwarding is enabled all the time and all other GUIs work just fine. And thank you for your clarification on the concept of server and client "in the X11 word". It makes a lot of sense and I just didn't give it a second thought! Best, Chen On Wed, Jul 1, 2015 at 6:47 PM, Dale Tronrud wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > >Both the ssh client and server must be set up with "X11Forwarding > yes". The message sounds like your local computer is not set up to > accept X11 tunneling. (By the way, in the X11 world the remote system > is the "client" and your local system the "server".) > > Dale Tronrud > > On 7/1/2015 3:40 PM, Chen Zhao wrote: > > Hi all, > > > > Sorry to bother you, but I am trying to fix a long-standing problem > > that I cannot run Coot and Pymol through Xming/PUTTY by SSH > > connection on a windows client. The error messages are pretty > > similar for both: Coot: PuTTY X11 proxy: unable to connect to > > forwarded X server: Network error: Connection refused > > (coot-real:23113): Gtk-WARNING **: cannot open display: > > localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to > > forwarded X server: Network error: Connection refused freeglut > > (pymol): failed to open display 'localhost:10.0' > > > > Does anybody have some ideas? > > > > Thank you so much, Chen > -BEGIN PGP SIGNATURE- > Version: GnuPG v2.0.22 (MingW32) > > iEYEARECAAYFAlWUbgYACgkQU5C0gGfAG10hVgCeLmuE4pHFrapu9biY9nHO/Bpi > 5O8An17UN+hgpr7/6A+mny+XOBfJV/T5 > =iTfz > -END PGP SIGNATURE- >
[ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?
Hi all, Sorry to bother you, but I am trying to fix a long-standing problem that I cannot run Coot and Pymol through Xming/PUTTY by SSH connection on a windows client. The error messages are pretty similar for both: Coot: PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused (coot-real:23113): Gtk-WARNING **: cannot open display: localhost:10.0 Pymol: PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused freeglut (pymol): failed to open display 'localhost:10.0' Does anybody have some ideas? Thank you so much, Chen
Re: [ccp4bb] MOLREP self-rotation matrix
Hi Sacha, Thanks you for your advice! I tried it and it does work. And thank you for your effort on this tool. It is really helpful! Have a nice day, Chen On Wed, May 20, 2015 at 3:11 AM, Alexandre OURJOUMTSEV wrote: > Dear Chen, > > > > Thank you for your confirmation (it is a pleasure, not everybody does it!). > > > > I am glad that it works for you. > > Now, if you wish/can spend 5 minutes more, you may (see > http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/convrot/Convrot.html): > > - Do the same (I mean – compile) three other fortran programs > of that package > > - Correct THE FIRST LINE of convrot5.tcl so that it indicates > the correct PATH to the command 'wish' of the Tcl/tk libraries (directory > where you have this program at your computer) > > > > Then normally the GUI version should work; it is more convenient than the > on-line fortran version alone. > > > > We understand that this is an obsolete way working with programs and by > this reason we are finishing its more modern python version (practically > done…). As for everybody, the problem is absence of time to do this ! > > > > Have a nice day, and good luck ! > > > Sacha > > > > > > *De :* Chen Zhao [mailto:c.z...@yale.edu] > *Envoyé :* mardi 19 mai 2015 18:00 > *À :* Alexandre OURJOUMTSEV > *Objet :* Re: [ccp4bb] MOLREP self-rotation matrix > > > > Dear Sacha, > > I am able to run the program now. Thank you so much! > > Have a nice day, > > Chen > > >
Re: [ccp4bb] MOLREP self-rotation matrix
Hah, this sounds good. I will try it out! Thank you so much! Best, Chen On Tue, May 19, 2015 at 10:22 AM, Eleanor Dodson wrote: > Any set of coordinates will do .. > pdbset just converts the eulerian or polar angles to a matrix.. > > In the example I gave > rota euler 10 20 30 > > corresponds to matrix. > ( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) >( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) >( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) > > > On 19 May 2015 at 15:11, Chen Zhao wrote: > >> Hi Eleanor, >> >> Thank you so much for your test! However, I am not starting with a PDB >> file. What I am doing self-RF on is just the Patterson map. So my problem >> is to convert the output Euler angles to orthogonal matrix. >> >> Thanks a lot for your time, >> Chen >> >> On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson < >> eleanor.dod...@york.ac.uk> wrote: >> >>> Actually it is pretty easy: >>> >>> Here is the log of pdbset >>> >>> [ccp4@roo job_55]$ pdbset xyzin part.pdb >>> ... >>> >>> Logical name: XYZIN File name: part.pdb >>> PDB file is being opened on unit 1 for INPUT. >>> >>> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE >>> >>> >>> RF RO >>> >>> 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 >>>-0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 >>> 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 >>>-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 >>> >>> rota euler 10 20 30 >>> Data line--- rota euler 10 20 30 >>> end >>> Data line--- end >>> >>> Logical name: XYZOUT File name: XYZOUT >>> PDB file is being opened on unit 2 for OUTPUT. >>> >>> >>> Coordinates will be transformed as follows: >>> >>>( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) >>>( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) >>>( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) >>> >>> >>> >>> Of course you still have to worry about the orthogonalisation code used >>> for the SELFROT search. >>> >>> polarrfn tells you what is chosen >>> >>> For triclinic, orthorhombic ext the choice is usually >>> >>> Z || c* X || a and Y chosen to make an orthogonal set >>> >>> >>> But for monoclinic it is often set >>> >>> Z || b* X || a and Y chosen to make an orthogonal set >>> >>> Eleanor >>> >>> >>> >>> On 18 May 2015 at 18:57, Chen Zhao wrote: >>> >>>> Sorry for the spaming... Just want to correct that I plan to say covert >>>> the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... >>>> >>>> On Mon, May 18, 2015 at 1:44 PM, Chen Zhao wrote: >>>> >>>>> I got some answers from the previous thread: >>>>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html >>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.html&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36U&s=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQ&e=> >>>>> >>>>> But I just want to make sure what I am doing... >>>>> >>>>> Thanks a lot, >>>>> Chen >>>>> >>>>> On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote: >>>>> >>>>>> Hi Eleanor, >>>>>> >>>>>> Yeah, the relationship of the XYZ with the unit cell axes is tricky >>>>>> too. Although I can get some clues by looking at the position of the >>>>>> crystallographic symmetry axes on the XY plane, it is better if I could >>>>>> find a definite answer... >>>>>> >>>>>> Thank you, >>>>>> Chen >>>>>> >>>>>> On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson < >>>>>> eleanor.dod...@york.ac.uk> wrote: >>>>>> >>>>>>> Hmm - there are programs which give you the matrix associated with >>>>>>> Eulerian or Polar angles. I think one is pdbset.. >>>>>>> >>>>>>> Or there is documentation in polarrfn or rotmat which describes how >>>>>>> to do it.. >>>>>>> >>>>>>> But remember there are conventions about which axes correspond to >>>>>>> the orthogonal X Y Z axes used to define the angles >>>>>>> >>>>>>> Eleanor >>>>>>> >>>>>>> >>>>>>> On 18 May 2015 at 17:04, Chen Zhao wrote: >>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am now trying to convert the NCS axis expressed by theta, phi, >>>>>>>> chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in >>>>>>>> order to >>>>>>>> feed into SOLVE. Would anybody suggest me a correct way to do it? >>>>>>>> >>>>>>>> Thank you so much in advance! >>>>>>>> >>>>>>>> Best, >>>>>>>> Chen >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
Re: [ccp4bb] MOLREP self-rotation matrix
Hi Eleanor, Thank you so much for your test! However, I am not starting with a PDB file. What I am doing self-RF on is just the Patterson map. So my problem is to convert the output Euler angles to orthogonal matrix. Thanks a lot for your time, Chen On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson wrote: > Actually it is pretty easy: > > Here is the log of pdbset > > [ccp4@roo job_55]$ pdbset xyzin part.pdb > ... > > Logical name: XYZIN File name: part.pdb > PDB file is being opened on unit 1 for INPUT. > > MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE > > > RF RO > > 0.016 0.009 -0.000 -0.000 61.922 -30.961 0.000 -0.000 >-0.000 0.019 -0.000 0.0000.000 53.626 0.000 0.000 > 0.000 -0.000 0.004 0.0000.000 0.000 248.752 -0.000 >-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000 > > rota euler 10 20 30 > Data line--- rota euler 10 20 30 > end > Data line--- end > > Logical name: XYZOUT File name: XYZOUT > PDB file is being opened on unit 2 for OUTPUT. > > > Coordinates will be transformed as follows: > >( 0.714610 -0.613092 0.336824 ) ( x ) ( 0.000 ) >( 0.633718 0.771281 0.059391 ) ( y ) + ( 0.000 ) >( -0.296198 0.171010 0.939693 ) ( z ) ( 0.000 ) > > > > Of course you still have to worry about the orthogonalisation code used > for the SELFROT search. > > polarrfn tells you what is chosen > > For triclinic, orthorhombic ext the choice is usually > > Z || c* X || a and Y chosen to make an orthogonal set > > > But for monoclinic it is often set > > Z || b* X || a and Y chosen to make an orthogonal set > > Eleanor > > > > On 18 May 2015 at 18:57, Chen Zhao wrote: > >> Sorry for the spaming... Just want to correct that I plan to say covert >> the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... >> >> On Mon, May 18, 2015 at 1:44 PM, Chen Zhao wrote: >> >>> I got some answers from the previous thread: >>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.html&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36U&s=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQ&e=> >>> >>> But I just want to make sure what I am doing... >>> >>> Thanks a lot, >>> Chen >>> >>> On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote: >>> >>>> Hi Eleanor, >>>> >>>> Yeah, the relationship of the XYZ with the unit cell axes is tricky >>>> too. Although I can get some clues by looking at the position of the >>>> crystallographic symmetry axes on the XY plane, it is better if I could >>>> find a definite answer... >>>> >>>> Thank you, >>>> Chen >>>> >>>> On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson < >>>> eleanor.dod...@york.ac.uk> wrote: >>>> >>>>> Hmm - there are programs which give you the matrix associated with >>>>> Eulerian or Polar angles. I think one is pdbset.. >>>>> >>>>> Or there is documentation in polarrfn or rotmat which describes how to >>>>> do it.. >>>>> >>>>> But remember there are conventions about which axes correspond to the >>>>> orthogonal X Y Z axes used to define the angles >>>>> >>>>> Eleanor >>>>> >>>>> >>>>> On 18 May 2015 at 17:04, Chen Zhao wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I am now trying to convert the NCS axis expressed by theta, phi, chi >>>>>> (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to >>>>>> feed into SOLVE. Would anybody suggest me a correct way to do it? >>>>>> >>>>>> Thank you so much in advance! >>>>>> >>>>>> Best, >>>>>> Chen >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
Re: [ccp4bb] MOLREP self-rotation matrix
Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao wrote: > I got some answers from the previous thread: > https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html > > But I just want to make sure what I am doing... > > Thanks a lot, > Chen > > On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote: > >> Hi Eleanor, >> >> Yeah, the relationship of the XYZ with the unit cell axes is tricky too. >> Although I can get some clues by looking at the position of the >> crystallographic symmetry axes on the XY plane, it is better if I could >> find a definite answer... >> >> Thank you, >> Chen >> >> On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson < >> eleanor.dod...@york.ac.uk> wrote: >> >>> Hmm - there are programs which give you the matrix associated with >>> Eulerian or Polar angles. I think one is pdbset.. >>> >>> Or there is documentation in polarrfn or rotmat which describes how to >>> do it.. >>> >>> But remember there are conventions about which axes correspond to the >>> orthogonal X Y Z axes used to define the angles >>> >>> Eleanor >>> >>> >>> On 18 May 2015 at 17:04, Chen Zhao wrote: >>> >>>> Hi all, >>>> >>>> I am now trying to convert the NCS axis expressed by theta, phi, chi >>>> (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to >>>> feed into SOLVE. Would anybody suggest me a correct way to do it? >>>> >>>> Thank you so much in advance! >>>> >>>> Best, >>>> Chen >>>> >>>> >>>> >>> >> >
Re: [ccp4bb] MOLREP self-rotation matrix
I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote: > Hi Eleanor, > > Yeah, the relationship of the XYZ with the unit cell axes is tricky too. > Although I can get some clues by looking at the position of the > crystallographic symmetry axes on the XY plane, it is better if I could > find a definite answer... > > Thank you, > Chen > > On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson > wrote: > >> Hmm - there are programs which give you the matrix associated with >> Eulerian or Polar angles. I think one is pdbset.. >> >> Or there is documentation in polarrfn or rotmat which describes how to do >> it.. >> >> But remember there are conventions about which axes correspond to the >> orthogonal X Y Z axes used to define the angles >> >> Eleanor >> >> >> On 18 May 2015 at 17:04, Chen Zhao wrote: >> >>> Hi all, >>> >>> I am now trying to convert the NCS axis expressed by theta, phi, chi (or >>> alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed >>> into SOLVE. Would anybody suggest me a correct way to do it? >>> >>> Thank you so much in advance! >>> >>> Best, >>> Chen >>> >>> >>> >> >
Re: [ccp4bb] MOLREP self-rotation matrix
Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson wrote: > Hmm - there are programs which give you the matrix associated with > Eulerian or Polar angles. I think one is pdbset.. > > Or there is documentation in polarrfn or rotmat which describes how to do > it.. > > But remember there are conventions about which axes correspond to the > orthogonal X Y Z axes used to define the angles > > Eleanor > > > On 18 May 2015 at 17:04, Chen Zhao wrote: > >> Hi all, >> >> I am now trying to convert the NCS axis expressed by theta, phi, chi (or >> alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed >> into SOLVE. Would anybody suggest me a correct way to do it? >> >> Thank you so much in advance! >> >> Best, >> Chen >> >> >> >
[ccp4bb] MOLREP self-rotation matrix
Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
[ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination
From: Chen Zhao Date: Thu, May 14, 2015 at 10:04 AM Subject: Re: [ccp4bb] XDS Rmeas in space group determination To: Kay Diederichs Hi Kay, Thanks a lot for your reply! I am a little surprised to learn that the centrosymmetry is always considered as a point groups symmetry component. That might explain why all the anomalous data I have seen have higher Rmeas than their native counterpart. I looked at both points you suggested and I found that the high Rmeas is because of radiation damage... Sorry about missing this point... But it is good for me to learn how the Friedel pairs are treated as equal in point group determination. Thank you very much, Chen On Thu, May 14, 2015 at 3:18 AM, Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Hi Chen, > > if Rmeas is high (like 50 and up) even in P1 then maybe the integration > was not right, or the indexing is offset by 1 in h or k or l ? > > To check the former, look at FRAME.cbf and see if the predictions match > the spots. > > To test the latter try > echo CENTRE | pointless XDS_ASCII.HKL > > best, > > Kay > > P.S. in XDS's space group determination, Friedels are indeed considered > symmetry-related. > > On Wed, 13 May 2015 19:24:30 -0400, Chen Zhao wrote: > > >> Hi Ethan, > >> > >> Thanks a lot for your detailed information. I am aware that in IDXREF > only the lattice symmetry was tried to be determined. I went back to check > the subtrees in IDXREF because even for P1 the Rmeas is very high, meaning > that the multiple measurements for the same reflections are already very > imprecise (test resolution 10-5). I therefore am worried about multiple > lattices. > >> > >> Also related to the probability thing you talked about, there is no > point group has significantly low Rmeas in this case. Or it is just because > even P1 has high Rmeas, so that the highest point group tried were > considered to be correct? If so, it sounds hard to determine the point > group in this case... > >> > >> Thank you so much, > >> Chen > >> > >> > >>>> On May 13, 2015, at 6:48 PM, Ethan A Merritt < > merr...@u.washington.edu> wrote: > >>>> > >>>> On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote: > >>>> Hi Ethan, > >>> > >>> Sorry, I'm coming in late on this so I might have missed an > >>> earlier explanation of exactly what programs are involved. > >>> > >>> > >>>> Yes. My question was simply whether it calculates the statistics > >>> > >>>> from completely unmerged intensities and just compare say h,k,l with > -h,-k,l (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe > so... > >>> > >>> What is "it"? > >>> > >>> If you mean the tables in IDXREF.LP, they only report the fit of points > >>> to a particular lattice. They do not compare the intensities of > >>> potential symmetry mates. Quoting from the program output: > >>> > >>> Note, that reflection integration is based only on orientation and > metric > >>> of the lattice. It does not require knowledge of the correct space > group! > >>> Thus, if no such information is provided by the user in XDS.INP, > >>> reflections are integrated assuming a triclinic reduced cell lattice; > >>> the space group is assigned automatically or by the user in the last > >>> step (CORRECT) when integrated intensities are available. > >>> > >>> If you mean the output from a later run of pointless/aimless, > >>> so far as I know it applies the symmetry operation being tested > >>> to all reflections, which means that Friedel/Bijvoet pairs are > >>> not compared. But I could be wrong on that point. > >>> > >>>> And what is a good number? Is 20 % OK? What about 30 % and even > higher? > >>> > >>> Still refering to output from pointless/aimless, the crucial point is > not > >>> the absolute number but rather how the agreement for the symmetry > operation > >>> being tested compares to the agreement for the identity operation. > >>> > >>> For example, here is the output for a lousy data set with a real > 2-fold: > >>> > >>> % > >>> Scores for each symmetry element > >>> > >>> Nelmt Lklhd Z-ccCCN RmeasSymmetry & operator (in > Lattice Cel
[ccp4bb] XDS Rmeas in space group determination
> Hi Ethan,
>
> Thanks a lot for your detailed information. I am aware that in IDXREF only
> the lattice symmetry was tried to be determined. I went back to check the
> subtrees in IDXREF because even for P1 the Rmeas is very high, meaning that
> the multiple measurements for the same reflections are already very imprecise
> (test resolution 10-5). I therefore am worried about multiple lattices.
>
> Also related to the probability thing you talked about, there is no point
> group has significantly low Rmeas in this case. Or it is just because even P1
> has high Rmeas, so that the highest point group tried were considered to be
> correct? If so, it sounds hard to determine the point group in this case...
>
> Thank you so much,
> Chen
>
>
>>> On May 13, 2015, at 6:48 PM, Ethan A Merritt
>>> wrote:
>>>
>>> On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote:
>>> Hi Ethan,
>>
>> Sorry, I'm coming in late on this so I might have missed an
>> earlier explanation of exactly what programs are involved.
>>
>>
>>> Yes. My question was simply whether it calculates the statistics
>>
>>> from completely unmerged intensities and just compare say h,k,l with
>>> -h,-k,l (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe
>>> so...
>>
>> What is "it"?
>>
>> If you mean the tables in IDXREF.LP, they only report the fit of points
>> to a particular lattice. They do not compare the intensities of
>> potential symmetry mates. Quoting from the program output:
>>
>> Note, that reflection integration is based only on orientation and metric
>> of the lattice. It does not require knowledge of the correct space group!
>> Thus, if no such information is provided by the user in XDS.INP,
>> reflections are integrated assuming a triclinic reduced cell lattice;
>> the space group is assigned automatically or by the user in the last
>> step (CORRECT) when integrated intensities are available.
>>
>> If you mean the output from a later run of pointless/aimless,
>> so far as I know it applies the symmetry operation being tested
>> to all reflections, which means that Friedel/Bijvoet pairs are
>> not compared. But I could be wrong on that point.
>>
>>> And what is a good number? Is 20 % OK? What about 30 % and even higher?
>>
>> Still refering to output from pointless/aimless, the crucial point is not
>> the absolute number but rather how the agreement for the symmetry operation
>> being tested compares to the agreement for the identity operation.
>>
>> For example, here is the output for a lousy data set with a real 2-fold:
>>
>> %
>> Scores for each symmetry element
>>
>> Nelmt Lklhd Z-ccCCN RmeasSymmetry & operator (in Lattice
>> Cell)
>>
>> 1 0.806 6.97 0.70 17852 0.516 identity
>> 2 0.919 7.67 0.77 21302 0.486 *** 2-fold k ( 0 1 0) {-h,k,-l}
>>
>> [snip]
>>
>> Laue Group Lklhd NetZc Zc+ Zc-CCCC- Rmeas R- Delta
>> ReindexOperator
>>
>> 1 P 1 2/m 1 *** 0.919 7.30 7.30 0.00 0.73 0.00 0.50 0.00 0.1
>> [-h,-l,-k]
>> 2 P -1 0.081 -0.69 6.97 7.67 0.70 0.77 0.52 0.49 0.0
>> [h,-k,-l]
>> %%
>>
>> In this case the program reports a 0.91 likelihood that the Laue
>> group is P2 even though the Rmeas is horrible.
>>
>> Ethan
>>
>>
>>> Thanks a lot,
>>> Chen
>>>
>>>
>>>>> On May 13, 2015, at 6:07 PM, Ethan A Merritt
>>>>> wrote:
>>>>>
>>>>> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
>>>>> Hi all,
>>>>>
>>>>> I am sorry about this question which I should have figured out earlier.
>>>>> For
>>>>> point group determination, does the Rmeas consider Fridel pairs
>>>>> differently?
>>>>
>>>> A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
>>>> This pairing is independent of space group.
>>>> So the agreement or lack of agreement between Friedel pairs is
>>>> not informative about selection of point group or space group.
>>>>
>>>> You may be thinking of a Bijvoet pair, which consists of
>>>> [hkl] and the Friedel mate of some symmetry equivalent of [hkl]
>
Re: [ccp4bb] XDS Rmeas in space group determination
Hi Ethan, Yes. My question was simply whether it calculates the statistics from completely unmerged intensities and just compare say h,k,l with -h,-k,l (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe so... And what is a good number? Is 20 % OK? What about 30 % and even higher? Thanks a lot, Chen > On May 13, 2015, at 6:07 PM, Ethan A Merritt wrote: > >> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote: >> Hi all, >> >> I am sorry about this question which I should have figured out earlier. For >> point group determination, does the Rmeas consider Fridel pairs >> differently? > > A Friedel pair consists of the [hkl] and [-h-k-l] reflections. > This pairing is independent of space group. > So the agreement or lack of agreement between Friedel pairs is > not informative about selection of point group or space group. > > You may be thinking of a Bijvoet pair, which consists of > [hkl] and the Friedel mate of some symmetry equivalent of [hkl] > within a particular spacegroup. > > But even in the presence of anomalous scattering I think that > Bijvoet pairs are expected to agree with each other better than > with a reflection not related by point group symmetry. > >> (although I think it should be...) This is because I saw a >> derivative dataset collected at peak (from a demo) whose Rmeas is quite >> high (>50 %) for all the space groups tested (including P1). However, the >> native dataset has only <10 % Rmeas. Should I worry about the derivative >> dataset? There seems to be multiple lattices in both datasets based on >> IDXREF. >> >> You inputs are really appreciated! >> >> Sincerely, >> Chen > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 >
[ccp4bb] XDS Rmeas in space group determination
Hi all, I am sorry about this question which I should have figured out earlier. For point group determination, does the Rmeas consider Fridel pairs differently? (although I think it should be...) This is because I saw a derivative dataset collected at peak (from a demo) whose Rmeas is quite high (>50 %) for all the space groups tested (including P1). However, the native dataset has only <10 % Rmeas. Should I worry about the derivative dataset? There seems to be multiple lattices in both datasets based on IDXREF. You inputs are really appreciated! Sincerely, Chen
Re: [ccp4bb] shelxd memory error
Hi Tim, Thanks a lot for your suggestion! I tried different versions later, and I found that the newest version doesn't work, but an old version works... I have no idea what is wrong, but anyway it is working now, and it is related to version... Thank you so much, Chen On Wed, May 13, 2015 at 3:02 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Chen, > > the fact that you differentiate between mp and non-mp version of > shelxd makes me assume you have a rather old version of shelxd > installed. Can you try again with the latest version of shelxd and > report if the (or any) error persists? > > Best regards, > Tim > > On 05/13/2015 04:26 AM, Chen Zhao wrote: > > Just an update. If I run shelxd from the command line the same > > error appears. However, if I change the shelxd to the mp version, > > the command line works but the hkl2map still doesn't work. I am > > more confused now. > > > > Your input is greatly appreciated! > > > > Best, Chen > > > > On Tue, May 12, 2015 at 5:11 PM, Chen Zhao > > wrote: > > > >> Hi all, > >> > >> I encountered a problem with shelxd (in hkl2map gui) installed in > >> a flash drive running 32 bit Ubuntu OS. > >> > >> The error message is: OMP: Error #29: Unable to set OMP thread > >> stack size to 268435456 OMP:System error #12: Cannot allocate > >> memory OMP:Hint: Try decreasing OMP_STACKSIZE > >> > >> The $OMP_STACKSIZE is 256m. However, other flash drives that are > >> supposed to be the same (cloned from the same parent flash drive, > >> although it is a while ago and somebody else used it and I don't > >> know what he did) also have $OMP_STACKSZIE as 256m. Could anybody > >> give me some clue on how to solve this problem? > >> > >> Sincerely, Chen > >> > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1 > > iD8DBQFVUvcMUxlJ7aRr7hoRAmgyAJ9fn7JA9eRPkhFngVa9DTIF4wajHwCgro2p > 6ELNQngITxTWQ7b61j+S7M4= > =Hh/O > -END PGP SIGNATURE- >
Re: [ccp4bb] shelxd memory error
Just an update. If I run shelxd from the command line the same error appears. However, if I change the shelxd to the mp version, the command line works but the hkl2map still doesn't work. I am more confused now. Your input is greatly appreciated! Best, Chen On Tue, May 12, 2015 at 5:11 PM, Chen Zhao wrote: > Hi all, > > I encountered a problem with shelxd (in hkl2map gui) installed in a flash > drive running 32 bit Ubuntu OS. > > The error message is: > OMP: Error #29: Unable to set OMP thread stack size to 268435456 > OMP:System error #12: Cannot allocate memory > OMP:Hint: Try decreasing OMP_STACKSIZE > > The $OMP_STACKSIZE is 256m. However, other flash drives that are supposed > to be the same (cloned from the same parent flash drive, although it is a > while ago and somebody else used it and I don't know what he did) also have > $OMP_STACKSZIE as 256m. Could anybody give me some clue on how to solve > this problem? > > Sincerely, > Chen >
[ccp4bb] shelxd memory error
Hi all, I encountered a problem with shelxd (in hkl2map gui) installed in a flash drive running 32 bit Ubuntu OS. The error message is: OMP: Error #29: Unable to set OMP thread stack size to 268435456 OMP:System error #12: Cannot allocate memory OMP:Hint: Try decreasing OMP_STACKSIZE The $OMP_STACKSIZE is 256m. However, other flash drives that are supposed to be the same (cloned from the same parent flash drive, although it is a while ago and somebody else used it and I don't know what he did) also have $OMP_STACKSZIE as 256m. Could anybody give me some clue on how to solve this problem? Sincerely, Chen
[ccp4bb] Clear project history
Hi all, Sorry for this small technical question. Would anyone tell me a simple way to clear all project history in CCP4? Where is the file recording this history stored? Thank you for your help! Best, Chen
Re: [ccp4bb] off topic: measuring angle between two nucleic acid helices
Hi Almudena, You can extract the vector for the helical aixs by 3DNA, and then calculate the angle between the vectors. I hope this help! Best, Chen On Wed, Mar 4, 2015 at 1:12 PM, Pavel Afonine wrote: > > I would like to ask if any of you know how to measure the angle between >> two nucleic acid helices? I am trying with pymol, but have not found a >> solution to it yet. >> > > phenix.angle might help, with or without effort on your side. > Pavel >
Re: [ccp4bb] A basic question about Fourier Transform
Dear Ethan, Zhijie and Keller, Thank you so much for your detailed reply! Now I think I have a much deeper view of this problem and understand the relationship between X-ray, XFEL and EM much better. I did learned a lot from your replies! Best, Chen On Wed, Jan 21, 2015 at 7:51 AM, Keller, Jacob wrote: > Phases can be deduced mathematically from a continuous transform, a la > David Sayre’s and others’ work. Compared to a crystallographic pattern, a > continuous pattern has huge amounts of information—every pixel (roxel?) > would be equivalent to a reflection, so instead of having ~10^4-5 data > points you would have, say, 10^8-12, all to define ~10^3-4 atoms. And no > b-factors to fit at 100K, since the molecule would not be moving at that > temp. Of course this would be totally impossible to actually measure, at > least for now (!). > > > > JPK > > > > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Chen > Zhao > *Sent:* Tuesday, January 20, 2015 11:47 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] A basic question about Fourier Transform > > > > Dear Steven, > > Thank you for your reply! I understand that it is nearly impossible to > measure the diffraction of a single molecule, and I am just bringing this > up as a thought experiment to help understand the basics in > crystallography. But I never thought that some molecules actually allow > such measurement because you can burn it over and over again without severe > damage. Thanks a lot for this piece of information. > > But for the phase problem, the difference is that, you can have magnetic > lens for the electrons in EM, but you cannot have any lenses for X-ray > beam. This is why I am still confused about this point. > > Thanks a lot again, > > Chen > > > > On Tue, Jan 20, 2015 at 11:21 PM, Steven Chou > wrote: > > I would say you cannot measure the diffraction pattern of a single > biological molecule accurately thus far, because biological molecules are > not strong scatters and can be damaged easily. For other molecules, > actually you can! > > In high-resolution electron microscopy, the diffraction pattern in the > back focal plane is actually the diffraction pattern of a projection of > your sample, which is usually composed of one to several hundred biological > molecules. For biological molecules, this pattern usually is dampened to > almost zero at a resolution between 30A-4A (actual resolution, not > theoretical); for some metal compounds, the resolution can reach up to 1 A, > or even better. > > The diffraction pattern in the back focal plane is the Fourier transform > (achieved by a convex lens) of the a 2D projection of your sample. If you > apply another Fourier transform (using another convex lens) to the > diffraction pattern, you can get the 2D image of your sample (which > contains both amplitude and phase). That is, in single particle EM (imaging > mode), people don't have the phase problem. In diffraction mode (2D > electron crystallography), only the diffraction pattern (intensity) is > recorded, so they also have the phase problem. > > > > HTH, > > > > Steven > > > > On Tue, Jan 20, 2015 at 10:18 PM, Chen Zhao wrote: > > Dear all, > > I am sorry about this slightly off-topic question. I am now a graduate TA > for crystallography course and one student asked me a question that I > didn't ask myself before. I don't have enough knowledge to precisely answer > this question, so I am seeking for help here. > > The question is, as I rephrased it, assuming we are able to measure the > diffraction pattern of a single molecule with acceptable accuracy and > precision (comparable to what we have now for the common crystals), is it > better than we measure the diffraction spots from a crystal, given that the > spots are just a sampling of the continuous pattern from a single molecule > and there is loss of information in the space between the spots that are > not sampled by the lattice? Of course this is more of a thought experiment, > so we don't need to consider that all measurement is discrete in nature > owing to the limitation of the pixel size. I kinda agree with him and I > have a feeling that this is related to the sampling theorem. I do > appreciate your valuable comments. If this is not true, why? If this is > true, what is its effect on electron density? > > Thank you so much for your attention and your help in advance! > > Best, > Chen > > > > -- > > Steven Chou > > > > > > >
Re: [ccp4bb] A basic question about Fourier Transform
Dear Steven, Thank you for your reply! I understand that it is nearly impossible to measure the diffraction of a single molecule, and I am just bringing this up as a thought experiment to help understand the basics in crystallography. But I never thought that some molecules actually allow such measurement because you can burn it over and over again without severe damage. Thanks a lot for this piece of information. But for the phase problem, the difference is that, you can have magnetic lens for the electrons in EM, but you cannot have any lenses for X-ray beam. This is why I am still confused about this point. Thanks a lot again, Chen On Tue, Jan 20, 2015 at 11:21 PM, Steven Chou wrote: > I would say you cannot measure the diffraction pattern of a single > biological molecule accurately thus far, because biological molecules are > not strong scatters and can be damaged easily. For other molecules, > actually you can! > > In high-resolution electron microscopy, the diffraction pattern in the > back focal plane is actually the diffraction pattern of a projection of > your sample, which is usually composed of one to several hundred biological > molecules. For biological molecules, this pattern usually is dampened to > almost zero at a resolution between 30A-4A (actual resolution, not > theoretical); for some metal compounds, the resolution can reach up to 1 A, > or even better. > > The diffraction pattern in the back focal plane is the Fourier transform > (achieved by a convex lens) of the a 2D projection of your sample. If you > apply another Fourier transform (using another convex lens) to the > diffraction pattern, you can get the 2D image of your sample (which > contains both amplitude and phase). That is, in single particle EM (imaging > mode), people don't have the phase problem. In diffraction mode (2D > electron crystallography), only the diffraction pattern (intensity) is > recorded, so they also have the phase problem. > > > HTH, > > Steven > > On Tue, Jan 20, 2015 at 10:18 PM, Chen Zhao wrote: > >> Dear all, >> >> I am sorry about this slightly off-topic question. I am now a graduate TA >> for crystallography course and one student asked me a question that I >> didn't ask myself before. I don't have enough knowledge to precisely answer >> this question, so I am seeking for help here. >> >> The question is, as I rephrased it, assuming we are able to measure the >> diffraction pattern of a single molecule with acceptable accuracy and >> precision (comparable to what we have now for the common crystals), is it >> better than we measure the diffraction spots from a crystal, given that the >> spots are just a sampling of the continuous pattern from a single molecule >> and there is loss of information in the space between the spots that are >> not sampled by the lattice? Of course this is more of a thought experiment, >> so we don't need to consider that all measurement is discrete in nature >> owing to the limitation of the pixel size. I kinda agree with him and I >> have a feeling that this is related to the sampling theorem. I do >> appreciate your valuable comments. If this is not true, why? If this is >> true, what is its effect on electron density? >> >> Thank you so much for your attention and your help in advance! >> >> Best, >> Chen >> > > > > -- > Steven Chou > > >
Re: [ccp4bb] A basic question about Fourier Transform
Hi Jacob, Thanks a lot for your reply! Yes, by comparable data quality I did mean the comparable resolution and SNR. I now understand the original question and kinda confirm what I thought. But I am also learning myself and I don't quite get why the continuous sampling would get rid of the phase problem. My first thought would be that mathematically speaking, the difference between solving the structure from a crystal diffraction pattern and solving the structure from a single molecule diffraction pattern only means the transition from a discrete Fourier summation to a continuous Fourier integral, but the phase term is always there. I am sorry for my lack of knowledge and I only knew the very basics in the sampling theorem many years ago. Another related question is, do different crystal lattices sample the reciprocal space equally well (or lose the same amount of information)? My intuition is yes because of the symmetry in the real space stays in the reciprocal space, but maybe I am wrong. Sorry for keeping bothering, Chen On Tue, Jan 20, 2015 at 10:41 PM, Keller, Jacob wrote: > >The question is, as I rephrased it, assuming we are able to measure > the diffraction pattern of a single molecule with acceptable accuracy and > precision (comparable to what we have now for the common crystals), is it > better than we measure the diffraction spots from a crystal, given that the > spots are just a sampling of the continuous pattern from a single molecule > and there is loss of information in the space between the spots that are > not sampled by the lattice? Of course this is more of a thought experiment, > so we don't need to consider that all measurement is discrete in nature > owing to the limitation of the pixel size. I kinda agree with him and I > have a feeling that this is related to the sampling theorem. I do > appreciate your valuable comments. If this is not true, why? If this is > true, what is its effect on electron density? > > This question depends on how you set your criteria for the goodness of > the single-molecule data; in a way by saying the data quality is comparable > to crystals, the question is tautological, since the cases would by > stipulation be the same. If you mean the resolution would be equal, and all > amplitudes would be of SNR similar to crystal data, of course the > continuously-sampled version would be far better. There would be no phase > problem (sampling theorem), and maps would be outstanding. > > > > This type of thing was, I think, the original vision of the XFEL > projects—you could check out those early papers for more details. > > > > JPK > > > > >
[ccp4bb] A basic question about Fourier Transform
Dear all, I am sorry about this slightly off-topic question. I am now a graduate TA for crystallography course and one student asked me a question that I didn't ask myself before. I don't have enough knowledge to precisely answer this question, so I am seeking for help here. The question is, as I rephrased it, assuming we are able to measure the diffraction pattern of a single molecule with acceptable accuracy and precision (comparable to what we have now for the common crystals), is it better than we measure the diffraction spots from a crystal, given that the spots are just a sampling of the continuous pattern from a single molecule and there is loss of information in the space between the spots that are not sampled by the lattice? Of course this is more of a thought experiment, so we don't need to consider that all measurement is discrete in nature owing to the limitation of the pixel size. I kinda agree with him and I have a feeling that this is related to the sampling theorem. I do appreciate your valuable comments. If this is not true, why? If this is true, what is its effect on electron density? Thank you so much for your attention and your help in advance! Best, Chen
Re: [ccp4bb] PROSMART spectrum bar
Dear Robert, These are great and all I want! Thank you for your PROSMART and it is really a nice tool. Best, Chen On Sun, Dec 14, 2014 at 5:05 AM, Robert Nicholls wrote: > > Hi Chen, > > could anybody suggest me an easy way to generate the spectrum bar for the > color-coded residue-wise scores? Generating a spectrum bar in Pymol seems > nontrivial to me… > > > There are some HTML/javascript files that will allow you to reproduce the > horizontal and vertical legends seen in the ProSMART publications. I've > made them available from our website, but here's a direct link: > > > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/docs/prosmart_legends.tar.gz > > You can open the "legend.html" file in a web browser, then zoom in and/or > export to whatever format you want. You can edit the "legend.css" file if > you want to adjust the text font. You can edit the values in the top of the > "legend.js" file in order to change the legend scale and colours so that > they correspond to your ProSMART run (if you have adjusted these > parameters). I hope this is an acceptable solution for you. Let me know if > you need further help with this. > > BTW, here is a rather unrelated question. what does the white color > represent (in default color setting)? Does it mean the residues that are > not included in the analysis? > > > You are correct. The white colour represents residues that were not > included in the analysis - these were not matched to any residues in the > other model. > > I might be careless, but I failed to find a documentation for this. > > > I'd say that the best resource for providing practical usage info is the > tutorial that's available from our website (see part 2 of the tutorial): > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > I'll try to update and expand on the documentation soon to help clarify > such issues. > > Best regards, > Rob > > > -- > Dr Robert A Nicholls > Career Development Fellow > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH > 07729 202999 > > > On 13 Dec 2014, at 23:55, Chen Zhao wrote: > > Hi all, > > Sorry for bothering you with this small technical question. I just got to > know PROSMART as a handy local structural alignment tool. But could anybody > suggest me an easy way to generate the spectrum bar for the color-coded > residue-wise scores? Generating a spectrum bar in Pymol seems nontrivial to > me... > > BTW, here is a rather unrelated question. what does the white color > represent (in default color setting)? Does it mean the residues that are > not included in the analysis? I might be careless, but I failed to find a > documentation for this. > > Thank you so much in advance! > > Best, > Chen > > >
[ccp4bb] PROSMART spectrum bar
Hi all, Sorry for bothering you with this small technical question. I just got to know PROSMART as a handy local structural alignment tool. But could anybody suggest me an easy way to generate the spectrum bar for the color-coded residue-wise scores? Generating a spectrum bar in Pymol seems nontrivial to me... BTW, here is a rather unrelated question. what does the white color represent (in default color setting)? Does it mean the residues that are not included in the analysis? I might be careless, but I failed to find a documentation for this. Thank you so much in advance! Best, Chen
Re: [ccp4bb] Command line tool for RMSD calculation
Dear all, Thanks a lot for your input. Later I found a R package called bio3d that is very suitable for my purpose. Best, Chen On Wed, Oct 15, 2014 at 5:53 PM, Steven Chou wrote: > Hi Chen, > I used SUPPOSE previously. It worked very well. The compositions of the > structures have to be the same! It works on Linux. > http://structbio.vanderbilt.edu/~jsmith/suppose/ > > If the compositions of your structures are different, you may first load > them to PyMOL, then align them use its commandline. > > http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ > > If the compositions/sequences of your structures are very very different, > but their overall structure are similar, you can do the alignment using a > PyMOL plugin called 'cealign'. It works on both Mac and Linux. > http://pymolwiki.org/index.php/Cealign > > > Here is my note on how to run SUPPOSE. > remove the outputs from the previous runs > rm -rf *.rot.pdb mean.pdb all.pdb > > # if the input file names are XXX.pdb, those of the output files are > XXX.rot.pdb and a mean.pdb > > > fit the structrue models based on the CA atoms, and then calculate > the RMSD of the backbone atoms > suppose -mat -rot -mean -fit ":11-52,85-97:CA" -calc ":11-52,85-97:C,CA,N" > restrt_*.pdb > # 0.639 > > fit the structrue models based on the CA atoms, and then calculte the > RMSD of the heavy atoms > suppose -mat -rot -mean -fit ":11-52,85-97:CA" -calc > ":11-52,85-97:C*,N*,O*,S*" restrt_*.pdb > # 1.23 > > # Do not visulize the rotated pdb files with molmol at this step, because > molmol will shift the individual files. > # That is, the output files have already been perfectly supperimposed, > # but molmol gives an illusion that they have not been rotated correctly. > > join the pdb with the AWK script > ./joinpdb -o all.pdb *.rot.pdb > # input files: *.rot.pdb > # output file: all.pdb > > display the rotated pdb with molmol now. > molmol all.pdb > # molmol can only display the combined pdb (i.e., 20 models in one file) > correctly!!! > > > HTH, > > Steven > > > > On Wed, Oct 15, 2014 at 4:05 PM, Chen Zhao wrote: > >> Dear all, >> >> I am just wondering whether there is a simple command line tool for RMSD >> calculation between two aligned structures? I just cannot find a good >> answer online, and ccp4bb can always impress me. >> >> Thank you so much in advance, >> Chen >> > > > > -- > Steven Chou > > >
[ccp4bb] Command line tool for RMSD calculation
Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen
Re: [ccp4bb] Get NCS rotational axis from PDB file?
Hi Dale, Thank you for your reply! Yes, the real term of all eigenvalues are very close to 1, and as I said in the previous email they matches a 2-fold rotational matrix. But I am just curious, would you mind if you give me a little bit of hint on what the imaginary space represent? Thank you so much, Chen On Mon, Sep 22, 2014 at 1:26 PM, Dale Tronrud wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > > On 9/22/2014 10:10 AM, Chen Zhao wrote: > > Hi all, > > > > I have a follow-up question here. I calculated the eigenvalues and > > the eigenvectors and some of them have imaginary terms. The real > > terms of the eigenvalues match a 2-fold rotation, but I am just > > wondering what the imaginary terms represent. It's been quite a > > while since I studied linear algebra. > > > >The eigenvalues for a rotation matrix will have one that is real > and the other two complex. The eigenvector that corresponds to the > real value is the rotation axis. The other two are not useful for > your purpose. > >By the way, that real eigenvalue has better be equal to one! > > Dale Tronrud > > > Thank you so much, Chen > > > > On Mon, Sep 22, 2014 at 10:41 AM, Philip Kiser > <mailto:p...@case.edu>> wrote: > > > > Cool. Glad to help. > > > > On Mon, Sep 22, 2014 at 10:34 AM, Chen Zhao > <mailto:c.z...@yale.edu>> wrote: > > > > Dear Philip, > > > > Please forgive me! Yes it is eigenvectors that I am looking for. I > > was deriving myself and came to the conclusion that R=A^(-1)R'A, > > but I just forgot it is eigenvectors, and I forgot what the > > eigenvector is originally for. Thank you so much! > > > > Sincerely, Chen > > > > On Mon, Sep 22, 2014 at 10:22 AM, Philip Kiser > <mailto:p...@case.edu>> wrote: > > > > Hi Chen, > > > > Wouldn't the fold of the NCS be clear from the PDB file? You could > > use superpose to superimpose one monomer onto the next member of > > the NCS group, and then take the rotation matrix output from that > > program to calculate the eigenvectors for the transformation. The > > NCS axis is parallel to one of those eigenvectors. > > > > Philip > > > > Philip > > > > On Mon, Sep 22, 2014 at 10:13 AM, Chen Zhao > <mailto:c.z...@yale.edu>> wrote: > > > > Dear all, > > > > Is there a software that can print out the position and the fold of > > a NCS rotational axis from a PDB file? (just something like molrep > > self-rotation on a reflection file) I cannot use molrep because the > > RMSD between the two copies are too high, and I just want to cut a > > certain region for calculation. I don't know whether calculated Fc > > from the truncated PDB works in molrep self-RF, but I am thinking > > whether there is a more straightforward way. > > > > Thanks a lot in advance! > > > > Sincerely, Chen > > > > > > > > > > > -BEGIN PGP SIGNATURE- > Version: GnuPG v2.0.22 (MingW32) > > iEYEARECAAYFAlQgW7QACgkQU5C0gGfAG13IzQCeNPJi+TDEe7v/vI5Pzwm+/Vfb > dDEAniquuYawYm3ogMUa8yylMz51xUDQ > =bFra > -END PGP SIGNATURE- >
Re: [ccp4bb] Get NCS rotational axis from PDB file?
Hi all, I have a follow-up question here. I calculated the eigenvalues and the eigenvectors and some of them have imaginary terms. The real terms of the eigenvalues match a 2-fold rotation, but I am just wondering what the imaginary terms represent. It's been quite a while since I studied linear algebra. Thank you so much, Chen On Mon, Sep 22, 2014 at 10:41 AM, Philip Kiser wrote: > Cool. Glad to help. > > On Mon, Sep 22, 2014 at 10:34 AM, Chen Zhao wrote: > >> Dear Philip, >> >> Please forgive me! Yes it is eigenvectors that I am looking for. I was >> deriving myself and came to the conclusion that R=A^(-1)R'A, but I just >> forgot it is eigenvectors, and I forgot what the eigenvector is originally >> for. Thank you so much! >> >> Sincerely, >> Chen >> >> On Mon, Sep 22, 2014 at 10:22 AM, Philip Kiser wrote: >> >>> Hi Chen, >>> >>> Wouldn't the fold of the NCS be clear from the PDB file? You could use >>> superpose to superimpose one monomer onto the next member of the NCS group, >>> and then take the rotation matrix output from that program to calculate the >>> eigenvectors for the transformation. The NCS axis is parallel to one of >>> those eigenvectors. >>> >>> Philip >>> >>> Philip >>> >>> On Mon, Sep 22, 2014 at 10:13 AM, Chen Zhao wrote: >>> >>>> Dear all, >>>> >>>> Is there a software that can print out the position and the fold of a >>>> NCS rotational axis from a PDB file? (just something like molrep >>>> self-rotation on a reflection file) I cannot use molrep because the RMSD >>>> between the two copies are too high, and I just want to cut a certain >>>> region for calculation. I don't know whether calculated Fc from the >>>> truncated PDB works in molrep self-RF, but I am thinking whether there is a >>>> more straightforward way. >>>> >>>> Thanks a lot in advance! >>>> >>>> Sincerely, >>>> Chen >>>> >>> >>> >> >
Re: [ccp4bb] Get NCS rotational axis from PDB file?
Dear Philip, Please forgive me! Yes it is eigenvectors that I am looking for. I was deriving myself and came to the conclusion that R=A^(-1)R'A, but I just forgot it is eigenvectors, and I forgot what the eigenvector is originally for. Thank you so much! Sincerely, Chen On Mon, Sep 22, 2014 at 10:22 AM, Philip Kiser wrote: > Hi Chen, > > Wouldn't the fold of the NCS be clear from the PDB file? You could use > superpose to superimpose one monomer onto the next member of the NCS group, > and then take the rotation matrix output from that program to calculate the > eigenvectors for the transformation. The NCS axis is parallel to one of > those eigenvectors. > > Philip > > Philip > > On Mon, Sep 22, 2014 at 10:13 AM, Chen Zhao wrote: > >> Dear all, >> >> Is there a software that can print out the position and the fold of a NCS >> rotational axis from a PDB file? (just something like molrep self-rotation >> on a reflection file) I cannot use molrep because the RMSD between the two >> copies are too high, and I just want to cut a certain region for >> calculation. I don't know whether calculated Fc from the truncated PDB >> works in molrep self-RF, but I am thinking whether there is a more >> straightforward way. >> >> Thanks a lot in advance! >> >> Sincerely, >> Chen >> > >
[ccp4bb] Get NCS rotational axis from PDB file?
Dear all, Is there a software that can print out the position and the fold of a NCS rotational axis from a PDB file? (just something like molrep self-rotation on a reflection file) I cannot use molrep because the RMSD between the two copies are too high, and I just want to cut a certain region for calculation. I don't know whether calculated Fc from the truncated PDB works in molrep self-RF, but I am thinking whether there is a more straightforward way. Thanks a lot in advance! Sincerely, Chen
Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix
I am sorry for my carelessness on the definition of Euler angles. I am just thinking of an Euler angle equivalent. Sorry for the confusion I have made. On Fri, Sep 5, 2014 at 3:34 PM, Eleanor Dodson wrote: > I don't think Eulerian angles are defined for a non-orthogonal axis > system? ? > > They are defined relative to perpendicular axes X Y Z > e.g. > Rotate coordinates by gamma about Z, beta about Y', alpha about Z". > > > Eleanor > > > > > > On 5 September 2014 16:27, Chen Zhao wrote: > >> Thank you Eleanor for your reply. I am actually considering how to >> describe a pseudo-NCS with an arbitrary rotational and translational >> relationship. I don't have to do this but I am just curious. It is more >> straightforward if I say how the two molecules are related by a rotation >> around unit cell axis than around orthogonal coordinate axis, which does >> not have an absolute physical meaning. >> >> The command line output after coot superpose prints out the rotational >> and translational matrices for both the orthogonal and fractional >> coordinate system. >> >> For using coordconv, my concern is that if I deal with a low-symmetry >> unit cell, which is not orthogonal by itself, the Euler angles for the >> fractional coordinate system and the orthogonal coordinate system should be >> different. If I just feed some numbers into coordconv, will it consider >> them as orthogonal coordinates? >> >> Thank you, >> Chen >> >> On Fri, Sep 5, 2014 at 6:24 AM, Eleanor Dodson > > wrote: >> >>> Rotation matrices are rarely specified in a fractional coordinate >>> system? The criteria for checking such a matrix is "Is the determinant 1?" >>> and this only holds for orthogonal matrices. >>> >>> >>> >>> I guess the way I would do this though. >>> >>> You presumably have two sets of fractional coordinates, before and after >>> rotation? >>> >>> There is a ccp4 program - coordconv which will read the fractional >>> coordinates and generate pdb format with the convention ncode = 1 (You may >>> need to fudge the fractional format I suppose..) >>> >>> You can then use superpose to match the two sets of coordinates and the >>> output will tell you the Eulerian angles used for the rotation! >>> >>> Lots of ways to kill cats! >>> Eleanor >>> >>> >>> >>> >>> >>> On 4 September 2014 21:21, Phil Jeffrey wrote: >>> >>>> The orthogonal/fractional matrix is outlined here: >>>> http://www.iucr.org/__data/assets/pdf_file/0009/7011/19_ >>>> 06_cowtan_coordinate_frames.pdf >>>> >>>> Sorry to say I apparently ditched my old Fortran o2f and f2o programs >>>> to do that. >>>> >>>> Bear in mind, however, that orthogonal has no fixed orientation with >>>> respect to fractional - for most space groups "ncode 1" is often used but >>>> for primitive monoclinic "ncode 3" is sometimes used, and I think the >>>> matrix shown in Kevin Cowtan's document above corresponds to "ncode 1". >>>> >>>> Phil Jeffrey >>>> Princeton >>>> >>>> >>>> On 9/4/14 3:55 PM, Chen Zhao wrote: >>>> >>>>> I am sorry, just to clarify, the fractional coordinate matrix I >>>>> referred >>>>> to is a rotational matrix in the fractional coordinate system. >>>>> >>>>> >>>>> On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao >>>> <mailto:c.z...@yale.edu>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I am just curious whether there are some tools extracting the Euler >>>>> angles from a fractional coordinate matrix. I have no luck >>>>> searching >>>>> it online. >>>>> >>>>> Alternatively, I found the analytical solution for the Euler angles >>>>> from an orthogonal coordinate matrix. So in the worst case, my >>>>> problem reduces to calculating the transformation matrix between >>>>> the >>>>> fractional and orthogonal coordinate system. I feel a little bit at >>>>> a loss because it is 6 years since I last studied linear algebra. >>>>> How can I calculate this for a specific unit cell? >>>>> >>>>> Thanks a lot in advance! >>>>> >>>>> Sincerely, >>>>> Chen >>>>> >>>>> >>>>> >>> >> >
Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix
Thank you Eleanor for your reply. I am actually considering how to describe a pseudo-NCS with an arbitrary rotational and translational relationship. I don't have to do this but I am just curious. It is more straightforward if I say how the two molecules are related by a rotation around unit cell axis than around orthogonal coordinate axis, which does not have an absolute physical meaning. The command line output after coot superpose prints out the rotational and translational matrices for both the orthogonal and fractional coordinate system. For using coordconv, my concern is that if I deal with a low-symmetry unit cell, which is not orthogonal by itself, the Euler angles for the fractional coordinate system and the orthogonal coordinate system should be different. If I just feed some numbers into coordconv, will it consider them as orthogonal coordinates? Thank you, Chen On Fri, Sep 5, 2014 at 6:24 AM, Eleanor Dodson wrote: > Rotation matrices are rarely specified in a fractional coordinate system? > The criteria for checking such a matrix is "Is the determinant 1?" and this > only holds for orthogonal matrices. > > > > I guess the way I would do this though. > > You presumably have two sets of fractional coordinates, before and after > rotation? > > There is a ccp4 program - coordconv which will read the fractional > coordinates and generate pdb format with the convention ncode = 1 (You may > need to fudge the fractional format I suppose..) > > You can then use superpose to match the two sets of coordinates and the > output will tell you the Eulerian angles used for the rotation! > > Lots of ways to kill cats! > Eleanor > > > > > > On 4 September 2014 21:21, Phil Jeffrey wrote: > >> The orthogonal/fractional matrix is outlined here: >> http://www.iucr.org/__data/assets/pdf_file/0009/7011/19_ >> 06_cowtan_coordinate_frames.pdf >> >> Sorry to say I apparently ditched my old Fortran o2f and f2o programs to >> do that. >> >> Bear in mind, however, that orthogonal has no fixed orientation with >> respect to fractional - for most space groups "ncode 1" is often used but >> for primitive monoclinic "ncode 3" is sometimes used, and I think the >> matrix shown in Kevin Cowtan's document above corresponds to "ncode 1". >> >> Phil Jeffrey >> Princeton >> >> >> On 9/4/14 3:55 PM, Chen Zhao wrote: >> >>> I am sorry, just to clarify, the fractional coordinate matrix I referred >>> to is a rotational matrix in the fractional coordinate system. >>> >>> >>> On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao >> <mailto:c.z...@yale.edu>> wrote: >>> >>> Hi all, >>> >>> I am just curious whether there are some tools extracting the Euler >>> angles from a fractional coordinate matrix. I have no luck searching >>> it online. >>> >>> Alternatively, I found the analytical solution for the Euler angles >>> from an orthogonal coordinate matrix. So in the worst case, my >>> problem reduces to calculating the transformation matrix between the >>> fractional and orthogonal coordinate system. I feel a little bit at >>> a loss because it is 6 years since I last studied linear algebra. >>> How can I calculate this for a specific unit cell? >>> >>> Thanks a lot in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >
Re: [ccp4bb] Extract Euler angles from fractional coordinate matrix
I am sorry, just to clarify, the fractional coordinate matrix I referred to is a rotational matrix in the fractional coordinate system. On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao wrote: > Hi all, > > I am just curious whether there are some tools extracting the Euler angles > from a fractional coordinate matrix. I have no luck searching it online. > > Alternatively, I found the analytical solution for the Euler angles from > an orthogonal coordinate matrix. So in the worst case, my problem reduces > to calculating the transformation matrix between the fractional and > orthogonal coordinate system. I feel a little bit at a loss because it is 6 > years since I last studied linear algebra. How can I calculate this for a > specific unit cell? > > Thanks a lot in advance! > > Sincerely, > Chen >
[ccp4bb] Extract Euler angles from fractional coordinate matrix
Hi all, I am just curious whether there are some tools extracting the Euler angles from a fractional coordinate matrix. I have no luck searching it online. Alternatively, I found the analytical solution for the Euler angles from an orthogonal coordinate matrix. So in the worst case, my problem reduces to calculating the transformation matrix between the fractional and orthogonal coordinate system. I feel a little bit at a loss because it is 6 years since I last studied linear algebra. How can I calculate this for a specific unit cell? Thanks a lot in advance! Sincerely, Chen
[ccp4bb] Twinning VS. Disorder
Dear all, Hello! I am kinda confused and am thinking about the definition of twinning and disorder. I am just a starting student and might make some fundamental mistakes. 1) Twinning is a macroscopic phenomenon and the result is the addition of the intensity from different lattices; disorder is a microscopic phenomenon and the result is the addition of structure factors from different crystal "domains". Is this statement valid? 2) I am now very confused about how to define the macroscopic versus the microscopic level when I think of the systematic absences introduced by translational operation. Or in other words, can the translational operation between the twin domains create systematic absences? My answer is probably no because the distance between the two domains are too far away compared to the coherent length of the X-ray, i.e. the addition of the intensity alone cannot make some spots disappear. Is it true? If yes, what is the x-ray coherence length at the synchrotron in general? 3) If the statement in 2) is valid, then if a "twinning operation" can introduce systematic absences, this should be a disorder instead of a twin based on the definitions in 1). Is this right? Your answers will be greatly appreciated! Sincerely, Chen
[ccp4bb] Phenix composite omit map
Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen
Re: [ccp4bb] AW: [ccp4bb] Space group problem?
By the way, I have another question related to the number of sites. I just rethought about what Herman mentioned, and I just realized that the number of sites, at least strong sites, could be guessed from an anomalous Patterson map. Therefore I looked at the anomalous Patterson of my data. The map indicates that the signal is very weak, and there are only 4 non-origin positive peaks (3 effective peaks, because 2 are symmetry equivalent), indicating there are at most 3 heavy atoms (3x2=6) if all of them contribute to the map. However, in shelxd, I can get optimal results from 6 sites out of the same data set. I am not sure whether this is because the anomalous Patterson is not sensitive enough. Now I am more confused about the criteria in choosing the parameters when running shelx and all other programs. What should be the general practice? Should I rely more on the anomalous Patterson or more on the better scores reported? When I tried to optimize the results by changing the parameters (either when locating sites or when phasing), am I more heading for the real signal or more simply tweaking the parameters? Maybe the golden standard would be whether you could solve the structure. Another question is, although from the Euler's equation I could understand negative Patterson peaks (maybe I am wrong), I am still not clear what negative Patterson peaks represent and why people generally don't talk about it. In the specific data I am talking about above, there is a negative Patterson peak at the same position as a positive Patterson peak with the same height. Is there any indication about this? Thank you so much for your attention! On Tue, Apr 1, 2014 at 2:00 PM, Nazia Nasir Phd2009,ProteinCrystall.Lab < nazia.nasi...@nii.ac.in> wrote: > Dear Jurgen, > > The beam position is fine. we have collected many data sets before and > after this data. Moreover, we the Technical scientist always checks the > beam position before we mount the crystals. > > Thanks > > > On Tue, Apr 1, 2014 at 11:23 PM, Jurgen Bosch wrote: > >> check your beam position >> .. >> Jürgen Bosch >> Johns Hopkins University >> Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> Johns Hopkins Malaria Research Institute >> 615 North Wolfe Street, W8708 >> Baltimore, MD 21205 >> Office: +1-410-614-4742 >> Lab: +1-410-614-4894 >> Fax: +1-410-955-2926 >> http://lupo.jhsph.edu >> >> On Apr 1, 2014, at 1:26 PM, Nazia Nasir Phd2009,ProteinCrystall.Lab < >> nazia.nasi...@nii.ac.in> wrote: >> >>Dear all, >> >> I am just taking advantage of this particular thread to add my query >> also. I hope you don't mind Chen. >> >> We haven't solved any structure in our lab using SAD phasing, so pardon >> me for sounding naive. >> >> I have a 6.5 A data of anomalous scattering with a 3.5 A data using the >> Cu anode.My crystals dont grow any better. I have around 10 Met distributed >> fairly evenly through out the sequence. So is it possible to get any >> anomalous signals form this data? >> Moreover, I am not able to index my 3.5A data at all. The spots don't fit >> well. What could be the problem? >> >> Hope this thread can be of benefit for both me and Chen. >> >> Thanks >> >> >> On Tue, Apr 1, 2014 at 8:21 PM, Chen Zhao wrote: >> >>> Dear Herman, >>> >>> Thank you so much for your suggestions. The density that passes through >>> the rotational axis is so strong and extended that can be considered as a >>> significant portion of the molecule. However, some density in the middle >>> might show some features. I have no experience and this could be only >>> artifact. >>> >>> The unit cell seems to be able to fit 1-2 molecules. But if there is >>> one molecule/ASU, the solvent content is about 89%, which is possible but >>> unlikely. Although the resolution of the crystal is not high, it is rather >>> rigid and easy to handle, which might indicate a not-too-high solvent >>> content. I soaked the native crystal with heavy atom compounds and I have >>> no clear idea of the relationship between metal binding and sequence, so I >>> don't know how many sites to expect. >>> >>> Best, >>> Chen >>> >>> >>> On Tue, Apr 1, 2014 at 9:42 AM, wrote: >>> >>>> Dear Chen, >>>> >>>> I am not an expert on SAD and MAD. However, at this stage I would not >>>> worry too much about density going through the 2-fold axis. There might be >>>>
Re: [ccp4bb] AW: [ccp4bb] Space group problem?
Dear Herman, Thank you so much for your suggestions. The density that passes through the rotational axis is so strong and extended that can be considered as a significant portion of the molecule. However, some density in the middle might show some features. I have no experience and this could be only artifact. The unit cell seems to be able to fit 1-2 molecules. But if there is one molecule/ASU, the solvent content is about 89%, which is possible but unlikely. Although the resolution of the crystal is not high, it is rather rigid and easy to handle, which might indicate a not-too-high solvent content. I soaked the native crystal with heavy atom compounds and I have no clear idea of the relationship between metal binding and sequence, so I don't know how many sites to expect. Best, Chen On Tue, Apr 1, 2014 at 9:42 AM, wrote: > Dear Chen, > > I am not an expert on SAD and MAD. However, at this stage I would not > worry too much about density going through the 2-fold axis. There might be > a sulfate ion or some other buffer component present at that position, or > it may just be an artifact that will go away once the structure has been > built and refined. > > > > The questions I would worry about is: how much too small is your unit > cell? Is it just crowded, say 25-30% solvent, or would your protein > molecule not fit at all? Does the amount of solvent as estimated from your > SAD/MAD maps agree with the amount of solvent obtained from the calculation > of the Matthews volume? How many (SeMet?) sites do you expect, 6, more, > less? If everything looks ok except that the unit cell is rather crowded, I > would go ahead and try to build the structure. > > However, if even a single protein molecule would not fit in your unit > cell, or you find many more sites than you can explain, you should start > worrying about twinning. Even than the structure can probably be solved, > but then you need some real experts! > > > > My 2 cents, > > Herman > > > > > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Chen Zhao > *Gesendet:* Montag, 31. März 2014 23:46 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] Space group problem? > > > > Dear all, > > I am now trying to phase a structure in C2 using anomalous scattering at > 5-6 A. It is hard to improve the derivative resolution at the moment. > Shelxd is able to locate 6 sites with a distinct CC and FOM. After density > modification in shelxe, the contrast of the two enantiomers is 0.59/0.38 > for SAD and 0.7/0.3 for MAD. When I looked at the electron density, the > maps from SAD and MAD are similar, and the solvent boundary is quite clear. > However, the problem is that the electron density blob passes through the > 2-fold rotation axis, even at 3 rmsd contour level. Also, the unit cell > seems to be too small for the molecule. I am afraid that the space group > assignment is wrong, but I am a beginner so I nearly have no clue. I did > reprocess the data in P1 and looked at the self-rotation function with a > radius at 200 A. From the list it seems that there is only one 2-fold > rotation axis. I am quite confused. Could anybody give me some hint of this > problem? > > Thanks a lot in advance! > > Sincerely, > > Chen >
Re: [ccp4bb] Space group problem?
Dear Savvas, Thank you for your reply and your nice protocol. I am also worried of this problem so I have already run my crystals on the gel for several times. The result is so clean that you can hardly draw any other conclusions except that the crystals are made up of the full-length molecule. But possibility remains regarding this concern if my molecule of interest is not in crystalline state but other molecules that cannot be stained are. Best, Chen On Tue, Apr 1, 2014 at 3:30 AM, Savvas Savvides wrote: > Dear Chen, > > how sure are you that your crystals contain the protein of interest? > Repeatedly washing harversted crystals in crystal stabilization solution > followed by SDS-PAGE coupled to appropriate staining protocols (e.g. > Coomassie, Silver staining) or western blotting can give a pretty > conclusive answer. > In our group, SDS-PAGE followed by Silver-staining is done routinely and > in most cases leads to conclusive results. Here is a summary of the > protocol: > > > - select a drop containing substantial crystalline material. The crystals > can be many and small (crystal shower) or few and large. > - prepare a PCR-tube with crystal stabilization buffer (e.g. 50 uL of > motherliquor containing a 10% higher concentration of precipitant). > - transfer all the crystalline material from the drop into the PCR-tube > using a pipet (You can use stabilization buffer from the PCR tube to > collect all crystals). One can also use a cryo-loop to harvest the crystals > if they are large enough to allow efficient harvesting. > - centrifuge the PCR-tube at low speed for 30-60 sec and observe the > crystals under the microscope to make sure they are at the bottom of the > PCR-tube. > - remove as much of the supernatant as you can using a pipet making sure > not to remove the crystals. Then add crystal stabilization buffer to wash > the crystals, and centrifuge again. > - repeat this washing procedure a few times (typicaly 3-4 times). > - after the final washing step, centrifugation and removal of the > supernatant, add Laemmli-buffer to the crystals and use this sample for > loading onto the SDS-PAGE gel. > - include a positive control (e.g. solubilize another drop directly in > Laemmli-buffer) and a negative control (final washing buffer). Including a > pre-crystallization sample of your protein as a control is also > recommended, to control for the integrity of the protein under > crystallization conditions. > - use silver staining to visualize the protein. > --- > > > best regards > Savvas > > > > On 31 Mar 2014, at 23:48, Chen Zhao wrote: > > > BTW, I forgot to mention that phenix.autosol also gave similar result. > > > > > > On Mon, Mar 31, 2014 at 5:46 PM, Chen Zhao wrote: > > Dear all, > > > > I am now trying to phase a structure in C2 using anomalous scattering at > 5-6 A. It is hard to improve the derivative resolution at the moment. > Shelxd is able to locate 6 sites with a distinct CC and FOM. After density > modification in shelxe, the contrast of the two enantiomers is 0.59/0.38 > for SAD and 0.7/0.3 for MAD. When I looked at the electron density, the > maps from SAD and MAD are similar, and the solvent boundary is quite clear. > However, the problem is that the electron density blob passes through the > 2-fold rotation axis, even at 3 rmsd contour level. Also, the unit cell > seems to be too small for the molecule. I am afraid that the space group > assignment is wrong, but I am a beginner so I nearly have no clue. I did > reprocess the data in P1 and looked at the self-rotation function with a > radius at 200 A. From the list it seems that there is only one 2-fold > rotation axis. I am quite confused. Could anybody give me some hint of this > problem? > > > > Thanks a lot in advance! > > > > Sincerely, > > Chen > > > >
Re: [ccp4bb] Space group problem?
BTW, I forgot to mention that phenix.autosol also gave similar result. On Mon, Mar 31, 2014 at 5:46 PM, Chen Zhao wrote: > Dear all, > > I am now trying to phase a structure in C2 using anomalous scattering at > 5-6 A. It is hard to improve the derivative resolution at the moment. > Shelxd is able to locate 6 sites with a distinct CC and FOM. After density > modification in shelxe, the contrast of the two enantiomers is 0.59/0.38 > for SAD and 0.7/0.3 for MAD. When I looked at the electron density, the > maps from SAD and MAD are similar, and the solvent boundary is quite clear. > However, the problem is that the electron density blob passes through the > 2-fold rotation axis, even at 3 rmsd contour level. Also, the unit cell > seems to be too small for the molecule. I am afraid that the space group > assignment is wrong, but I am a beginner so I nearly have no clue. I did > reprocess the data in P1 and looked at the self-rotation function with a > radius at 200 A. From the list it seems that there is only one 2-fold > rotation axis. I am quite confused. Could anybody give me some hint of this > problem? > > Thanks a lot in advance! > > Sincerely, > Chen >
[ccp4bb] Space group problem?
Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC and FOM. After density modification in shelxe, the contrast of the two enantiomers is 0.59/0.38 for SAD and 0.7/0.3 for MAD. When I looked at the electron density, the maps from SAD and MAD are similar, and the solvent boundary is quite clear. However, the problem is that the electron density blob passes through the 2-fold rotation axis, even at 3 rmsd contour level. Also, the unit cell seems to be too small for the molecule. I am afraid that the space group assignment is wrong, but I am a beginner so I nearly have no clue. I did reprocess the data in P1 and looked at the self-rotation function with a radius at 200 A. From the list it seems that there is only one 2-fold rotation axis. I am quite confused. Could anybody give me some hint of this problem? Thanks a lot in advance! Sincerely, Chen
Re: [ccp4bb] Trouble cleaving SUMO tag off of membrane protein
Sorry for my typo, it is Ulp1-SMT3 complex... On Sun, Feb 16, 2014 at 10:54 PM, Chen Zhao wrote: > By the way, I have an unrelated question. In the crystal structures > containing yeast SUMO (including Ulp1-SMT1 complex: 1EUV), the first ~19 > residues are absent. I am curious whether people tried a SUMO tag with > these residues deleted. I am using the vector from invitrogen which seems > to have the full-length ySUMO. > > Thank you, > Chen > > > On Sun, Feb 16, 2014 at 10:38 PM, Matthew Bratkowski > wrote: > >> Hi Raji, >> >> I have no experience with membrane proteins, but I have used SUMO tags >> frequently. Unlike other proteases that cleave at a specific site >> (thrombin, TEV, etc.), Ulp1 recognizes the tertiary structure of SUMO for >> cleavage. So if only about 50% of your protein is cleaved, this may >> indicate that about 50% of your protein is misfolded. You may just try to >> take the cleaved protein and use it and forget about recovering the >> uncleaved portion. While your yield will obviously be substantially >> reduced, you only really want correctly folded protein for structural or >> functional studies, and the inability of Ulp1 to cleave the SUMO tag could >> serve as means of removing misfolded protein from your sample. >> >> Matt >> >> >> On Sun, Feb 16, 2014 at 9:58 AM, Raji Edayathumangalam > > wrote: >> >>> Hi Everyone, >>> >>> After several attempts to cleave the SUMO tag off my membrane protein >>> under various conditions (different reducing agents, enzyme-to-substrate >>> ratios, etc.) and after reading the manual and troubleshooting guide, I'm >>> reaching out to the ccp4bb community. >>> >>> Experiment: I dialyze the mixture of SUMO-membrane protein and Ulp1 >>> Express protease against buffer containing 20mM Tris pH 7, 150mM NaCl, 1mM >>> DTT or 2mM beta-mercaptoethanol and 0.02% DDM at 4C overnight (14-18 >>> hours). I am currently using an enzyme-to-substrate molar ratio of >>> 1-to-15-20. >>> >>> Problem: With buffer containing 1mM DTT, I get about 50% tag-cleaved >>> protein and 50% tagged protein. With buffer containing 2mM bME, I get about >>> 30% tag-cleaved protein and 70% tagged protein. >>> >>> Couple of things: >>> (1) Side-by-side cleavage of a SUMO-tagged control soluble protein by >>> the same batch of Ulp1 works to 100% completion. >>> (2) Detergent (0.02% DDM) did not interfere at all with cleavage of the >>> SUMO-tagged control soluble protein. >>> (3) I cannot set up the cleavage reaction at 30C or 37C and must stick >>> with 4C, a protocol that I have used successfully in the past with >>> SUMO-tagged soluble proteins. >>> >>> Although membrane proteins supposedly form a protein-detergent complex, >>> I wonder if some of my protein is in micelles and if the random orientation >>> of my SUMO-tagged protein in micelles may be the cause for incomplete >>> digestion. I've also suspected that some of my membrane protein may be >>> misfolded and oligomeric/aggregated, making the cleavage site inaccessible >>> to the protease. >>> >>> But suppose the above explanations are not the problem in my case and >>> that it's a technical issue and I am missing something very simple. >>> Therefore, I am planning to set up more reactions ramping up the ratio of >>> enzyme-to-substrate, increasing amount of bME (I prefer bME over DTT since >>> I need to rebind the cleaved mixture to His-affinity resin) and decreasing >>> the NaCl concentration to 100mM or lower (although 250mM NaCl did not >>> interfere with cleavage of control protein). >>> >>> Have folks working with SUMO-tagged membrane protein encountered similar >>> problems? I am purifying membrane protein from 30L bacterial culture and >>> the yields are not all that great. So, if possible, I'd like to get the >>> cleavage reaction to completion so that I don't have to suffer a 50% loss >>> of protein at this step. I have a construct for my membrane protein without >>> a SUMO tag and the expression is abysmal. >>> >>> Thanks very much for your time and suggestions! >>> Raji >>> >>> -- >>> Raji Edayathumangalam >>> Instructor in Neurology, Harvard Medical School >>> Research Associate, Brigham and Women's Hospital >>> Visiting Research Scholar, Brandeis University >>> >>> >> >
Re: [ccp4bb] Trouble cleaving SUMO tag off of membrane protein
By the way, I have an unrelated question. In the crystal structures containing yeast SUMO (including Ulp1-SMT1 complex: 1EUV), the first ~19 residues are absent. I am curious whether people tried a SUMO tag with these residues deleted. I am using the vector from invitrogen which seems to have the full-length ySUMO. Thank you, Chen On Sun, Feb 16, 2014 at 10:38 PM, Matthew Bratkowski wrote: > Hi Raji, > > I have no experience with membrane proteins, but I have used SUMO tags > frequently. Unlike other proteases that cleave at a specific site > (thrombin, TEV, etc.), Ulp1 recognizes the tertiary structure of SUMO for > cleavage. So if only about 50% of your protein is cleaved, this may > indicate that about 50% of your protein is misfolded. You may just try to > take the cleaved protein and use it and forget about recovering the > uncleaved portion. While your yield will obviously be substantially > reduced, you only really want correctly folded protein for structural or > functional studies, and the inability of Ulp1 to cleave the SUMO tag could > serve as means of removing misfolded protein from your sample. > > Matt > > > On Sun, Feb 16, 2014 at 9:58 AM, Raji Edayathumangalam > wrote: > >> Hi Everyone, >> >> After several attempts to cleave the SUMO tag off my membrane protein >> under various conditions (different reducing agents, enzyme-to-substrate >> ratios, etc.) and after reading the manual and troubleshooting guide, I'm >> reaching out to the ccp4bb community. >> >> Experiment: I dialyze the mixture of SUMO-membrane protein and Ulp1 >> Express protease against buffer containing 20mM Tris pH 7, 150mM NaCl, 1mM >> DTT or 2mM beta-mercaptoethanol and 0.02% DDM at 4C overnight (14-18 >> hours). I am currently using an enzyme-to-substrate molar ratio of >> 1-to-15-20. >> >> Problem: With buffer containing 1mM DTT, I get about 50% tag-cleaved >> protein and 50% tagged protein. With buffer containing 2mM bME, I get about >> 30% tag-cleaved protein and 70% tagged protein. >> >> Couple of things: >> (1) Side-by-side cleavage of a SUMO-tagged control soluble protein by the >> same batch of Ulp1 works to 100% completion. >> (2) Detergent (0.02% DDM) did not interfere at all with cleavage of the >> SUMO-tagged control soluble protein. >> (3) I cannot set up the cleavage reaction at 30C or 37C and must stick >> with 4C, a protocol that I have used successfully in the past with >> SUMO-tagged soluble proteins. >> >> Although membrane proteins supposedly form a protein-detergent complex, I >> wonder if some of my protein is in micelles and if the random orientation >> of my SUMO-tagged protein in micelles may be the cause for incomplete >> digestion. I've also suspected that some of my membrane protein may be >> misfolded and oligomeric/aggregated, making the cleavage site inaccessible >> to the protease. >> >> But suppose the above explanations are not the problem in my case and >> that it's a technical issue and I am missing something very simple. >> Therefore, I am planning to set up more reactions ramping up the ratio of >> enzyme-to-substrate, increasing amount of bME (I prefer bME over DTT since >> I need to rebind the cleaved mixture to His-affinity resin) and decreasing >> the NaCl concentration to 100mM or lower (although 250mM NaCl did not >> interfere with cleavage of control protein). >> >> Have folks working with SUMO-tagged membrane protein encountered similar >> problems? I am purifying membrane protein from 30L bacterial culture and >> the yields are not all that great. So, if possible, I'd like to get the >> cleavage reaction to completion so that I don't have to suffer a 50% loss >> of protein at this step. I have a construct for my membrane protein without >> a SUMO tag and the expression is abysmal. >> >> Thanks very much for your time and suggestions! >> Raji >> >> -- >> Raji Edayathumangalam >> Instructor in Neurology, Harvard Medical School >> Research Associate, Brigham and Women's Hospital >> Visiting Research Scholar, Brandeis University >> >> >
Re: [ccp4bb] Control the crystallization process in the presence of small volatile organic molecules
Dear Mark, Thank you so much for your reply. Interestingly, after several days I posted this question, I found both my previous crystals and precipitant completely dissolved, but instead much larger crystals start to appear. However, most of them are intergrown together, only few are single. And I think I have to get the right timing and freeze them soon, otherwise it may dissolve again. For cryoprotectant, I am also thinking of starting from low molecular weight PEG. Hopefully at least I could manage to get one or two crystals out of a drop. Finger crossed... Best, Chen On Fri, Jan 24, 2014 at 6:31 PM, Mark van der Woerd wrote: > Chen, > > Dioxane is not easy to work with, exactly for the reasons you describe. > > There is one thing you did not mention, which I know to be an additional > issue: the quality of the dioxane. I do not know if you need good quality > (whatever that is) but it is a fact that crystallization works with dioxane > from some manufacturer/lots and not with others. I have never figured out > why this is so. > > For a paper on kinetics and reservoir volume discussion, I would read the > work by Forsythe et al ( > http://journals.iucr.org/d/issues/2002/10/01/ic0013/vidsup.html, > doi:10.1107/S0907444902014208)<http://dx.doi.org/10.1107/S0907444902014208> > Basically you will find that this paper says that well volume does not > matter much. Content of your drop matters a lot. In your case, having a > very volatile component, equilibration would be really fast. > > One way to get away from all that is to do batch experiments, where there > is no active transport from a drop into a well. But your question remains > very good: you need an "oil" (?) that will not permit water or a volatile > organic substance to escape. I am not sure what would do the trick. > > Dioxane is a decent cryo-protectant by itself. I would think about adding > "gooey" things like low molecular weight PEG to try to get the drops better > behaved. Evaporation of the dioxane will still be an issue, but with a > higher viscosity you may not have to "chase your crystals" through the > drop. > > Hope this helps a little. > > Mark > > > > -Original Message- > From: Chen Zhao > To: CCP4BB > Sent: Wed, Jan 22, 2014 11:00 pm > Subject: [ccp4bb] Control the crystallization process in the presence of > small volatile organic molecules > >Dear all, > > I am now optimizing a hit which contains about 30% 1,4-dioxane using > hanging-drop vapor diffusion at 25 degree. I am having a hard time to > reproduce the results: most of the times the drops are either dry in one > day or full of precipitate, and only occasionally could I get small > crystals. Is there a way to control the vapor diffusion process, like using > oil to seal the reservoir? (I know paraffin is permeable to dioxane) Also > if someone could refer me to studies on the effects of reservoir volume and > surface area to the crystallization kinetics, that would be very helpful. > > I am also seeking for recommendations for freezing crystals in this > condition. What kind of cryoprotectant has a higher chance? Another problem > is that when I tried to freeze the crystals, the drop dries super rapidly, > and the crystals will dissolve if I add reservoir buffer. But I would > assume good cryoprotectant could do the job. On the other hand, this points > back to my previous question on "dioxane-impermeable" oil. If this magic > oil exists, I could use it to seal the drop when freezing. > > Thank you for help! > > Sincerely, > Chen >
[ccp4bb] Control the crystallization process in the presence of small volatile organic molecules
Dear all, I am now optimizing a hit which contains about 30% 1,4-dioxane using hanging-drop vapor diffusion at 25 degree. I am having a hard time to reproduce the results: most of the times the drops are either dry in one day or full of precipitate, and only occasionally could I get small crystals. Is there a way to control the vapor diffusion process, like using oil to seal the reservoir? (I know paraffin is permeable to dioxane) Also if someone could refer me to studies on the effects of reservoir volume and surface area to the crystallization kinetics, that would be very helpful. I am also seeking for recommendations for freezing crystals in this condition. What kind of cryoprotectant has a higher chance? Another problem is that when I tried to freeze the crystals, the drop dries super rapidly, and the crystals will dissolve if I add reservoir buffer. But I would assume good cryoprotectant could do the job. On the other hand, this points back to my previous question on "dioxane-impermeable" oil. If this magic oil exists, I could use it to seal the drop when freezing. Thank you for help! Sincerely, Chen
Re: [ccp4bb] CELL_NOW Download
Thank you all for your replies! I will look into them. Best, Chen On Mon, Jan 6, 2014 at 5:31 AM, Navdeep Sidhu wrote: > Dear Chen, > > To download CELL_NOW, please contact Bruker, <http://www.bruker.com/>. > For a relevant tutorial for use in twinning, see e.g. Regine Herbst-Irmer's > Introduction to Twinning at < > http://shelx.uni-ac.gwdg.de/~rherbst/twin/twin_introduction.pdf>. In > conjunction with CELL_NOW, I've also found the Bruker program RLATT helpful > in handling twins. > > Best regards, > Navdeep > > > --- > On Sun, Jan 05, 2014 at 11:14:27PM -0500, Chen Zhao wrote: > > Dear all, > > > > Could anyone give me some instructions for how to download CELL_NOW? It > > doesn't seem to be obvious... > > > > Thank you for your help! > > > > Sincerely, > > Chen > > > --- > Navdeep S. Sidhu > Departments of Structural Chemistry >& Pediatrics II > University of Goettingen > Germany > --- >
[ccp4bb] CELL_NOW Download
Dear all, Could anyone give me some instructions for how to download CELL_NOW? It doesn't seem to be obvious... Thank you for your help! Sincerely, Chen
[ccp4bb] CC and PATFOM in shelxd
Dear all, I am a 2nd year PhD student who just started working on crystallography. I am now trying to solve a structure by SAD. The data quality is poor, with a resolution of 4.9 A and anomalous signal up to 5.5-6 A. I am using hkl2map to locate the heavy atoms, and I have a few questions concerning the CC and PATFOM in shelxd. 1) I do have several "solutions" whose CC seems to be well separated from the majority (highest CCall/CCweak=35.8/16.5), however, their PATFOM are rather low. On the other hand, I got a well separated PATFOM, but its CCall is only 25.4. (see attached) How could this happen? I tried to search online for how shelxd calculates CC and PATFOM but didn't get a clear answer. 2) In the native dataset of crystals from similar conditions, pseudo-translation is detected (34.36% off-origin peak compared to the origin peak in the native Patterson map). Would this pseudo-translation peak bias the Patterson seeding in shelxd? I switched off the Patterson seeding and got worse CCall but better CCweak (30.4/19.3). Is this an intrinsic trend in shelxd or can it tell something about the data? Does this pseudo-translation peak have something to do with the extremely high PATFOM mentioned in 1)? Your answers will be greatly appreciated. Sincerely, Chen <><>
Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?
Thank you all for your helps, It seems that either COOT with modified PDB file or PDBSET is able to do most of the tricks for me. And thank Edward for sharing you useful files! I have to do a little bit more homework on xtaldraw though. Chen On Thu, Aug 1, 2013 at 9:17 AM, Edward A. Berry wrote: > It's not ideal but we have been using a program called XtalDraw on windows > for this, to display the different lattices and to build up the content of > the unit cell from a small molecule of 2 or 3 atoms by applying the > different space group symmetries. The students can edit the coordinates > file (not pdb format unfortunately) to change the symmetry and see what > happens in a hexagonal lattice as p1 goes to p3, p6, p6(1) etc. I put > figures made starting with a screenshot of xtaldraw, and some of the simple > coordinates files we used (plain text) > in > http://sb20.lbl.gov/berry/**xtaldraw/<http://sb20.lbl.gov/berry/xtaldraw/>. > The figures look 2D because in projection, but the lattice is actually > 3D, rotatable by mouse or arrow keys. > In principle I guess the same thing could be done with O or coot > generating symmetry mates within a sphere, and using real pdb files. > > > Chen Zhao wrote: > >> Dear all, >> >> I have been trying to search for some softwares/applications that can >> display the crystal space group "lattice" based on >> the input of cell dimension and space group. Ideally, it can also apply >> the arbitrary symmetry operation to a molecule >> with given orientation and position in the unit cell. It would be perfect >> if it can output a PDB file. Does anybody >> heard of something like that? >> >> I know it might not be too hard to be realized with a script simply >> modifying the coordinates, but unluckily I am not a >> programmer. And actually, even some simple PDB files of different space >> group, in which molecules are represented as >> dots, would be very helpful. >> >> Thank you so much! >> >> Sincerely, >> Chen Zhao >> >
[ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?
Dear all, I have been trying to search for some softwares/applications that can display the crystal space group "lattice" based on the input of cell dimension and space group. Ideally, it can also apply the arbitrary symmetry operation to a molecule with given orientation and position in the unit cell. It would be perfect if it can output a PDB file. Does anybody heard of something like that? I know it might not be too hard to be realized with a script simply modifying the coordinates, but unluckily I am not a programmer. And actually, even some simple PDB files of different space group, in which molecules are represented as dots, would be very helpful. Thank you so much! Sincerely, Chen Zhao
Re: [ccp4bb] Output of Phaser
Dear Prof. Read, Thank you for your detailed explaination. I think now I am clear about what each set of scores represent. But what do you mean by what the .sol should show? I did "make it up" by selecting two solutions sets from two different runs, and I am sorry for not making it clear at the begining. Thank you so much! Sincerely, Chen On Wed, Jul 31, 2013 at 6:35 AM, Randy Read wrote: > Dear Chen, > > For each component that is placed, Phaser reports the Z-scores for the > rotation function (RFZ) and translation function (TFZ), along with the > number of packing clashes (PAK) at this point and the LLG. For the top > solution at that point in the search, Phaser also reports the > TFZ-equivalent (TFZ=) score, which is what the Z-score would have been for > the translation search if the refined orientation from the rigid-body > refinement had been used. We introduced the TFZ-equivalent to eliminate > the dependence of the TFZ on the quality of the orientation used for the > particular translation search that (after refinement) ended up giving the > best solution. However, it takes some CPU time to compute a random > sampling of translations for that orientation, so we only do it for one > solution after adding each component. > > Your .sol file doesn't quite make sense in terms of what it should show. > Did you make it up to illustrate your point? What you might see is that, > for the top solution, the first LLG value (from placing the first > component) is lower the the corresponding LLG value for a solution lower in > the final list. However, you might see a TFZ== entry immediately after the > first LLG for whichever solution had the highest LLG at that point in the > search. If a solution that was worse after placing the first component > ends up with the top LLG after adding the second component to that > solution, then there will be a TFZ== entry after the second LLG value > (corresponding to the LLG after placing the second component. > > I hope that helps! There's also an explanation on our Phaser Wiki: > http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Annotation, > which gets into some even more obscure aspects of this annotation line. > > Randy Read > > On 31 Jul 2013, at 01:24, Chen Zhao wrote: > > Dear all, > > I am sorry for my new-comer question, but I am not clear what the multiple > RFZ, TFZ, PAK and LLG scores belong to after each solution set in the > phaser output (eg. .sol) file. My bet is that each of them corresponds to > each of the solutions listed below, but I am not sure. Also I know that > TFZ== represents the TFZ score based on the refined orientation, but why > does it sometimes appear in the middle instead of at the end? > > One example could look like this: > > SOLU SET *RFZ=5.4 TFZ=3.6 PAK=0 LLG=67* TFZ==1.8 *RFZ=2.2 TFZ=5.1 PAK=3 > LLG=91* LLG=102 > SOLU SPAC XXX > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU ENSE ensemble1 VRMS X > SOLU ENSE ensemble2 VRMS X > > SOLU SET* RFZ=4.2 TFZ=2.8 PAK=0 LLG=51* *RFZ=3.1 TFZ=5.1 PAK=1 LLG=71 > LLG=86 *TFZ==5.3 > SOLU SPAC XXX > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU ENSE ensemble1 VRMS X > SOLU ENSE ensemble2 VRMS X > > Thank you so much! > > Sincerely, > Chen > > > -- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills RoadE-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >
[ccp4bb] Output of Phaser
Dear all, I am sorry for my new-comer question, but I am not clear what the multiple RFZ, TFZ, PAK and LLG scores belong to after each solution set in the phaser output (eg. .sol) file. My bet is that each of them corresponds to each of the solutions listed below, but I am not sure. Also I know that TFZ== represents the TFZ score based on the refined orientation, but why does it sometimes appear in the middle instead of at the end? One example could look like this: SOLU SET *RFZ=5.4 TFZ=3.6 PAK=0 LLG=67* TFZ==1.8 *RFZ=2.2 TFZ=5.1 PAK=3 LLG=91* LLG=102 SOLU SPAC XXX SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X SOLU ENSE ensemble1 VRMS X SOLU ENSE ensemble2 VRMS X SOLU SET* RFZ=4.2 TFZ=2.8 PAK=0 LLG=51* *RFZ=3.1 TFZ=5.1 PAK=1 LLG=71 LLG=86 *TFZ==5.3 SOLU SPAC XXX SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X SOLU ENSE ensemble1 VRMS X SOLU ENSE ensemble2 VRMS X Thank you so much! Sincerely, Chen
[ccp4bb] Map Alignment
Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the "Superpose maps" utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen
[ccp4bb] RNA 3D structure alignment
Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single "aligned" structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
[ccp4bb] [Rendering Problem] Pymol & VMD conflicts Coot
Hi all, I am sorry that I ask something a little bit irrelevant here. I am a newbie in Linux, and recently installed Coot, Pymol and VMD on Ubuntu 12.04. It took me a while to figure out a strange conflict among them on my machine. If I remove the mesa-swx11 package, Coot becomes crazily slow. However, if I include that package, which requires the remove of mesa-glx, the backgrounds of Pymol and VMD becomes transparent, and you can barely see the molecule. Does anyone have some suggestions? Thank you so much! Best, Chen
[ccp4bb] [Rendering Problem] Pymol & VMD conflicts Coot
Hi all, I am sorry that I ask something a little bit irrelevant here. I am a newbie in Linux, and recently installed Coot, Pymol and VMD on Ubuntu 12.04. It took me a while to figure out a strange conflict among them on my machine. If I remove the mesa-swx11 package, Coot becomes crazily slow. However, if I include that package, which requires the remove of mesa-glx, the backgrounds of Pymol and VMD becomes transparent, and you can barely see the molecule. Does anyone have some suggestions? Thank you so much! Best, Chen
