Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear Robbie, I use pdbset in scripts from time to time, mainly to generate symmetry equivalent copies. I use sftools on the command line more frequently, because it allows a lot of mathematical operations on data in mtz files. I also use sftools to produce lists of average data values against resolution (that I plot then with gnuplot). I can't recall having used coordconv at all. Best regards, Dirk. On 8/26/21 12:29 PM, Robbie Joosten wrote: Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar functionality. Could you answer a few questions: - Do you use any of these tools? - If so, how often? (Few times a week, month, year, or less than once a year). - Which functionality of program X do you use? - Would you like a graphical interface to that functionality or are you happy to use the command line? Personal example: I use pdbset a few times a month, but only the "noise" function. I don't need a graphical interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. Again, only from the command line. Feel free to send your answers directly to me or to the bulletin board if you want to start a discussion. Tips on alternative CCP4 tools to achieve similar effects are probably also interesting for other BB users. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Jeffrey, just using thin shells of reflections for the test set might not be enough to eliminate any correlation to working set reflections. The distance of the test set reflections in reciprocal space, after applying the NCS rotations in reciprocal space, to any reflections of the working set should be large enough to be uncorrelated. A typical maximum distance for correlation in reciprocal space is the first zero (root) of the Fourier transform of the approximated spherical shape of the protein molecule, the so-called G-function (see [1) and [2]). However, this means, that shells should be thicker than 2 times this distance to blindly exclude any potential correlation between test set and working set reflection in reciprocal space. This would be way too expensive! An better way to select uncorrelated reflections is described in [3] (same reference that Kay has given), where for each test set reflection, after applying the NCS rotations in reciprocal space, the distances to the working set reflections are taken into account, and test and working set reflections are chosen such that their distances are large enough to be uncorrelated. Best regards, Dirk. [1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962) [2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966) [3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006) On 8/27/21 4:47 PM, Kay Diederichs wrote: Hi Jeffrey, good question. Both twinning and NCS may couple reflections across free and working sets, and this should be avoided by proper selection - otherwise Rfree is biased towards Rwork. Selecting thin shells should be a good option, and can be done in SFTOOLS (or DATAMAN, or SHELXPRO). How much does it matter? Actually I started to search the literature after reading your question, and expected that one of Z. Dauter's papers would enlighten me, but until a minute ago couldn't find the one(s) that I thought existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227–238 which is relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta Cryst. (2020). D76, 653-667 where they indeed selected thin shells. Best wishes, Kay On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno wrote: Hi Kay, Can you also comment on Rfree set selection? It seems thin shell might be preferred in these cases? jbb Jeffrey B. Bonanno, Ph.D. Department of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 off. 718-430-2452 fax. 718-430-8565 email jeffrey.bona...@einsteinmed.org To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Omit maps in phenix and ccp4
Dear Eleanor, setting occupancies of omitted atoms to zero has the danger of leaving a hole with the shape of these atoms in the bulk solvent mask, leading to positive difference density just because of the missing bulk solvent density. Since the days of X-PLOR, I always removed the omitted atoms. I never tried this with REFMAC5, though. Cheers, Dirk. On 07.04.21 11:46, Eleanor Dodson wrote: Well - I use COOT for this sort of task, and dont trust the automated tools. my procedure is load COOT - probably after a refinement cycle set occupancy of ligand(s) to 0.00 ( Measures - residue information - change occupancy) Look at the environment critically . eg if an ARG or other bulky side chain nearby , or waters etc selectively set occupancies to 0.00 Doo some more cycles of refinement with this coordinate set to remove any memory of the ligand. Look at the map - if the ligand and other zero occ atoms is still in the right place reinstate them, or try to reinterpret density.. Eleanor On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund <mailto:bjarte.l...@uit.no>> wrote: Dear Hari, With regards to 1) Is 15 the number of atoms in your molecule? Or is it the number of hydrogens? The CIF file may have the wrong residue name or lack the hydrogens depending on how you built the ligand-protein complex. There is also a phenixbb for phenix questions, http://www.phenix-online.org/mailman/listinfo/phenixbb <http://www.phenix-online.org/mailman/listinfo/phenixbb> Kind regards, Bjarte Aarmo Lund Postdoc UiT The Arctic University of Norway *From:* CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *Hari shankar *Sent:* Wednesday, April 7, 2021 08:47 *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* [ccp4bb] Omit maps in phenix and ccp4 Dear All, I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have tried phenix for this purpose but get this error message consistently. "Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary." This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to work. 1. Is there something I have missed out that can solve this issue? 2. Is there a program in CCP4i that can be used to generate the required omit maps? 3. In general, how do I omit 3.5 ang of the space around the ligand during this map calculations? Thank you so much for your time. Hari To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density
ected to outline a strategy for every eventuality a priori - that sounds more like the design of an automated pipeline, not advice that users should be expected follow. In summary, it's unadvisable to put all eggs in one basket (of one type of map, Polder or otherwise). If an experienced user likes a particular tool because it's worked well for them in the past, it doesn't mean that they shouldn't try other tools now (in this case: view other types of maps) the next time they encounter a problem. Especially given that tools in our field are still very much evolving over time. Different approaches may have more value and provide more insight in different circumstances. Best regards, Rob To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [xds] how to specify measuring angle
Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). without knowing the correct value for the OSCILLATION_RANGE, data processing might run through but produces non-sense results, independent of the data processing program you use. So, it is absolutely important to know the correct value for the oscillation range per frame. Cheers, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: Going back to Coot 0.8
Hi Paul,
thanks - I've setup my own key bindings, already ;-)
Cheers,
Dirk.
On 11.09.20 12:34, Paul Emsley wrote:
Maybe because I've never attended a Coot course? And maybe because,
I've even never searched for Coot tutorials because the usage of Coot
was (almost) always very intuitive? I am open for any new developments
OK "Pro Tip of the Day!" then...
Edit -> Settings -> Install Template Key Bindings # you need only do
this once.
(this is how I move around in Coot)
Fast navigation by residue: Ctrl-G {Type a number in the little box}
Enter -> Coot jumps to that residue number
Fast navigation by blob: {Point at a blob with your mouse cursor} G ->
Coot brings blob to screen centre
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Gene Center Munich
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76998
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strubio.userweb.mwn.de
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Re: [ccp4bb] AW: Going back to Coot 0.8
rience in our lab. What experience is that? I am still in the dark about you think is now worse. Personally, I did would not like to judge here, as so far, I did not have had enough time to get into the new RSR of coot 0.9.x by myself. But many colleagues did not like the new refinement module maybe just as they are used to the method in all coot versions before. You have a Ferrari parked beside your house but you want to to take the bus to work because that's what you've always done. Or maybe the Ferrari is parked around the back and you don't know it's there? I just thought if it wouldn't be an option to let the user decide what kind of RSR implementation she/he would like to use and give them the choice via an option in coot preferences? That would be possible but not easy. Unlike much of the CCP4 suite, Coot is Free Software. But, again... why would you want to take the bus? Explain. regards, Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Help With Setting up a Stereo view system_walkthrough
MAIL.AC.UK> *Subject:*[ccp4bb] Help With Setting up a Stereo view system Dear colleagues. I would like to check if some one can help me with the setup of my hardware stereo system in Coot under Ubuntu 14 With the help of a friend I collect a bunch of second hand stuff. 1 NVIDIA 3D Video 2 system. 1 Monitor ASUS VG248 conectes through the display port 1 NVIDIA QUADRO 4000 video card. After connecting everything and having a nightmare to install the Legacy Drivers 390.138 And following this instructions https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo I run nvidia-xconfig --stereo=10 I connected the emitter both by USB and the DIN 3 pin conector I connected the monitor through the Display Port I reboot and , the emitter finally shows the green light I can run nvidia-settings and I have the control panel I see Stereo 3D Vision Stereo but only the left cube running. But when I activate hardware stereo nothing works. Does anybody have a clue of what to do? Thanks in advance, Marian Marian Oliva CSIC-Centro de Investigaciones Biológicas Margarita Salas 9, Ramiro de Maeztu 28040-Madrid (Spain) phone: 0034 91 8373112 (x4380) e-mail: mar...@cib.csic.es <mailto:mar...@cib.csic.es> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Help With Setting up a Stereo view system
Dear Marian Oliva,
in my experience, MATE, XFCE and Plasma 5/KDE work well with 3D stereo
if the compositor is disabled. You don't even have to disable COMPOSITE
in the xorg.conf - for those desktops, it is sufficient to disable
composite in the respective desktop/compositor/window manager settings
(tested with Debian Stable and CentOS 8; unfortunately, I can't access
my documents for more details).
For Gnome 3, the picture is somewhat mixed: the gnome3 shell crashes if
you disable composite in xorg.conf. However, if you use a recent Fedora
or CentOS 8 (which is based on relatively recent Fedoras), 3D stereo
works under Gnome 3 out-of-the-box. Upon switching 3D stereo on/off, you
will notice a delay of ~1 second, before a message appears that stereo
has been enabled/disabled. I guess, in these distributions, the
compositor is somehow switched in the background without crashing the
session.
Independent of the desktop, for Fedora/CentOS 8, it might be necessary
to place a udev rule to give write permissions to the USB emitter for
regular users. So, if 3D stereo works under root, but not under a
regular user, you should create a rule like
/etc/udev/rules.d/98-nvstusb.rules, with the contents
# NVIDIA 3D Vision USB IR Emitter
SUBSYSTEM=="usb", ATTR{idVendor}=="0955", ATTR{idProduct}=="0007",
MODE="0666"
Cheers,
Dirk.
On 30.07.20 14:46, Marian Oliva wrote:
Dear colleagues.
I would like to check if some one can help me with the setup of my
hardware stereo system in Coot under Ubuntu 14
With the help of a friend I collect a bunch of second hand stuff.
1 NVIDIA 3D Video 2 system.
1 Monitor ASUS VG248 conectes through the display port
1 NVIDIA QUADRO 4000 video card.
After connecting everything and having a nightmare to install the
Legacy Drivers 390.138
And following this instructions
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
I run nvidia-xconfig --stereo=10
I connected the emitter both by USB and the DIN 3 pin conector
I connected the monitor through the Display Port
I reboot and , the emitter finally shows the green light
I can run nvidia-settings and I have the control panel
I see Stereo 3D Vision Stereo but only the left cube running.
But when I activate hardware stereo nothing works.
Does anybody have a clue of what to do?
Thanks in advance,
Marian
Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)
phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es <mailto:mar...@cib.csic.es>
**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
ficheros adjuntos, pueden contener información protegida para el uso
exclusivo de su destinatario. Se prohíbe la distribución, reproducción
o cualquier otro tipo de transmisión por parte de otra persona que no
sea el destinatario. Si usted recibe por error este correo, se
ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any
attachments may contain confidential and privileged information for
the sole use of the designated recipient named above. Distribution,
reproduction or any other use of this transmission by any party other
than the intended recipient is prohibited. If you are not the intended
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***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
WWW:www.genzentrum.lmu.de
strubio.userweb.mwn.de
***
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Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
Dear Kay & Gerard, the only reason, why I want to count differently, is to distinguish between true and pseudo-multiplicity. Apparently, I get on thin ice by trying to define "identical" reflections ... maybe, instead, we should start working with unmerged data in all programs. If I remember correctly, this is something that Gerard proposed long time ago for phasing programs. Best wishes, Dirk. On 01.07.20 11:52, Kay Diederichs wrote: Dear Dirk, one cannot fully correct radiation damage. Normal scaling procedures take care of the average decay by a smooth resolution-dependant function. Zero-dose extrapolation goes beyond that but needs all symmetry mates - this does not fulfill your definition of "identical". If we really could correct radiation damage then we could collect data to high resolution from all crystals just by using very high dose, and solve structures much more easily. How often you count a reflection is up to you; I don't see what you gain by this. best, Kay Am 01.07.20 um 11:42 schrieb Dirk Kostrewa: Dear Gerard and Kay, yes, you are both right - I have totally forgotten radiation damage! And correcting for this really makes a difference! However, if radiation damage is corrected for reflections measured at different time points under the same geometry, does anything speak against it, to average them and count them only once (say, for crystals measured multiple rounds of 360 degrees to find identical geometries)? Best wishes, Dirk. On 01.07.20 11:02, Gerard Bricogne wrote: Dear Dirk, Aren't you for getting about radiation damage? The n measurements of the same hkl with the same geometry would not be equivalent, although they would enable the tracking of radiation damage without the confounding with absorption effects that comes from considering symmetry-related hkls. I mentioned that in my second message yesterday. The notion of "identical" reflections measurements is problematic for the same reason that Heraclitus wrote (something like) "You cannot step twice into the same river". With best wishes, Gerard. -- On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote: Dear Herman, I think, your MPR proposal is a great idea and would like to second it! And I would also like to propose that data processing programs just average "identical" reflections measured under the same geometry and count them only once (*), so that, in the end, we will get a realistic number of truly independent measurements. Cheers, Dirk. (*) I don't see a difference between measuring the same reflection with the same geometry n-times and measuring it n-times as long (apart from, maybe, catching instabilities in the experimental setup). Just averaging such "identical" reflections would simplify the subsequent scaling process with equivalent reflections that were measured under different geometry. On 01.07.20 09:32, Schreuder, Herman /DE wrote: Dear Bernard and other bulletin board members, As Gerard mentioned, current data processing programs and table 1’s do not make this distinction, but of course, you are free to ask the community to introduce it. My proposal to use “measurements per reflections” is not a joke. It exactly describes what is meant by the parameter and it is easily understood even by lay people like journal editors and referees, without the need of lengthy explanations like the ones we have seen in this thread. I really would like to ask you to consider replacing multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread about completeness of data sets to be hijacked by a discussion on whether use the name multiplicity of redundancy for the number of measurements per reflection. My 2 cents, Herman *Von:* CCP4 bulletin board *Im Auftrag von *Bernhard Rupp *Gesendet:* Dienstag, 30. Juni 2020 17:50 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset? *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk <mailto:owner-ccp...@jiscmail.ac.uk> .…but there is a difference whether I measure the same identical hkl over again or ‘preferably in more than one symmetry-equivalent position’, to quote the IUCr. So do we have a MPSR for the same reflection and a MPRR for the related reflections? Cacophonically yours, BR *From:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell *Sent:* Tuesday, June 30, 2020 08:36 *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset? Dear Herman, I think that MPR is a very neat and tidy, excellent, proposal. Moreover it uses the word “measurements”, and we are an experimental based science. I support it. Great. Greetings, John Emeritus Professor John R Helliwell DSc On 30 Jun 2020, at 1
Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
Dear Gerard and Kay, yes, you are both right - I have totally forgotten radiation damage! And correcting for this really makes a difference! However, if radiation damage is corrected for reflections measured at different time points under the same geometry, does anything speak against it, to average them and count them only once (say, for crystals measured multiple rounds of 360 degrees to find identical geometries)? Best wishes, Dirk. On 01.07.20 11:02, Gerard Bricogne wrote: Dear Dirk, Aren't you for getting about radiation damage? The n measurements of the same hkl with the same geometry would not be equivalent, although they would enable the tracking of radiation damage without the confounding with absorption effects that comes from considering symmetry-related hkls. I mentioned that in my second message yesterday. The notion of "identical" reflections measurements is problematic for the same reason that Heraclitus wrote (something like) "You cannot step twice into the same river". With best wishes, Gerard. -- On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote: Dear Herman, I think, your MPR proposal is a great idea and would like to second it! And I would also like to propose that data processing programs just average "identical" reflections measured under the same geometry and count them only once (*), so that, in the end, we will get a realistic number of truly independent measurements. Cheers, Dirk. (*) I don't see a difference between measuring the same reflection with the same geometry n-times and measuring it n-times as long (apart from, maybe, catching instabilities in the experimental setup). Just averaging such "identical" reflections would simplify the subsequent scaling process with equivalent reflections that were measured under different geometry. On 01.07.20 09:32, Schreuder, Herman /DE wrote: Dear Bernard and other bulletin board members, As Gerard mentioned, current data processing programs and table 1’s do not make this distinction, but of course, you are free to ask the community to introduce it. My proposal to use “measurements per reflections” is not a joke. It exactly describes what is meant by the parameter and it is easily understood even by lay people like journal editors and referees, without the need of lengthy explanations like the ones we have seen in this thread. I really would like to ask you to consider replacing multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread about completeness of data sets to be hijacked by a discussion on whether use the name multiplicity of redundancy for the number of measurements per reflection. My 2 cents, Herman *Von:* CCP4 bulletin board *Im Auftrag von *Bernhard Rupp *Gesendet:* Dienstag, 30. Juni 2020 17:50 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset? *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk <mailto:owner-ccp...@jiscmail.ac.uk> .…but there is a difference whether I measure the same identical hkl over again or ‘preferably in more than one symmetry-equivalent position’, to quote the IUCr. So do we have a MPSR for the same reflection and a MPRR for the related reflections? Cacophonically yours, BR *From:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell *Sent:* Tuesday, June 30, 2020 08:36 *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset? Dear Herman, I think that MPR is a very neat and tidy, excellent, proposal. Moreover it uses the word “measurements”, and we are an experimental based science. I support it. Great. Greetings, John Emeritus Professor John R Helliwell DSc On 30 Jun 2020, at 15:10, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear BB, Since there does not seem a generally accepted term for the subject of this discussions, and since even the IUCR scriptures do not give any guidance, I would propose to introduce a completely new term: Measurements per reflection or MPR This term is politically neutral, should adequately describe this particular statistic and is not associated with entrenched traditions at either side of the Atlantic. What do you think? Herman *Von:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *John R Helliwell *Gesendet:* Dienstag, 30. Juni 2020 14:34 *An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Betreff:* [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset? *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk <mailto:owner-ccp...@jiscmail.ac.uk> Dear Colleagues, In an effort to break this naming deadlock,
Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
Po=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=J0zDXf_fmFuuuSdL_f3Rux6-Dkg9g4Myb2J6inlBYOY=Ib310E3JW-V0qyXGEQchrvA7HBHF9JKxtpRbxK4HkMo=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=J0zDXf_fmFuuuSdL_f3Rux6-Dkg9g4Myb2J6inlBYOY=Ib310E3JW-V0qyXGEQchrvA7HBHF9JKxtpRbxK4HkMo=> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Space group/Unit cell
Dear Maria, are you sure, it's I222? From the extinction rules, you can't distinguish between I222 and I2(1)2(1)2(1). Best regards, Dirk. On 22.05.20 12:08, Demou, Maria wrote: Dear all, I have a question that may have a straight forward answer, and was wondering if this is a common issue. We have a protein crystallised in I222 space group. This is CRP, but the monomer/pentamer is not predicted to fit in this space group. Is there a possibility of the lipid cubic phase being crystallised on it's own, or is there any other obvious reason? Thank you, Maria To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] nVidia 3D Vision2 glasses
rsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de ** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] nVidia 3D Vision2 glasses
Hi Matthias, although, Nvidia announced that the final driver with 3D stereo is the 418 driver, the more recent drivers (at least up to 440) under Linux (CentOS 7.7) apparently still support quad-buffered 3D stereo on our Quadro cards. This is in line with the 3D Vision End-of-Life FAQ <https://nvidia.custhelp.com/app/answers/detail/a_id/4845/~/3d-vision-end-of-life---faq> on the Nvidia site. Best regards, Dirk Kostrewa. On 1/9/20 10:37 AM, Barone, Matthias wrote: Hi Patricia All modern graphics cards still support 3D vision, but you are correct that nvidia is addressing critical issues in release 418 only till April. So if you got a new card, you should not run into problems anytime soon. Just make sure the card is supported with the new kernel packages before updating and stick to the driver release 418. I did so for the last 7 years and just recently had to refurbish the card as it was no longer supported by centos 7.7.1908 So, I dont have an alternative yet either.. Best, matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 *From:* CCP4 bulletin board on behalf of Patricia Borges *Sent:* Wednesday, January 8, 2020 7:25:20 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] nVidia 3D Vision2 glasses Dear all, Does anyone knows any alternative to the nVidia 3D Vision2 glasses for a Ubuntu workstation, since these are at the moment discontinued? Thanks a lot for the help, Best regards Patricia To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de ** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Dear colleagues, since approximately end of last year, there is indeed a 3D stereo problem under CentOS/Scientific Linux 7.6. I found the odd reason for this by a small warning message in the Xorg-log file and some trial-and-error and just want to share this with you, in case, you come across the same problem: My xorg.conf contains the usual switch-off of the composite extension, since this is incompatible with 3D stereo: Section "Extensions" Option "Composite" "Disable" EndSection However, in recent Xorg-log files, there is a warning that the extension "Composite" is not recognized, but the extension "COMPOSITE" is loaded. This doesn't lead to 3D stereo problems on the KDE desktop, but disables 3D stereo on the MATE and probably the XFCE desktop. The solution is both odd and easy - you have to modify the composite option in your xorg.conf as follows: Section "Extensions" Option "COMPOSITE" "Disable" EndSection I have no idea, since when Xorg is case-sensitive, or whether this has anything to do with the Nvidia driver (I use the one from ELRepo). Anyway, this solution appears to work. Best wishes, Dirk. On 20.12.18 22:28, Kay Diederichs wrote: Unfortunately, monitors with built-in emitter are no longer being manufactured. The NVIDIA website has not been updated for years. So that path leads nowhere. Stereo has worked well for us (for existing monitors with built-in emitter, and with Quadro cards /USB emitter) until and including CentOS 7.5. Recently, this stopped after updating to CentOS 7.6 - coot finds the stereo-capable hardware and reports the switch to stereo, but the monitor does not flip the pictures. We are investigating. We are using the Nvidia drivers through the EPEL repository. best, Kay On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller wrote: I can see two possible paths here: 1) Make the card work with an emitter or 2) Switch to a monitor with a built-in emitter Datasheet on the graphics card: <https://www.nvidia.com/content/dam/en-zz/Solutions/design-visualization/productspage/quadro/quadro-desktop/quadro-pascal-p4000-data-sheet-us-nvidia-704358-r2-web.pdf> "3D Stereo support with Stereo Connector1 ... 1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket" The task then is to identify the correct bracket to work with this card, and find a source for purchase. Something like this: https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html "PNY Technoligies Stereo Bracket for Quadro FX 3800" Is this part also compatible with the Quadro P4000? I do not know. http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf "NVidia 3D Stereo Bracket... Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200, M4000, M5000, M6000, P4000, P5000, P6000 graphics cards" Seems promising. - Here is a web page listing compatible monitors. You can filter for those with "built-in emitter" https://www.nvidia.com/object/3d-vision-displays.html On 12/20/18 3:45 PM, Adarsh Kumar wrote: Hello everyone We have just purchased a Dell workstation for crystallography data analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. Please help me out with this one. Some relevant information is as follows: OS: Ubuntu 16.04 LTS Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) Monitor: Asus VG248QE Thanks and regards Adarsh Kumar Suo Lab Florida State University College of Medicine To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-
[ccp4bb] Fwd: Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Sorry for spamming the CCP4BB with this e-mail meant for Kay, only - I accidentally used the "Reply All" button instead of the "Reply" button ... ;-) Anyway, I wish the CCP4 community a Happy New Year! Cheers, Dirk. Forwarded Message Subject: Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation Date: Mon, 7 Jan 2019 14:12:05 +0100 From: Dirk Kostrewa Reply-To: dirk.kostr...@lmu.de To: CCP4BB@JISCMAIL.AC.UK Lieber Kay, ich wünsche Dir ein Frohes und Gesundes Neues Jahr! Ich staune auch, dass es anscheinend keine "3D-Ready"-Monitore mehr gibt! Wir haben einmal versuchsweise einen 144 Hz ASUS Monitor ohne "3D-Ready" gekauft - leider hat da die Synchronisation mit der Stereo-Brille nicht funktioniert ... Mit unseren alten 3D-Ready-Monitoren haben wir unter Scientific Linux 7.6 bisher keine 3D Stereo-Probleme beobachten können. Die Nvidia-Treiber kommen aus dem ELRepo-Repository. Habt Ihr die Stereo-Probleme noch? Liebe Grüße, Dirk. On 20.12.18 22:28, Kay Diederichs wrote: Unfortunately, monitors with built-in emitter are no longer being manufactured. The NVIDIA website has not been updated for years. So that path leads nowhere. Stereo has worked well for us (for existing monitors with built-in emitter, and with Quadro cards /USB emitter) until and including CentOS 7.5. Recently, this stopped after updating to CentOS 7.6 - coot finds the stereo-capable hardware and reports the switch to stereo, but the monitor does not flip the pictures. We are investigating. We are using the Nvidia drivers through the EPEL repository. best, Kay On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller wrote: I can see two possible paths here: 1) Make the card work with an emitter or 2) Switch to a monitor with a built-in emitter Datasheet on the graphics card: <https://www.nvidia.com/content/dam/en-zz/Solutions/design-visualization/productspage/quadro/quadro-desktop/quadro-pascal-p4000-data-sheet-us-nvidia-704358-r2-web.pdf> "3D Stereo support with Stereo Connector1 ... 1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket" The task then is to identify the correct bracket to work with this card, and find a source for purchase. Something like this: https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html "PNY Technoligies Stereo Bracket for Quadro FX 3800" Is this part also compatible with the Quadro P4000? I do not know. http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf "NVidia 3D Stereo Bracket... Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200, M4000, M5000, M6000, P4000, P5000, P6000 graphics cards" Seems promising. - Here is a web page listing compatible monitors. You can filter for those with "built-in emitter" https://www.nvidia.com/object/3d-vision-displays.html On 12/20/18 3:45 PM, Adarsh Kumar wrote: Hello everyone We have just purchased a Dell workstation for crystallography data analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. Please help me out with this one. Some relevant informationis as follows: OS: Ubuntu 16.04 LTS Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) Monitor: Asus VG248QE Thanks and regards Adarsh Kumar Suo Lab Florida State University College of Medicine To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de ** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 #
Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation
Lieber Kay, ich wünsche Dir ein Frohes und Gesundes Neues Jahr! Ich staune auch, dass es anscheinend keine "3D-Ready"-Monitore mehr gibt! Wir haben einmal versuchsweise einen 144 Hz ASUS Monitor ohne "3D-Ready" gekauft - leider hat da die Synchronisation mit der Stereo-Brille nicht funktioniert ... Mit unseren alten 3D-Ready-Monitoren haben wir unter Scientific Linux 7.6 bisher keine 3D Stereo-Probleme beobachten können. Die Nvidia-Treiber kommen aus dem ELRepo-Repository. Habt Ihr die Stereo-Probleme noch? Liebe Grüße, Dirk. On 20.12.18 22:28, Kay Diederichs wrote: Unfortunately, monitors with built-in emitter are no longer being manufactured. The NVIDIA website has not been updated for years. So that path leads nowhere. Stereo has worked well for us (for existing monitors with built-in emitter, and with Quadro cards /USB emitter) until and including CentOS 7.5. Recently, this stopped after updating to CentOS 7.6 - coot finds the stereo-capable hardware and reports the switch to stereo, but the monitor does not flip the pictures. We are investigating. We are using the Nvidia drivers through the EPEL repository. best, Kay On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller wrote: I can see two possible paths here: 1) Make the card work with an emitter or 2) Switch to a monitor with a built-in emitter Datasheet on the graphics card: <https://www.nvidia.com/content/dam/en-zz/Solutions/design-visualization/productspage/quadro/quadro-desktop/quadro-pascal-p4000-data-sheet-us-nvidia-704358-r2-web.pdf> "3D Stereo support with Stereo Connector1 ... 1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket" The task then is to identify the correct bracket to work with this card, and find a source for purchase. Something like this: https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html "PNY Technoligies Stereo Bracket for Quadro FX 3800" Is this part also compatible with the Quadro P4000? I do not know. http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf "NVidia 3D Stereo Bracket... Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200, M4000, M5000, M6000, P4000, P5000, P6000 graphics cards" Seems promising. - Here is a web page listing compatible monitors. You can filter for those with "built-in emitter" https://www.nvidia.com/object/3d-vision-displays.html On 12/20/18 3:45 PM, Adarsh Kumar wrote: Hello everyone We have just purchased a Dell workstation for crystallography data analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but failed to do so. Please help me out with this one. Some relevant information is as follows: OS: Ubuntu 16.04 LTS Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket) Monitor: Asus VG248QE Thanks and regards Adarsh Kumar Suo Lab Florida State University College of Medicine To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- ** Dr. Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de ** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?
Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa <kostr...@genzentrum.lmu.de> Reply-To: Dirk Kostrewa <kostr...@genzentrum.lmu.de> To: CCP4BB@JISCMAIL.AC.UK Dear CCP4ers, I want to check the validity of the refinement of anisotropic B-factors vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This test uses the generalised R-factors (assuming unit weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the end of refinement, one could also use the similar ratio of the usual R-factors, I really would like to check the ratio of the RG-values after refinement. As far as I can see, this value is not reported by the usual refinement programs. Is there a program that reads an mtz file with Fo and refined Fc and just calculates RG? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Calculation of generalised R-factor?
Dear Robbie, thanks for your reply. According to the REFMAC5 manual, the weighted R-factor is just: weighted R factor = sum w ||F_o -|F_c ||/sum w |F_o | So, unfortunately, it is not the generalised R-factor. Do you have a reference for that follow-up paper? PDB_REDO does too much for my purpose ... Cheers, Dirk. On 20.12.2016 15:37, Robbie Joosten wrote: The value for the Hamilton test is written by Refmac as the weighted R-factor. There was a follow-up paper that showed that you shouldn’t use the normal R-factor for the Hamilton test. PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac logfiles to the bselect program to do your own Hamilton test. Cheers, Robbie Sent from my Windows 10 phone *Van: *Keller, Jacob <mailto:kell...@janelia.hhmi.org> *Verzonden: *dinsdag 20 december 2016 14:23 *Aan: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Onderwerp: *Re: [ccp4bb] Calculation of generalised R-factor? I'd be interested as well. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Tuesday, December 20, 2016 8:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculation of generalised R-factor? Dear CCP4ers, I want to check the validity of the refinement of anisotropic B-factors vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This test uses the generalised R-factors (assuming unit weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the end of refinement, one could also use the similar ratio of the usual R-factors, I really would like to check the ratio of the RG-values after refinement. As far as I can see, this value is not reported by the usual refinement programs. Is there a program that reads an mtz file with Fo and refined Fc and just calculates RG? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de <http://www.genzentrum.lmu.de> *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Calculation of generalised R-factor?
Dear CCP4ers, I want to check the validity of the refinement of anisotropic B-factors vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This test uses the generalised R-factors (assuming unit weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the end of refinement, one could also use the similar ratio of the usual R-factors, I really would like to check the ratio of the RG-values after refinement. As far as I can see, this value is not reported by the usual refinement programs. Is there a program that reads an mtz file with Fo and refined Fc and just calculates RG? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] AW: [ccp4bb] Rfree below Rwork
stresses the independence assumption of the free set. Am I correct in believing that Rfree *may* be smaller than Rcryst even in the absence of a major mistake? My hope is that the combined wisdom of ccp4bb followers can point out my possible mistake, suggest tests that I may perform to avoid them and, possibly, arguments in defense of a crystallographic model with Rfree Rcryst. Many thanks, Wolfram Tempel -- === * * * Gerard Bricogne g...@globalphasing.com mailto:g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 tel:%2B44-%280%291223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 tel:%2B44-%280%291223-366889 * * * === To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] [SUSPECTED SPAM] Re: [ccp4bb] nVidia quadro Update for Linux
, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. -- -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Bulk solvent
- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Armando Albert Sent: Friday, January 09, 2015 12:56 AM To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bulk solvent Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Bulk solvent
Dear Bernhard, further thinking about the Babinet scaling effects, I have to correct my conclusion in the last sentence: On 12.01.2015 14:21, Dirk Kostrewa wrote: If, however, the unmodelled part is less well ordered (which is the more common case), it's contribution will mainly affect the model's Fcalc at low resolution. If the overall scaling is dominated by the high resolution terms (which is usually the case), the unmodelled part will not have an effect on the overall scale factor of the model's Fcalc, leaving only the Fcalc at low resolution somewhat too low. Since lowering the model's Fcalc scale factor at low resolution is the main purpose of the Babinet solvent correction, this will lead to an _underestimation_ (!) of the Babinet bulk solvent contribution scale factor (ksol). This, in principle, should increase, or overestimate, the signal of the difference densities at low resolution, which might also help with interpretation of the unmodelled part. The underestimation of the Babinet bulk solvent scale factor is equivalent to an overestimation of the contrast between protein and solvent and should therefore lead to an overestimation of the Fcalc at low resolution. If scaling is still dominated by the high resolution terms, this should lead to a decrease, or underestimation, of the structure factor differences at low resolution, which would reduce the overall signal of the difference densities. But still, this will be an overall effect and not restricted to the location of the unmodelled part. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Bulk solvent
On 09.01.2015 08:56, Armando Albert wrote: Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando Dear Armando, yes: the mask bulk solvent correction depends on the proper calculation of a protein mask. The bulk solvent density is then assigned outside the protein mask. This mask calculation is based on one or two radii around the protein atoms and is always a compromise. Sometimes, the protein mask misses really empty cavities usually surrounded by hydrophobic residues, wrongly filling these cavities with bulk solvent density. This results in relatively large blobs with negative difference density. Sometimes, the protein mask covers narrow cavities really filled with bulk solvent electron density, which is then missing in the model. This results in positive difference densities, that are not easy to interpret. The Babinet bulk solvent correction only uses two parameters, is less effective in describing the contribution of the bulk solvent to the scattering, but is free of these artefacts. I use the Babinet bulk solvent correction sometimes as a control if I'm not sure about the origin of possibly important difference density peaks in narrow regions. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] twin or untwinned
... and please check, whether phenix.xtriage recognized the input data as intensities or as amplitudes. In case of doubt, convert the intensives first into an mtz file with Fs instead of Is and run phenix.xtriage on the mtz file. Best regards, Dirk. Am 03.07.2014 13:36, schrieb Tim Gruene: Hi Yamei, did you by any chance feed the output file from XDS into xtriage? It would indicate the data were twinned even for a near perfect insulin test crystal. After discussion with the developers I understand that phenix does not seem to handle unmerged data well. With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL Mean |L| :0.392 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.219 (untwinned: 0.333; perfect twin: 0.200) after pointless and merging with aimless: Mean |L| :0.492 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.322 (untwinned: 0.333; perfect twin: 0.200) As workaround, run the data through pointless/aimless first. Best, Tim On 07/03/2014 05:04 AM, Yamei Yu wrote: HI all, I have a data set processed to P42 21 2 (the space group was suggested by pointless ). then I use phenix.xtriage to analysis the data. I was confused by the phenix.xtriage result. According to the following number it is twin data, but why it couldn’t find any possible twin law? Determining possible twin laws. 0 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 0 twin operator were found Mean |L| :0.378 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.205 (untwinned: 0.333; perfect twin: 0.200) How could be that? Is it twin or no twin? Please find the log file of phenix.xtrage in attachment. Thank you so much for your suggestion! Yamei Yu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] twin or untwinned
Hi Tim, yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL intensities as amplitudes, producing very different output statistics, compared both to the XDS statistics and to an mtz file with amplitudes created from that XDS file. I've contacted a phenix developer a few weeks ago, but got no reply, yet (maybe, my e-mail got lost). Cheers, Dirk. Am 03.07.2014 13:46, schrieb Tim Gruene: Hi Dirk, that would truely be very sad - the XDS file format is such a beautiful, self-contained and well documented format for diffraction data that a misinterpretation should really not happen. Cheers, Tim On 07/03/2014 01:42 PM, Dirk Kostrewa wrote: ... and please check, whether phenix.xtriage recognized the input data as intensities or as amplitudes. In case of doubt, convert the intensives first into an mtz file with Fs instead of Is and run phenix.xtriage on the mtz file. Best regards, Dirk. Am 03.07.2014 13:36, schrieb Tim Gruene: Hi Yamei, did you by any chance feed the output file from XDS into xtriage? It would indicate the data were twinned even for a near perfect insulin test crystal. After discussion with the developers I understand that phenix does not seem to handle unmerged data well. With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL Mean |L| :0.392 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.219 (untwinned: 0.333; perfect twin: 0.200) after pointless and merging with aimless: Mean |L| :0.492 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.322 (untwinned: 0.333; perfect twin: 0.200) As workaround, run the data through pointless/aimless first. Best, Tim On 07/03/2014 05:04 AM, Yamei Yu wrote: HI all, I have a data set processed to P42 21 2 (the space group was suggested by pointless ). then I use phenix.xtriage to analysis the data. I was confused by the phenix.xtriage result. According to the following number it is twin data, but why it couldn’t find any possible twin law? Determining possible twin laws. 0 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 0 twin operator were found Mean |L| :0.378 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.205 (untwinned: 0.333; perfect twin: 0.200) How could be that? Is it twin or no twin? Please find the log file of phenix.xtrage in attachment. Thank you so much for your suggestion! Yamei Yu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] twinning fun
Dear Bert Van-Den-Berg, as far as I understand this, if you have true P622, process the data in P6 and then test for twinning, both the Britton-test and H-test will indicate perfect merohedral twinning. This is because the Britton-test checks for a sudden increase of negative intensities after de-twinning, which happens only at twin fractions close to 0.5 if the intensities used for de-twinning are the same. But this is true if they are related by crystallographic symmetry. The H-test relates the absolute difference to the sum of the presumably twinned intensities, which gives 0 for intensities related by crystallographic symmetry, again resulting in twin fractions close to 0.5. In other words, intensities related by crystallographic symmetry would indicate perfect twinning in both of these tests. A better test for perfect merohedral twinning would be the ratio of I^2/I^2 which should be 2 for untwinned and 1.5 for perfectly twinned data, tested in the higher space group. These values are reported by data processing programs like XDS. Please, be aware that these ratios have rather strange values if you have an unusually high background (loop fiber diffraction, ice rings, etc.) or extremely weak data. For a really good discussion of twin tests, see Yeates, Methods. Enzymol. 276, 344-358, 1997. Best regards, Dirk. Am 28.01.14 18:26, schrieb Bert Van-Den-Berg: Dear all, I recently collected several datasets for a protein that needs experimental phasing. The crystals are hexagonal plates, and (automatic) data processing suggests with high confidence that the space group is P622. This is where the fun begins. For some datasets (processed in P622), the intensity distributions are normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is no twinning (twinning fractions 0.05). However, for other datasets (same cell dimensions), the intensity distributions are not normal (eg Z-scores 10). Given that twinning is not possible in P622, this suggests to me that the real space group could be P6 with (near) perfect twinning. If I now process the normal L-test P622 datasets in P6, the twin-law based tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), suggesting all my data is twinned. Does this make sense (ie can one have twinning with normal intensity distributions)? If it does, would the normal L-test datasets have a higher probability of being solvable? Is there any strategy for experimental phasing of (near) perfect twins? SAD would be more suitable than SIR/MIR? (I also have potential heavy atom derivatives). Thanks for any insights! Bert -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Fractional coordinate shift with two-character chain names?
Dear Martyn, Pavel and other interested, I think, an official extension by the PDB to two characters for the chain names and 5 digits for residues would really help. I'm currently working on a structure with 6x15 chains (through NCS) - it is huge and only a few programs can handle this by extending the PDB format. The last PDB format revision 3.3 http://www.wwpdb.org/documentation/format33/sect9.html#ATOM still only allows one character for the chain name and four digits for the residue number. More bigger structures will be published in the future and an official human-readable extended PDB format would really help. Cheers, Dirk. Am 30.08.13 18:14, schrieb MARTYN SYMMONS: Hold your horsemen! Does not this option save us from 'formatagedon'? We currently only have single letters or numbers for chains. But we could easily agree to switch to double letters. And long chains can be a sequence of letter number permutations such as A1, A2, A3 etc (actually I notice single numbers are allowed for the PDB - although are deprecated until all the letters have been used). We could allow the first character to be a number as well - so 11 12 13 as a valid sequence.for a single polymer. Conversely we could expand the atom identifier to include letters as is the case with most computing identifiers - however not many programs seem to pay attention to the atom 'numbers' in any case. Cheers Martyn Martyn Symmons (not Winn) Cambridge *From:* Dirk Kostrewa kostr...@genzentrum.lmu.de *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Friday, 30 August 2013, 15:36 *Subject:* Re: [ccp4bb] Fractional coordinate shift with two-character chain names? Hi Martyn, excellent - this worked! Many thanks! Cheers, Dirk. Am 30.08.13 16:04, schrieb Martyn Winn: IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may be something specific in pdbset which interferes. You can try pdbcur as an alternative. Something like: pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb eof translate * frac 0 0.2 0 end eof I just tried it on a little example, and it works for me. Cheers Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: 30 August 2013 14:41 To: ccp4bb Subject: [ccp4bb] Fractional coordinate shift with two-character chain names? Dear CCP4ers, I want to apply a fractional coordinate shift along a polar b-axis with coordinates that have non-standard two-character chain names, such as AA, AB, and so forth. Unfortunately, neither the old USF moleman2 nor the actual CCP4 pdbset can handle these chain names. To my knowledge, only COOT and PHENIX can cope with them. Before I start writing my own little jiffy, is there a quick way to use COOT or PHENIX to apply a fractional coordinate shift, or could you tell me, which other program I can use in this special case? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Fractional coordinate shift with two-character chain names?
Dear CCP4ers, I want to apply a fractional coordinate shift along a polar b-axis with coordinates that have non-standard two-character chain names, such as AA, AB, and so forth. Unfortunately, neither the old USF moleman2 nor the actual CCP4 pdbset can handle these chain names. To my knowledge, only COOT and PHENIX can cope with them. Before I start writing my own little jiffy, is there a quick way to use COOT or PHENIX to apply a fractional coordinate shift, or could you tell me, which other program I can use in this special case? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Fractional coordinate shift with two-character chain names?
Hi Martyn, excellent - this worked! Many thanks! Cheers, Dirk. Am 30.08.13 16:04, schrieb Martyn Winn: IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may be something specific in pdbset which interferes. You can try pdbcur as an alternative. Something like: pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb eof translate * frac 0 0.2 0 end eof I just tried it on a little example, and it works for me. Cheers Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: 30 August 2013 14:41 To: ccp4bb Subject: [ccp4bb] Fractional coordinate shift with two-character chain names? Dear CCP4ers, I want to apply a fractional coordinate shift along a polar b-axis with coordinates that have non-standard two-character chain names, such as AA, AB, and so forth. Unfortunately, neither the old USF moleman2 nor the actual CCP4 pdbset can handle these chain names. To my knowledge, only COOT and PHENIX can cope with them. Before I start writing my own little jiffy, is there a quick way to use COOT or PHENIX to apply a fractional coordinate shift, or could you tell me, which other program I can use in this special case? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster
We have a very similar setup, and I can only second Kay's experience. Best regards, Dirk. Am 31.07.13 13:36, schrieb Kay Diederichs: I have a very different experience with NFS: we are using Gigabit Ethernet, and a 64bit RHEL6 clone with ECC memory as a file server; it has RAID1 ext4 home directories and RAID6 ext4 for synchrotron data. We have had zero performance or reliability problems with this in a computer lab with ~ 10 workstations, and I have seen 115 MB/sec file transfers via NFS, at peak times. Just make sure to export using the async option. HTH, Kay On Wed, 31 Jul 2013 09:21:48 +0900, Francois Berenger beren...@riken.jp wrote: Be careful that running data intensive jobs over NFS is super slow (at least an order of magnitude compared to writing things on a local disk). Not only the computation is slow, but you may be slowing down all other users of the cluster too... F. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Concerns about statistics
Dear Andrea, I agree with Tim and still cut the resolution at I/sigma=2. In my experience, including higher resolution shells with poorer signal-to-noise never changed the apparent resolution of the electron density maps. In addition, the high resolution limit at I/sigma=2 coincides very well with the point where the Fo vs. Fo +Gauss(0,1)*sigma(Fo) correlation coefficient curve, reported by BUSTER, crosses the recommended lower limit of 0.9. And please note, CC*=0.5 corresponds to CC(1/2)=0.143. In my very limited experience, I/sigma=2 corresponds to roughly CC(1/2)~0.7. Although I'm very excited about the CC(1/2) or CC* paper by Karplus Diederichs, I still prefer to be on the save side, until it has been verified in numerous cases, that choosing high resolution cutoffs based on CC(1/2) really leads to higher resolution structures. The recommended procedure to include small resolution increments in refinement to decide the high resolution cutoff is very time-consuming. Best regards, Dirk. Am 13.06.13 17:15, schrieb Andrea Edwards: Hello group, I have some rather (embarrassingly) basic questions to ask. Mainly.. when deciding the resolution limit, which statistics are the most important? I have always been taught that the highest resolution bin should be chosen with I/sig no less than 2.0, Rmerg no less than 40%, and %Completeness should be as high as possible. However, I am currently encountered with a set of statistics that are clearly outside this criteria. Is it acceptable cut off resolution using I/sig as low as 1.5 as long as the completeness is greater than 75%? Another way to put this.. if % completeness is the new criteria for choosing your resolution limit (instead of Rmerg or I/sig), then what %completeness is too low to be considered? Also, I am aware that Rmerg increases with redundancy, is it acceptable to report Rmerg (or Rsym) at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution bin of these crystals? I appreciate any comments. -A -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Single-Gaussian Atomic Scattering Factors?
Dear colleagues, for a very simple calculation, I want to use a single-Gaussian atomic scattering factor approximation (for nitrogen). I only find 2- or 5-Gaussian approximations. Could you please give me a pointer to values of single-Gaussian atomic scattering factor approximations? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Coot Release 0.7 in CCP4 Software Update?
Dear CCP4 developers, this question might be interesting for many CCP4/Coot users: will the Coot release 0.7 and future releases be made available to CCP4 users via the CCP4 software update? Best regards, Dirk. Original-Nachricht Betreff:[COOT] Release 0.7 Datum: Sat, 29 Sep 2012 10:49:45 +0100 Von:Paul Emsley paul.ems...@bioch.ox.ac.uk Antwort an: Paul Emsley paul.ems...@bioch.ox.ac.uk An: c...@jiscmail.ac.uk Hi Coot-users, We are pleased to announce Release 0.7 of Coot. Source: http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz Binaries: http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ Mac 10.8: http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip Now stick a fork in me (as they say)... Paul. A few notes: o FEATURE: RCrane [RNA builder] o FEATURE: Cootaneer [RNA builder] o FEATURE: Het-groups are now represented with bond orders. o FEATURE: Ligand Builder - working in conjunction with cprodrg. o FEATURE: JLigand interface. o CHANGE: symmetry operator number are no longer zero indexed. Add trans component to symmetry file names. o CHANGE: Dotted surfaces now are coloured by atom type and are at atomic radii rather than 1A. o CHANGE: map transformation no longer has symmetry overwrite problems. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** smime.p7s Description: S/MIME Kryptografische Unterschrift
Re: [ccp4bb] Coot Release 0.7 in CCP4 Software Update?
Dear Eugene, thank you for your kind reply and your explanation! Since the CCP4 download site offers Coot either as a stand-alone-package or via the new package manager, I was hoping that new Coot releases could also be handled by the wonderful CCP4 software update. A software update mechanism for Coot, be it part of CCP4 or part of Coot, would help the software administrator :-). A related question just crossed my mind: when will Coot and CCP4mg become part of the CCP4 core packages? Best regards, Dirk. P.S.: I've sent Paul Emsley a CC of this little conversation. Am 01.10.12 13:13, schrieb eugene.krissi...@stfc.ac.uk: Thanks for nice question. Currently, CCP4 update is applicable only to what is distributed as CCP4 core, which guarantees a definite location in $CCP4 directory. Also, updates are not supposed to deliver releases (upgrades), but rather smallish changes between them. Coot is not part of CCP4 core, and in fact, is distributed in many different ways, therefore, CCP4 update mechanism cannot be applied to Coot straightforwardly, and it is unlikely to be applicable to Coot upgrades (e.g., 0.7 to 08). However, the updater may be made a part of Coot package, which is something completely doable in principle, in which case it can deliver fixes for current release. Eugene On 1 Oct 2012, at 09:46, Dirk Kostrewa wrote: Dear CCP4 developers, this question might be interesting for many CCP4/Coot users: will the Coot release 0.7 and future releases be made available to CCP4 users via the CCP4 software update? Best regards, Dirk. Original-Nachricht Betreff:[COOT] Release 0.7 Datum: Sat, 29 Sep 2012 10:49:45 +0100 Von:Paul Emsley paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk Antwort an: Paul Emsley paul.ems...@bioch.ox.ac.ukmailto:paul.ems...@bioch.ox.ac.uk An: c...@jiscmail.ac.ukmailto:c...@jiscmail.ac.uk Hi Coot-users, We are pleased to announce Release 0.7 of Coot. Source: http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz Binaries: http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ Mac 10.8: http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip Now stick a fork in me (as they say)... Paul. A few notes: o FEATURE: RCrane [RNA builder] o FEATURE: Cootaneer [RNA builder] o FEATURE: Het-groups are now represented with bond orders. o FEATURE: Ligand Builder - working in conjunction with cprodrg. o FEATURE: JLigand interface. o CHANGE: symmetry operator number are no longer zero indexed. Add trans component to symmetry file names. o CHANGE: Dotted surfaces now are coloured by atom type and are at atomic radii rather than 1A. o CHANGE: map transformation no longer has symmetry overwrite problems. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de/ *** -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** smime.p7s Description: S/MIME Kryptografische Unterschrift
Re: [ccp4bb] Which Coot for Scientific Linux 6.3
Dear Fred David, the new CCP4 Package Manager works perfectly on SL 6.3, as does the wonderful new CCP4 Update program! The file command for the coot-real executable (version 0.6.2) tells me: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped I hope that helps a little bit. Best regards, Dirk. Am 20.09.12 14:37, schrieb David Waterman: Dear Fred, You may like to try the CCP4 Package Manager, available from the downloads page: http://www.ccp4.ac.uk/download/#os=linux This allows installation of CCP4 components, including Coot, automatically and will attempt to identify the appropriate version for you (disclaimer: I have not tried this on SL 6.3, so can't tell you in advance what you'll get) Cheers -- David On 19 September 2012 17:12, Fred. Vellieux frederic.velli...@ibs.fr mailto:frederic.velli...@ibs.fr wrote: Hi all, The question is in the Subject line of this email: which version of Coot should I download and install on a Scientific Linux 6.3 box ? Ta very much in advance, F.V. -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 tel:%2B33%20438789605 Fax: +33 438785494 tel:%2B33%20438785494 -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** smime.p7s Description: S/MIME Kryptografische Unterschrift
Re: [ccp4bb] CNS installation
Dear Fulvio Saccoccia, along the lines of Ian Tickle's reply: there should be a script cns_solve_env_sh using /bin/sh, which is usually a soft-link to /bin/bash. I use this script for setup of CNS under bash. Best regards, Dirk. Am 12.07.12 16:49, schrieb fulvio saccoccia: Dear ccp4 users, I tried to install CNS under Debian 64bit. I followed the installation giude as reported by CNS developers but I received the following message when souurcing cns_solve_env: bash: setenv: command not found bash: setenv: command not found bash: cns_solve_env: line 32: syntax error near unexpected token `setenv' bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH ` $CNS_SOLVE/bin/getarch`' I know that the script would set all variables; it is indicated for csh (or tcsh) shell. I tried to run the script under a csh shell but I received a different error: Word too long The above statement is also received if a bash-optimized script is run. Does anyone have experience in CNS installation and environment setting? Any advice? Thanks in advance Fulvio Saccoccia Dept. of Biochemical Sciences Sapienza University of Rome, Italy -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Allister Crow, in cases like these, I would recommend to apply the Babinet bulk solvent correction instead of the mask bulk solvent correction as a control (Refmac5 - Scaling - Use Babinet scaling; uncheck Calculcate the contribution from the solvent region). The Babinet bulk solvent correction only uses two overall scaling factors and is usually simple, robust and, in my experience, does not show any local difference density artefacts. The mask bulk solvent correction is more powerful, but, depending on the project and the various mask radii for generating and shrinking the mask, could produce false positive or negative difference density. To exclude these cases, you can always calculate the Babinet bulk solvent correction as a control. Best regards, Dirk. Am 16.04.12 12:37, schrieb Allister Crow: Board members, I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins. I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied. I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters). My questions are therefore: 1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6? 2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities? Best wishes, and thanks in advance for all your help, - Allister Crow -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] proper or improper ncs?
Hi Francis, a quick insertion of your rotation matrix into CONVROT (by Alexandre Urzhumtsev) gives the following equivalent polar rotation angles (definition as in X-PLOR/CNS or Rossmann, 1962): phi,psi,kappa : 111.86 128.68 133.38 291.86 51.32 226.62 For a proper two-fold, a kappa of 180 degrees would be expected. This looks (very) improper to me. Best regards, Dirk. Am 21.02.12 14:47, schrieb Francis E Reyes: Hi all This structure has the following ncs (output via phenix.simple_ncs_from_pdb) OPERATOR 1 CENTER: 18.3443 -55.4605 23.0986 ROTA 1:1.0.0. ROTA 2:0.1.0. ROTA 3:0.0.1. TRANS: 0.0.0. OPERATOR 2 CENTER: 37.0405 -23.8676 -14.9388 ROTA 1: -0.5444 -0.22020.8094 ROTA 2:0.8330 -0.02780.5526 ROTA 3: -0.09910.97510.1985 TRANS:45.3456 -78.7231 53.0085 It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying to rationalize the lack of peaks on the self rotation maps). Any help would be appreciated. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Freezing crystal
Dear Jürgen, Am 07.02.12 16:58, schrieb Bosch, Juergen: snip Then one last remark, LN2 versus cryo-stream freeze. Dipping in LN2 leads to a quicker freeze of your material. /snip Are you sure? There was a publication by Warkentin et al. [1] about a cold gas layer above liquid nitrogen that reduces the expected cooling rate a lot! My very personal experience is, that cryo-cooling in the N2-stream worked better for me than in LN2 in a variety of projects - but the reason could just be me ;-) Best regards, Dirk. [1] Matthew Warkentin, Viatcheslav Berejnov, Naji S Husseini, and Robert E Thorne: Hyperquenching for protein cryocrystallography, J. Appl. Crystallogr., 39, 805-811 (2006) -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA ⁄ RNA molecule that are flexible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the final electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
My understanding of coherence is a constant phase relation between waves. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. Best regards, Dirk. Am 12.01.12 11:27, schrieb Bernhard Rupp (Hofkristallrat a.D.): Does out of phase imply incoherent scattering? I though it means inelastic Compton scattering? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Thursday, January 12, 2012 1:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NMR review Dear Bernhard, Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.): Dear All, I read an interesting statement in an NMR review: regions of a protein or DNA / RNA molecule that are ?exible in the crystal do not provide coherent X-ray scattering and hence do not contribute to the ?nal electron density map. Thus, for all intents and purposes, they can effectively be ignored. Besides that I was not aware that disorder across molecules implies incoherence in scattering, I think this is quite some strong tobacco coming from what is primarily a crystallization screening tool ;-) That doesn't sound wrong to me: the flexible parts are at different relative positions in the unit cells and thus their partial-structure scattering waves do not have a constant phase relation to each other, i.e., they don't give a coherent contribution to the total scattering. But I don't agree to their conclusion, since disorder doesn't necessarily mean, that there won't be any interpretable electron density left. The floppy parts could still be interpreted at an effective lower resolution and thus will not be ignored. Maybe the authors were annoyed by a vanishing NMR signal because the macromolecule crystallized in the NMR test tube ;-) Best regards, Dirk. Cheers, BR PS: I am grappling with the meaning of resolution in NMR. I can see that it could be related to comparable data/parameter ratios, although I am even less clear about the weights of NMR restraint weights than in the case of MX... some cross-trained person out there who can explain? -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] NMR review
I'm not a physicist - but isn't (in)coherence also used to describe the property of sources of electromagnetic waves with constant wavelength? For instance, an incoherent sodium vapour light source (only looking at one emission band) compared to a coherent Laser, or the incoherent emission from a conventional X-ray source or an X-ray undulator compared to a Free-electron-X-ray-Laser? If yes, then we could describe diffraction from a crystal in a similar way by treating the crystal as a light-source, both with coherent and incoherent scattering from the well-ordered and disordered parts, respectively, without any need to change the wavelength. In this analogy, the ordered part would have the coherence of a Laser, whereas the disordered part would have the incoherence of a vapour lamp. Best regards, Dirk. Am 12.01.12 11:57, schrieb Ian Tickle: On 12 January 2012 10:33, Dirk Kostrewakostr...@genzentrum.lmu.de wrote: My understanding of coherence is a constant phase relation between waves. Correct. For a perfect crystal all the unit cells are identical so they scatter in phase and this gives rise to the interference effect we see as Bragg spots, as you say arising from a constant phase relation in specific directions. For a disordered crystal the unit cells are not the same: this destroys the interference effect but there's still a constant phase relation in any specified direction so it's still coherent. Of course, this breaks down for inelastic scattering, but (in)coherence can also be described without any change in wavelength. That's not the definition of incoherence used by the physicists. Of course you're free to redefine it but I think that just confuses everyone. Cheers -- IAn -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Sub-angstrom resolution
Dear Colin, Am 10.01.12 18:08, schrieb Colin Nave: snip 3. The structure factors are lower for large unit cells. This will mean they will be harder to detect, particularly if there is a high background. /snip But aren't the total structure factors of a unit cell the sum of the atomic structure factors? For a larger unit cell (assuming a similar solvent content), I would then expect larger structure factors. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Distinguish NH4 from Na?
Dear Jacob, for NH4+, you would expect a (partial) tetrahedral coordination with typical H-bond distances of ~2.9 A. For Na+, you would expect a (partial) octahedral coordination with Metal-to-ligand distances of ~2.4 A (see Harding, Acta Cryst., D62, 678-682 (2006); Harding, Acta Cryst., D58, 872-874 (2002); Glusker, Advances in Protein Chemistry, 42, 1-76 (1991)). But depending on your data resolution and quality, and on the completeness of the coordination sphere, it might be difficult to distinguish between them. Best regards, Dirk. Am 16.11.11 19:20, schrieb Jacob Keller: Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] [PyMOL] Putting a protein molecule into a grid and traversing through the grid
Hi Anasuya, at least, Gerard Kleywegt's program moleman2 from the Uppsala Software Factory http://xray.bmc.uu.se/usf/ has a command XYz ALign_inertia_axes should do your first task. From the moleman2 manual: This will move the currently selected atoms such that their centre-of-gravity is at the origin (0,0,0); then it will calculate the three principal inertia axes, and align the selected atoms such that these axes coincide with the X, Y and Z axis. This alignment is done such that the major inertia axis coincides with the X-axis (largest eigenvalue), and the minor inertia axis coincides with the Z-axis (smallest eigenvalue). Best regards, Dirk. Am 27.10.11 14:17, schrieb Anasuya Dighe: how do i put a protein molecule inside a cube with x-axis spanning till the largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis spanning till the largest z-coordinate? Once i do this, can i divide the larger cube(i.e. the one holding the entire protein) into smaller ones of lesser dimensions? Say, 5A x 5A x 5A? Once i generate these smaller cubes, is there a way via pymol, by which i can navigate through the protein molecule, (smaller)cube by (smaller)cube? As in, can pymol be used to tell me which residues are lying in which (smaller) cube and so on? Can all this be done in a single pymol window/script? please let me know. Thanks -Anasuya -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Linux vs MacOS for crystallographic software
Yes, SHARP and BUSTER both work on a Mac. Cheers, Dirk. Am 29.09.11 09:45, schrieb Sebastiano Pasqualato: On Sep 29, 2011, at 2:48 AM, Nat Echols wrote: I don't know of any macromolecular crystallography programs that don't run on Mac - Hey there, does this mean that SHARP works on a Mac? ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] question regarding secondary-structure restraints
Dear Nat, yes, I fully agree - all these restraints that improve the geometry either by restraining to high-resolution structures or by introducing H-bond restraints for secondary structures are very useful for low-resolution structures! I see your argument with the Ramachandran plot. But imagine a set of very strong non-bonding/bonding restraints that would result in an absolutely clean Ramachandran plot for any structure, then the Ramachandran plot would become useless even in the absence of any phi/psi-restraints. So, I prefer to err a bit on the safe side here by saying not a truly independent measure. Personally, I think, that ALL refinement programs, including the real-space refinement in Coot, would benefit from inclusion of proper H-bonding terms (something, that for instance the very old X-Plor version did), since this would automatically restrain secondary structures and other hydrophilic interactions to some reasonable geometry, even at very low resolution. Best regards, Dirk. Am 26.09.11 16:17, schrieb Nat Echols: On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de wrote: when I played with H-bond restraints for secondary structures for the refinement of a 4.3 A structure (only a few weeks before they were introduced in phenix), I've made the following observation: at low resolution without H-bond restraints for secondary structures, the carbonyl groups of these secondary structures take the liberty within their globbish electron densities to deviate from their ideal H-bond conformation, resulting in a tight belt of outliers around the preferred Ramachandran regions, with typical deviations of only a few degrees. Introducing the additional H-bond restraints for maintaining secondary structures pulls these outlier carbonyl groups back into the preferred Ramachandran regions. In my case, the number of Ramachandran outliers was reduced to less than one half! Although, these H-bond restraints do not directly include information about allowed Ramachandran regions, the Ramachandran plot is actually affected by these restraints. Thus, at least in my opinion, the Ramachandran plot is then not a truly independent measure for model quality, anymore. The same holds true for all geometrical restraints, of course. It depends on how strictly you assess the independence of validation criteria. The Ramachandran plot is considered valid in most cases because refinement programs traditionally do not restrain phi and psi angles, so we need to rely on the accuracy of the data (and our placement of atoms) and various complementary geometry restraints (especially nonbonded) to keep residues in the favorable regions of the plot. There are a variety of ways to make the plot better by modification of the model and/or restraints (adding hydrogens, increasing the weight on the nonbonded restraints, secondary structure restraints, etc.), none of which are as drastic as directly restraining the model to the plot. I don't really view this as biasing the plot, for two reasons: a) the quantity being measured is independent of the quantity restrained, and b) at least in my hands, these modifications never completely fix the problem of Ramachandran outliers. (It's the loop regions that are really awful.) Anyway, I don't think anyone should feel bad about using this kind of restraint at low resolution. The caveat is that of all the specialized restraints that we (Jeff Headd and I) have been testing for low-resolution refinement (in Phenix), nothing works nearly as well in preserving good geometry, and usually improving the R-factors, as restraining model parameters to a related high-resolution structure, when one is available. Fortunately, every modern refinement program has this ability in some form, and I expect that this is going to have the most impact in improving the overall quality of low-resolution structures. -Nat -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Protein structure solved by computer gamers (and phaser)!
Great! Maybe, they should add an extra term for correlation of Fcalc to Fobs (or LLG or R) to their game. I wonder, if structures could be solved ab inition by players, then :-). Best regards, Dirk. Am 19.09.11 12:33, schrieb Kevin Cowtan: Crystal structure of a monomeric retroviral protease solved by protein folding game players The paper (Nature SB): http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf The game: http://fold.it/portal/ -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] PIR - was Re: [ccp4bb] Another paper structure retracted
Dear Phil, I remember one case where reading a sequence file in PIR format failed, although I did my best to have the right format. It turned out, that the error message about the wrong PIR format was misleading - the real cause was a non-standard amino acid letter, in this case a X. Maybe, you could check your sequence for this ... Best regards, Dirk. Am 12.08.11 11:16, schrieb Phil Evans: I was missing the semicolon, but it still fails On 12 Aug 2011, at 10:12, Antony Oliver wrote: Interesting iPhone formatting things going on... Let's try again... First line is greater than symbol followed by some text about your protein then closed with a semicolon. The next line is blank. The next line contains your amino acid sequence, which you can also close with an optional asterisk. Sent from my iPhone On 12 Aug 2011, at 10:06, Antony Oliverantony.oli...@sussex.ac.uk wrote: PIR is fairly similar to Fasta, from addled memory the format is... protein name; empty line MPREIL...rest of amino acid sequence with an optional asterisk to mark the sequence end. Tony Sent from my iPhone On 12 Aug 2011, at 09:14, Phil Evansp...@mrc-lmb.cam.ac.uk wrote: Can anyone get this server to work? For me it keeps complaining that my sequence file is not a PIR file. The file looks OK to me, but I've never really understood what a PIR file is Phil On 12 Aug 2011, at 01:39, Kevin Jin wrote: Should we really have some crystallographers to review and qc those structures before the formal releasing? JCSG has set a very good mechanism for this issue. There is a sever for self check. http://smb.slac.stanford.edu/jcsg/QC/ On Thu, Aug 11, 2011 at 4:58 PM, Jacob Kellerj-kell...@fsm.northwestern.edu wrote: I think they fudged the data in this paper... JPK On Thu, Aug 11, 2011 at 6:30 PM, David Schullerdj...@cornell.edu wrote: link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1 Ferric C. Fang Arturo Casadevall Retracted Science and the Retraction Index Infec. Immun. doi:10.1128/IAI.05661-11 Abstract: Articles may be retracted when their findings are no longer considered trustworthy due to scientific misconduct or error, they plagiarize previously published work, or are found to violate ethical guidelines. Using a novel measure that we call the “retraction index,” we found that the frequency of retraction varies among journals and shows a strong correlation with the journal impact factor. ... (with special attention to Figure 1, Retraction Index vs. Impact Factor) -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Vonrhein:
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
[ccp4bb] Lattice sampling and resolution - a seeming paradox?
Dear colleagues, I just stumbled across a simple question and a seeming paradox for me in crystallography, that puzzles me. Maybe, it is also interesting for you. The simple question is: is the discrete sampling of the continuous molecular Fourier transform imposed by the crystal lattice sufficient to get the desired information at a given resolution? From my old lectures in Biophysics at the University, I know it has been theoretically proven, but I don't recall the argument, anymore. I looked into a couple of crystallography books and I couldn't find the answer in any of those. Maybe, you can help me out. Let's do a simple gedankenexperiment/thought experiment in the 1-dimensional crystal case with unit cell length a, and desired information at resolution d. According to Braggs law, the resolution for a first order reflection (n=1) is: 1/d = 2*sin(theta)/lambda with 2*sin(theta)/lambda being the length of the scattering vector |S|, which gives: 1/d = |S| In the 1-dimensional crystal, we sample the continuous molecular transform at discrete reciprocal lattice points according to the von Laue condition, S*a = h, which gives |S| = h/a here. In other words, the unit cell with length a is subdivided into h evenly spaced crystallographic planes with distance d = a/h. Now, the discrete sampling by the crystallographic planes a/h is only 1x the resolution d. According to the Nyquist-Shannon sampling theorem in Fourier transformation, in order to get a desired information at a given frequency, we would need a discrete sampling frequency of *twice* that frequency (the Nyquist frequency). In crystallography, this Nyquist frequency is also used, for instance, in the calculation of electron density maps on a discrete grid, where the grid spacing for an electron density map at resolution d should be = d/2. For calculating that electron density map by Fourier transformation, all coefficients from -h to +h would be used, which gives twice the number of Fourier coefficients, but the underlying sampling of the unit cell along a with maximum index |h| is still only a/h! This leads to my seeming paradox: according to Braggs law and the von Laue conditions, I get the information at resolution d already with a 1x sampling a/h, but according to the Nyquist-Shannon sampling theory, I would need a 2x sampling a/(2h). So what is the argument again, that the sampling of the continuous molecular transform imposed by the crystal lattice is sufficient to get the desired information at a given resolution? I would be very grateful for your help! Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?
Dear Ian, oh, yes, thank you - you are absolutely right! I really confused the sampling of the molecular transform with the sampling of the electron density in the unit cell! Sometimes I don't see the wood for the trees! Let me then shift my question from the sampling of the molecular transform to the sampling of the electron density within the unit cell. For the 1-dimensional case, this is discretely sampled at a/h for resolution d, which is still 1x sampling and not 2x sampling, as required according to Nyquist-Shannon. Where is my error in reasoning, here? Best regards, Dirk. Am 15.04.11 14:25, schrieb Ian Tickle: Hi Dirk I think you're confusing the sampling of the molecular transform with the sampling of the electron density. You say In the 1-dimensional crystal, we sample the continuous molecular transform at discrete reciprocal lattice points according to the von Laue condition, S*a = h. In fact the sampling of the molecular transform has nothing to do with h, it's sampled at points separated by a* = 1/a in the 1-D case. Cheers -- Ian On Fri, Apr 15, 2011 at 12:20 PM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Dear colleagues, I just stumbled across a simple question and a seeming paradox for me in crystallography, that puzzles me. Maybe, it is also interesting for you. The simple question is: is the discrete sampling of the continuous molecular Fourier transform imposed by the crystal lattice sufficient to get the desired information at a given resolution? From my old lectures in Biophysics at the University, I know it has been theoretically proven, but I don't recall the argument, anymore. I looked into a couple of crystallography books and I couldn't find the answer in any of those. Maybe, you can help me out. Let's do a simple gedankenexperiment/thought experiment in the 1-dimensional crystal case with unit cell length a, and desired information at resolution d. According to Braggs law, the resolution for a first order reflection (n=1) is: 1/d = 2*sin(theta)/lambda with 2*sin(theta)/lambda being the length of the scattering vector |S|, which gives: 1/d = |S| In the 1-dimensional crystal, we sample the continuous molecular transform at discrete reciprocal lattice points according to the von Laue condition, S*a = h, which gives |S| = h/a here. In other words, the unit cell with length a is subdivided into h evenly spaced crystallographic planes with distance d = a/h. Now, the discrete sampling by the crystallographic planes a/h is only 1x the resolution d. According to the Nyquist-Shannon sampling theorem in Fourier transformation, in order to get a desired information at a given frequency, we would need a discrete sampling frequency of *twice* that frequency (the Nyquist frequency). In crystallography, this Nyquist frequency is also used, for instance, in the calculation of electron density maps on a discrete grid, where the grid spacing for an electron density map at resolution d should be= d/2. For calculating that electron density map by Fourier transformation, all coefficients from -h to +h would be used, which gives twice the number of Fourier coefficients, but the underlying sampling of the unit cell along a with maximum index |h| is still only a/h! This leads to my seeming paradox: according to Braggs law and the von Laue conditions, I get the information at resolution d already with a 1x sampling a/h, but according to the Nyquist-Shannon sampling theory, I would need a 2x sampling a/(2h). So what is the argument again, that the sampling of the continuous molecular transform imposed by the crystal lattice is sufficient to get the desired information at a given resolution? I would be very grateful for your help! Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?
Dear colleagues of the CCP4BB, many thanks for all your replies - I really got lost in the trees (or wood?) and you helped me out with all your kind responses! I should really leave for the weekend ... Have a nice weekend, too! Best regards, Dirk. Am 15.04.11 13:20, schrieb Dirk Kostrewa: Dear colleagues, I just stumbled across a simple question and a seeming paradox for me in crystallography, that puzzles me. Maybe, it is also interesting for you. The simple question is: is the discrete sampling of the continuous molecular Fourier transform imposed by the crystal lattice sufficient to get the desired information at a given resolution? From my old lectures in Biophysics at the University, I know it has been theoretically proven, but I don't recall the argument, anymore. I looked into a couple of crystallography books and I couldn't find the answer in any of those. Maybe, you can help me out. Let's do a simple gedankenexperiment/thought experiment in the 1-dimensional crystal case with unit cell length a, and desired information at resolution d. According to Braggs law, the resolution for a first order reflection (n=1) is: 1/d = 2*sin(theta)/lambda with 2*sin(theta)/lambda being the length of the scattering vector |S|, which gives: 1/d = |S| In the 1-dimensional crystal, we sample the continuous molecular transform at discrete reciprocal lattice points according to the von Laue condition, S*a = h, which gives |S| = h/a here. In other words, the unit cell with length a is subdivided into h evenly spaced crystallographic planes with distance d = a/h. Now, the discrete sampling by the crystallographic planes a/h is only 1x the resolution d. According to the Nyquist-Shannon sampling theorem in Fourier transformation, in order to get a desired information at a given frequency, we would need a discrete sampling frequency of *twice* that frequency (the Nyquist frequency). In crystallography, this Nyquist frequency is also used, for instance, in the calculation of electron density maps on a discrete grid, where the grid spacing for an electron density map at resolution d should be = d/2. For calculating that electron density map by Fourier transformation, all coefficients from -h to +h would be used, which gives twice the number of Fourier coefficients, but the underlying sampling of the unit cell along a with maximum index |h| is still only a/h! This leads to my seeming paradox: according to Braggs law and the von Laue conditions, I get the information at resolution d already with a 1x sampling a/h, but according to the Nyquist-Shannon sampling theory, I would need a 2x sampling a/(2h). So what is the argument again, that the sampling of the continuous molecular transform imposed by the crystal lattice is sufficient to get the desired information at a given resolution? I would be very grateful for your help! Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
Hi Ethan, many thanks for that - your Dark Matter really (en)lightened my day! I wonder, how many pdb records in the future will contain the corresponding remark lines that your incredible perl script produces :-) Best regards, Dirk. Am 01.04.11 08:06, schrieb Ethan Merritt: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Density sharpening with Truncate?
Dear Randy, thanks for your comment - a good point with the likelihood target estimated from E-values! So, in principle, there shouldn't be any difference in maximum-likelihood refinement using sharpened data or not. However, for curiosity, in one case at 4.3 A resolution and a sharpening B-factor of ~100 A**2, I compared ML refinement against the sharpened data with ML refinement against the original data and subsequent map sharpening: the R-factors were almost identical, and so were the electron density maps in most places. But in a some places, the maps were slightly different, with slightly less (!) model-bias and slightly clearer densities for the refinement against sharpened data. But those judgements were very subjective, and since a true structure at really high resolution is not available, I never could quantify this. Either, this was only anecdotal evidence, or there is still room for improvement in existing ML refinement programs. Best regards, Dirk. Am 28.02.11 11:40, schrieb Randy Read: Hi, I'm on Garib's side here. The way the maximum likelihood targets work, the variances are defined relative to the average intensity in a resolution shell, so if you change the falloff the variances will change in the same way. In fact, one way to implement maximum likelihood refinement is in terms of E-values, from which the falloff has been removed. If your B-factors didn't run into hard limits (which, as Garib points out, they will when you make the data non-physical) you would end up with the same model if you refined against sharpened data, except the B-factors would be lower. The other thing that will change if you sharpen the data is that the R-factors will be higher, because the poorly-fit higher-resolution terms will contribute more to the sums. And that's probably not what you want when you might already have a hard time getting a low resolution structure past the freeR police! This is a case where intuition can lead you astray. Intuition might suggest that, if you sharpen the data, the refinement program should pay more attention to fitting the high resolution detail, but the likelihood target doesn't look at the data the same way you do when you look at a map. The fact that you can define the target in terms of E-values means that, if your model and data are both good, the likelihood target can be thought of as sharpening the data anyway. Best wishes, Randy Read On 28 Feb 2011, at 09:02, Dirk Kostrewa wrote: Dear CCP4ers, I really would sharpen the structure factors, not only the electron density maps. The simple reason is: if sharpening emphasizes enough information at higher resolution to help interpreting the electron density maps, refinement will also benefit from this information. Of course, the mean B-factor of the refined structure will be lower by the sharpening B-factor, but since B-factor sharpening is usually done with lower resolution data, the Wilson B-factor is usually very high, and thus far, I didn't run into problems with B-factors crashing at the lower limit. The sharpening B-factor can easily reach values in the -100s A**2, not only -10 to -50 A**2. Axel Brunger has published several papers about how to estimate a good sharpening B-factor (a recent one with references is Brunger et al. Acta Cryst D65, 128-133). He usually describes map sharpening, but B-factor sharpening of structure factors seems to be done routinely for virus structures in Steve Harrisons lab. One word of caution: the B-factor sharpening should be correctly described not only in the publication but also in the PDB deposition (if refinement was done against sharpened structure factors, the refinement statistics can only be reproduced using these structure factors). The original structure factors can be easily reproduced by applying back the negative sharpening B-factor. Best regards, Dirk. Am 26.02.11 01:09, schrieb Garib N Murshudov: I would not sharpen structure factors before refinement. It may cause problems with B value refinement (a lot of B values may stuck around 2 or minimum B). One must remember that not all atoms in crystal have same Bvalue. There is a distribution of Bvalues. However maps can be sharpened after refinement. It can be done directly in coot (I hope this version of coot is now widely available). Or if you are using refmac for refinement you can use: mapc sharpen # regularised map sharpening. Bvalues and regularisation parameters are calculated automatically or mapc sharpenBvalue # regularised map sharpening with specified Bvalue or mapc sharpenBvalue mapc sharpen alphavalue=0.1# regularisation paramater. alpha=0 is simple sharpening. I am sure other programs have similar options. (I know CNS has and it has been used successfully by many people) regards Garib P.S. These options available from refmac v5.6 available from; www.ysbl.york.ac.uk/refmac/data/refmac_experimental
Re: [ccp4bb] strange density
An additional information would be to calculate an anomalous difference map: at typical synchrotron wavelenght of ~1 A, Ni would have ~2 electrons f'', whereas Cl would have only ~0.2 electrons f''. So, a strong anomalous difference density peak would be more consistent with Ni than with Cl. However, if the data set was collected on a home source with CuKalpha wavelength, such a map would be not be very helpful here, because the Ni signal is about as weak as the Cl signal. Best regards, Dirk. Am 24.02.11 16:37, schrieb Gloria Borgstahl: I'm voting with Roger this time. If I were you I would model a nickel in there (unless you have a better candidate) if it is right, the distances to the His should be like seen in a SOD active site. Then you can model the bonds and waters. You may need partial occupancy on the metal. Reminds me of the time I found a 6th water in MnSOD as I was making the token electron denisty figure of the active site. Found myself doing more refinement and a much better paper. On Thu, Feb 24, 2011 at 8:15 AM, Roger Rowlett rrowl...@colgate.edu mailto:rrowl...@colgate.edu wrote: This looks suspiciously like a metal ion with 3 or more resolved water ligands. It's hard to tell from the images provided, but it looks like the metal could be close to octahedral, with 2 His and 3 water ligands well-defined. The estimated metal-nitrogen bond distances might help narrow down the metal ion. For example, tetrahedral Zn(II) has a Zn-N bond distance of around 2.0 A. I suppose this could be a Mg(II) ion, since that is in your crystallization mix, but I think that Mg(II) typically prefers harder protein ligands, e.g., carboxylates. Zn(II) is a very common contaminant in solution, however, and should not necessarily be discounted; indeed Zn(II) and other first row transition metal ions would be expected to have a reasonable affinity for medium hard/soft ligands such as vicinial His residues. Cheers. On 2/23/2011 7:34 PM, Alex Singer wrote: cocrystallized in 2.5mM Glycero-3Phosphocholine and cryoprotected by dipping in -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu mailto:rrowl...@colgate.edu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Postdoc position at the Gene Center Munich
Dear CCP4ers, on behalf of Patrick Cramer, I send a Postdoc position offer, given below. Please, do not respond to me, but to the e-mail addresses given in the job description. Best regards, Dirk Kostrewa. *** Applications are invited for a RESEARCH SCIENTIST (POSTDOC) POSITION IN CRYSTALLOGRAPHY to work on multi-component complexes and study the mechanisms of gene transcription in the lab of Patrick Cramer at the Gene Center of the University of Munich (www.LMB.uni-muenchen.de/cramer). We look for a collaborative person with a background in X-ray crystallography, documented by at least one significant first-author publication. We offer a stimulating environment on a leading European life science campus, and a longer-term perspective (2-5 years). There are possibilities to join ongoing projects of high scientific significance, to participate in networks of excellence at the national and international level, and to contribute to teaching. Thus this position can prepare for an independent career. Applications including a one-page CV, list of publications, and email addresses of two referees should be sent to R. Menacher (menac...@lmb.uni-muenchen.de). Questions may be sent to Patrick Cramer (cra...@lmb.uni-muenchen.de). Deadline for applications is March 1st, 2011.
[ccp4bb] PDB deposition ADIT without frames?
Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump between the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] PDB deposition ADIT without frames?
Thanks a lot for your suggestions! Meanwhile, my colleague entered the desired sequence information into the first website without frames, and after that, the usual frame layout re-appeared! I don't know whether this is a bug or intended ... Best regards, Dirk. Am 15.02.11 17:00, schrieb Dirk Kostrewa: Dear CCP4ers, a colleague of mine is just going through the PDB deposition process using the usual ADIT website. In contrast to my experience and to the ADIT turorial, she has only one frame in the browser. The left frame with the overview is missing. So, there is no way to jump between the different deposition fields, which makes deposition a nightmare. Has anybody else noticed that? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Counting of geometrical restraints?
Dear Ian other CCP4ers, I want to get a riddle about counting geometrical restraints solved, which emerged in my head after a recent discussion http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17534.html on this board about the effect of NCS on the data:parameter ratio. This discussion quickly centered around the 1998 Acta Cryst paper about R-factor ratios [1]. So, here is my riddle: On one hand, geometrical restraints can be counted as observations. Refinement programs use differences between model geometry and ideal geometry restraints as least-squares targets, in a similar way to differences between model structure factor amplitudes and observed structure factor amplitudes. Model refinement is possible using geometrical restraints only, in the complete absence of observed structure factor amplitudes (idealization; whether this makes sense, is a different question). Geometrical restraints are also counted as observations in [1], both in Table 1 and in the text (for example in formula 2). On the other hand, it is shown in that paper, summarized in Table 2, that for the Rfree/Rwork ratios, geometrical restraints effectively reduce the number of refinement parameters, with a smooth transition from restraints to constraints via the residual term Drest. This implies that geometrical restraints can be counted as reducing the numbers of parameters, not as increasing the number of observations, which was also brought up as an argument in the aforementioned discussion. Thus, on one hand, geometrical restraints can be counted as observations, on the other hand they can be counted as reducing the number of parameters. The riddle for me is, that these two ways of counting are mutually exclusive alternatives - so, which one is the right one? I would be grateful, if you, Ian, or any other crystallographer on this board could help me (and maybe others) to solve this riddle. Best regards, Dirk. [1] Tickle, Laskowski, Moss. Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement, Acta Cryst., D54, 547-557 (1998) -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Merging data to increase multiplicity
Hi Bert, here is one anecdotal evidence: a couple of years ago, I had one real in-house 3 A data set from a crystal after a quick iodide soak and processed the images with denzo/scalepack, mosflm/scala and xds/xscale. I got lower Rsym, higher I/sig(I) and better anomalous signal with xds. More importantly, I could solve the iodide substructure easily with SHELXC/D at different high resolution limits up to 3.5 A with the xds data set. For the other data sets, I had to cut the higher resolution limit down to 4-5 A, and there were fewer solutions for the substructure. Best regards, Dirk. Am 28.01.11 14:37, schrieb Van Den Berg, Bert: I have heard this before. I'm wondering though, does anybody know of a systematic study where different data processing programs are compared with real-life, non-lysozyme data? Bert On 1/28/11 7:58 AM, Bosch, Juergen jubo...@jhsph.edu wrote: I was a bit reductive with my statement (iPhone) The equation below is suppose to read: If you have bad data, then you need to process with XDS in order to get the maximum out of your data. Thanks Tim, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ http://web.me.com/bosch_lab/ On Jan 28, 2011, at 7:44 AM, Tim Gruene wrote: Dear Jürgen, is this an assignment operator or an equal sign? For if it's the latter it could read that the result of processing data with XDS are bad data, which is rather rude and probably not what you meant. Tim On Fri, Jan 28, 2011 at 06:55:43AM -0500, Jürgen Bosch wrote: Bad data = processing with XDS Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jan 28, 2011, at 6:46, José Trincão trin...@dq.fct.unl.pt wrote: Hello all, I have been trying to squeeze the most out of a bad data set (P1, anisotropic, crystals not reproducible). I had very incomplete data due to high mosaicity and lots of overlaps. The completeness was about 80% overall to ~3A. Yesterday I noticed that I could process the data much better fixing the mosaicity to 0.5 in imosflm. I got about 95% complete up to 2.5A but with a multiplicity of 1.7. I tried to integrate the same data fixing the mosaicity at different values ranging from 0.2 to 0.6 and saw the trend in completeness, Rmerge and multiplicity. Now, is there any reason why I should not just merge all these together and feed them to scala in order to increase multiplicity? Am I missing something? Thanks for any comments! Jose José Trincão, PhDCQFB@FCT-UNL 2829-516 Caparica, Portugal It's very hard to make predictions... especially about the future - Niels Bohr -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] High Rmerge with thin frames
Dear Sergei, since your Rmerge is high at low resolution even in P1, my guess is, that there was a problem either with the crystal or with the data collection. Fine slicing should improve the data quality, because your get a better description of the reference profiles and reduce the background. Different merging of fine-sliced images into coarser-sliced images was already systematically done by Wolfgang Kabsch, with the result, that finer slices gave better results, although slices much finer than half the full mosaicity angle of a reflection didn't improve the results much further (I've heard a talk given by Wolfgang, but never found a publication about these results). There is a publication in 1999 about fine-slicing by Jim Pflugrath, that you might want to read about this (Acta Cryst D55, 1718-1725). So, merging fine-sliced images into coarse-sliced probably won't help. Anyway, good luck! Dirk. Am 05.11.10 09:40, schrieb Sergei Strelkov: Dear All, I am processing a dataset collected (not by me) with 0.1 degree oscillations. The diffraction is quite weak even though there is a clean diffraction pattern to about 3A. Either Mosflm or XDS processes the data readily with +/- default settings but both yield a high overall Rmerge of about 0.23 in the expected symmetry. Processing in P1 yields an overall Rmerge of ~0.18, but what is especially disappointing is that Rmerge is as high as 0.15 at ~5A resolution already. The question is, how can we process the data so that the merging statistics becomes more reasonable? Apparent mosaicity turns out to be ~0.5A. My naive way of thinking is to try treating each five consecutive frames as a single 0.5 degree frame. Does anyone have experience with this? Many thanks in advance, Sergei -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Off-Topic: CNS MAXLEV error
Dear CCP4ers, sorry for this off-topic question, but maybe, somebody can answer this: I want to refine some self-defined dummy-atoms (scatter.lib, topology, parameter: all copypaste from water and modified) with CNS and get the following enigmatic error message: %CONNE2 error encountered: MAXLEV exceeded Does anyone could point me to a direction what that means? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Against Method (R)
Hi Robbie, yes, the apparently larger radius of convergence in real space refinement impresses me, too. Therefore, I usually do local real space refinement after manually correcting errors, either with Moloc at lower resolution or with Coot at higher resolution, prior to reciprocal space refinement. If I recall correctly, real space refinement was introduced by Robert Diamond in the 60s long before reciprocal space refinement. In the 90s Michael Chapman tried to revive it, but without much success, as far as I know. With the fast computers today, maybe the time has come again for real space refinement ... Best regards, Dirk. Am 29.10.10 08:03, schrieb Robbie Joosten: Hi Bart, I agree with the building strategy you propose, but at some point it stops helping and a bit more attention to detail is needed. Reciprocal space refinement doesn't seem to do the fine details. It always surprises me how much atoms still move when you real-space refine a refined model, especially the waters. I admit this is not a fair comparison. High resolution data helps, but better data makes it tempting to put too little effort in optimising the model. I've seen some horribly obvious errors in hi-res models (more than 10 sigma difference density peaks for misplaced side chains). At the same time there are quite a lot of low-res models that are exceptionally good. Cheers, Robbie Date: Thu, 28 Oct 2010 16:32:04 -0600 From: bart.ha...@ualberta.ca Subject: Re: [ccp4bb] Against Method (R) To: CCP4BB@JISCMAIL.AC.UK On 10-10-28 04:09 PM, Ethan Merritt wrote: This I can answer based on experience. One can take the coordinates from a structure refined at near atomic resolution (~1.0A), including multiple conformations, partial occupancy waters, etc, and use it to calculate R factors against a lower resolution (say 2.5A) data set collected from an isomorphous crystal. The R factors from this total-rigid-body replacement will be better than anything you could get from refinement against the lower resolution data. In fact, refinement from this starting point will just make the R factors worse. What this tells us is that the crystallographic residuals can recognize a better model when they see one. But our refinement programs are not good enough to produce such a better model in the first place. Worsr, they are not even good enough to avoid degrading the model. That's essentially the same thing Bart said, perhaps a little more pessimistic :-) cheers, Ethan Not pessimistic at all, just realistic and perhaps even optimistic for methods developers as apparently there is still quite a bit of progress that can be made by improving the search strategy during refinement. During manual refinement I normally tell students not to bother about translating/rotating/torsioning atoms by just a tiny bit to make it fit better. Likewise there is no point in moving atoms a little bit to correct a distorted bond or bond length. If it needed to move that little bit the refinement program would have done it for you. Look for discreet errors in the problematic residue or its neighbors: peptide flips, 120 degree changes in side chain dihedrals, etc. If you can find and fix one of those errors a lot of the stereochemical distortions and non-ideal fit to density surrounding that residue will suddenly disappear as well. The benefit of high resolution is that it is much easier to pick up and fix such errors (or not make them in the first place) Bart -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Against Method (R)
Dear George, thanks a lot! I see the point, that in reciprocal space refinement one could refine directly against the observed intensities and sigmas. But in principle, one could do iterative real space refinement, structure factor and intensity calculation for refinement statistics and weights, calculation of an improved electron density map (but that requires Fs again ...), and so forth until some convergence criterion is met. I wonder, which refinement scheme is more efficient. The missing reflections in map calculation is something that we have to live with, and unless the data are severely incomplete, I must admit, that I don't worry too much. The twinning problem is really severe! Here, I don't see how this could be done in a clever way in real space. Interesting discussion ... Best wishes, Dirk. Am 29.10.10 10:41, schrieb George M. Sheldrick: Dear Dirk, There are good reasons why real space refinement has never become popular. With reciprocal space refinement, you refine directly against what you measured, taking the standard uncertainly of each individual intensity into account. In this context I was pleased to read in CCP4bb that REFMAC will soon be refining against intensities (like SHELXL). Then the assumptions made (e.g. no distortion of the expected intensity distribution by e.g. NCS or twinning) and even 'bugs' in (c)truncate will no longer matter. If for some reason a reflection wasn't measured, then simply leaving it out it does not invalidate a recoprocal space refinement. The same applies to reflections that are reserved for Rfree. In contrast, the electron density is only theoretically correct if all reflections between 0,0,0 and infinity are included in the Fourier summation, For a twin it is even worse, because we don't know how to partition the difference between Fo^2 and Fc^2 between the twin components. None of the attempts to work around these problems are entirely convincing. Maps and real space refinement are invaluable in the intermediate stages of model building and correction, but the final refinement should be performed in reciprocal space. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 29 Oct 2010, Dirk Kostrewa wrote: Hi Robbie, yes, the apparently larger radius of convergence in real space refinement impresses me, too. Therefore, I usually do local real space refinement after manually correcting errors, either with Moloc at lower resolution or with Coot at higher resolution, prior to reciprocal space refinement. If I recall correctly, real space refinement was introduced by Robert Diamond in the 60s long before reciprocal space refinement. In the 90s Michael Chapman tried to revive it, but without much success, as far as I know. With the fast computers today, maybe the time has come again for real space refinement ... Best regards, Dirk. Am 29.10.10 08:03, schrieb Robbie Joosten: Hi Bart, I agree with the building strategy you propose, but at some point it stops helping and a bit more attention to detail is needed. Reciprocal space refinement doesn't seem to do the fine details. It always surprises me how much atoms still move when you real-space refine a refined model, especially the waters. I admit this is not a fair comparison. High resolution data helps, but better data makes it tempting to put too little effort in optimising the model. I've seen some horribly obvious errors in hi-res models (more than 10 sigma difference density peaks for misplaced side chains). At the same time there are quite a lot of low-res models that are exceptionally good. Cheers, Robbie Date: Thu, 28 Oct 2010 16:32:04 -0600 From: bart.ha...@ualberta.ca Subject: Re: [ccp4bb] Against Method (R) To: CCP4BB@JISCMAIL.AC.UK On 10-10-28 04:09 PM, Ethan Merritt wrote: This I can answer based on experience. One can take the coordinates from a structure refined at near atomic resolution (~1.0A), including multiple conformations, partial occupancy waters, etc, and use it to calculate R factors against a lower resolution (say 2.5A) data set collected from an isomorphous crystal. The R factors from this total-rigid-body replacement will be better than anything you could get from refinement against the lower resolution data. In fact, refinement from this starting point will just make the R factors worse. What this tells us is that the crystallographic residuals can recognize a better model when they see one. But our refinement programs are not good enough to produce such a better model in the first place. Worsr, they are not even good enough to avoid degrading the model. That's essentially the same thing Bart said, perhaps a little more pessimistic :-) cheers, Ethan Not pessimistic at all, just realistic and perhaps even optimistic for methods developers as apparently there is still
Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]
Hi Tim, sorry for my late reply - I just came back to the lab. In the Babinet bulk solvent correction, no bulk solvent phases are used, it is entirely based on amplitudes and strictly only valid if the phases of the bulk solvent are opposite to the ones of the protein. And as Sasha Urzhumtsev pointed out, this assumption is only valid at very low resolution. The mask bulk solvent correction is a vector sum including the phases of the bulk solvent mask, which makes a difference at medium resolution (up to ~4.5 A, or so). As far as I can see, your formulas given below do not distinguish between amplitude (modulus) and vector bulk solvent corrections. Personally, I really don't see any physical sense in using both corrections together, except for compensating any potential scaling problems at low resolution. If the model is basically complete and correct, the mask bulk solvent correction is usually superior to the Babinet bulk solvent correction (see, for example, my old and small CCP4 Newsletter contribution http://www.ccp4.ac.uk/newsletters/newsletter34/bsdk_text.html). However, there are also good reasons for using the Babinet bulk solvent correction (it should be an option in ALL refinement programs!): - it requires only two parameters and can be used in any case - in rigid body refinement, the mask lags behind; here, I always use the Babinet BS correction - channels could show false positive density, because the mask left them empty - this depends heavily on the choice of radii to determine/shrink the bulk solvent mask; in such cases, I always calculate a Babinet BS correction as a control Best regards, Dirk. Am 23.10.10 22:14, schrieb Tim Fenn: On Sat, 23 Oct 2010 10:05:15 -0700 Pavel Afoninepafon...@gmail.com wrote: Hi Tim, ...but I hope this answers the question: Babinet's vs. the flat model? Use them together! ;) thanks a lot for your reply. Could you please explain the *physical* meaning of using both models together? I can try! Typically, we model the bulk solvent using a real space mask that is set to 1 in the bulk solvent region and 0 in the protein. This gets Fourier transformed, symmetrized and added in to the scattering factors from the molecule (Equation 1 in the paper, page 6 in your presentation): Ftot = Fc + ks*Fs*exp(-Bs*s^2/4) which works great and is how things are usually coded in most macromolecular software, no problems or arguments there. However, we can come from the opposite - but equivalent! - direction of Babinet's principle, which tells us the bulk solvent can also be modeled by inverting everything: set the bulk solvent region to 0 and the protein region to 1 in the real space mask, apply a Fourier transform to that and then invert the phase: Ftot = Fc - ks*Fm*exp(-Bs*s^2/4) (I'm using Fm to distinguish it from Fs, due to the inversion of 0's and 1's in the real space mask) This is equation 2 in the paper. So we're still using the flat model to compute Fm, and we're using Babinet's principle to add it in to the structure factors - although its better described as adding the inverse (thus the minus sign in the second equation) of the complement (Fm rather than Fs). These two equations are exactly equivalent, without any loss of generality. So, I would argue the flat model and Babinet's are very much congruous. Also take a look at the description/discussion in the paper regarding Figure 2 (which helped me think about things at first). The big difference is that Babinet's is usually applied as: Ftot = Fc - ks*Fc*exp(-Bs*s^2/4) which, I would argue, isn't quite right - the bulk solvent doesn't scatter like protein, but it does get the shape right. Which I think is why Fokine and Urzhumtsev point out that at high resolution this form would start to show disagreement with the data. I haven't looked at this explicitly though, so we still haven't answered that question! We didn't want to spend much time on it in the paper, our main goal was to try out the differentiable models we describe. The Babinet trick was a convenient way to make coding easier. Anyway, I hope this helps explain it a bit more, and again: sorry for the long-windedness. Regards, Tim -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Fill map/mask with dummy atoms?
Dear colleagues, many thanks for all of your kind support, following my request about placing dummy atoms into en EM-map! Here is a short summary: Frederic Vellieux kindly offered me to use his programs with clever positioning of atoms in a density. Paul Emsley pointed to a program findwaters, that comes with Coot, with option --flood to fill a density with waters. John Tanner pointed to a USF program FLOOD from the VOIDOO packages for filling cavities with water. Victor Lamzin sent me a script for ARP/wARP for placing dummy atoms into a map. Alex Shkumatov pointed to two SAXS programs, em2dam and vol2pdb, to convert low resolution maps into dummy atoms. Now, I have plenty of options to play with! Best regards, Dirk. Am 13.10.10 13:49, schrieb Dirk Kostrewa: ... maybe, to clarifiy my question a little bit: I want to fill an essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't work. I would need a program that fills this map with dummy atoms for a few things that I want to try with this atomic representation. Best regards, Dirk. Am 13.10.10 13:00, schrieb Dirk Kostrewa: Dear CCP4ers, is there a program around that allows to fill an input map or mask with dummy atoms? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Question regarding S-SAD
Dear Kornelius, a few thoughts that come to my mind: - Are you sure about the space group P6? For proteins, P6_1, P6_2, ..., P6_5 are more usual. - Did you try both hands of the Se-sites? In case of space group P6_n, you have to invert both the handedness of the sites _and_ of the space group, resulting in P6_(6-n) (i.e. P6_5 instead of P6_1). - I wouldn't worry about the mosaicity. Best regards, Dirk. Am 18.10.10 14:03, schrieb Kornelius Zeth: Dear all, we have collected S-SAD data (2x4000 Frames, 0.1 degrees, wedges of 40 Frames, Rf between 3-5% overall) and received a dataset to 2.5 A which is complete with a redundancy of 30-40. Space group is P6 and the AU 120 residues, 6 Mets. Native data are up to 1.9 A Sharp and Phenix both return the expected number of sites and given the phasing power to approx. 3.8 A after HA refinement I was hoping to get some maps which I could use for tracing the structure. However DM, Solomon and Resolve all fail to significantly improve the phases and densities look not as if they can be traced. There is some partial twinning of 15%. What I noticed was that the spot profiles in XDS looked not as the are supposed to, presumably because the mosaicity of the spots are 0.4-0.6 and spot integration may be hampered. Still, merging Rfactors are brilliant. Any hints + ideas are welcome! Best wishes Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Fill map/mask with dummy atoms?
Dear CCP4ers, is there a program around that allows to fill an input map or mask with dummy atoms? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Fwd: [ccp4bb] Fill map/mask with dummy atoms?
... maybe, to clarifiy my question a little bit: I want to fill an essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't work. I would need a program that fills this map with dummy atoms for a few things that I want to try with this atomic representation. Best regards, Dirk. Am 13.10.10 13:00, schrieb Dirk Kostrewa: Dear CCP4ers, is there a program around that allows to fill an input map or mask with dummy atoms? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Difference map
Hi Intekhab Alam, an Fobs-Fobs' map usually works only if the two crystals are isomorphous, which means that there are neither large cell constant changes nor any other larger structural changes (like overall rotations, domain movements, other rearrangements) than the bound compound (ligand, heavy atom, ...). Scaleit produces a plot of Riso against resolution which ideally should resemble the scattering curve of the bound compound (~ like an atomic scattering curve for instance), plus a mild increase at high resolution due to the increasing noise component at higher resolution. If the curve starts at high Riso values and increases steeply, this would indicate anisomorphism, and there is probably no chance to detect your compound signal. All this is qualitative, but you could estimate the expected change with the Crick-Magdoff equation by replacing the heavy atoms with a sum over your compound atoms. The Crick-Magdoff equations has been recently discussed on this board: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg10039.html Good luck, Dirk. Am 29.09.10 09:09, schrieb intekhab alam: Hi Folks I have a query regarding the difference map between the two structures ligand bound data (2.5A) and native (2.8A). I tried to calculate the fourier difference map between two data sets ligand bound- native. The protocol in CCP4 that i used is as: 1.merge the mtz file of native nad ligand bound using cad 2. scaling this combine file with scaleit program followed by map generation uisng fft. I got the map but i did not find the fu;ll map of the ligand,i can only see small density nera the ligand binding site at 5 sigma level. I have calculated omit map that cleraly showed the ligand. why is such discrepency in the two cases, is there is something missing from the calculation. kindly help me out. Thanks and regards Intekhab alam -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio
Dear Ian, many thanks for your explanations - they've changed my view! I was always a bit puzzled by the supposedly contradictory transition between restraints and constraints with increasing weight, which has been clarified by their effect on the number of parameters, and not on the number of observations. Interestingly, in your Acta Cryst paper, restraints are also counted as observations (for instance, in Table 1 and §2.3), but in the derived residuals and ratios, it's clear that they reduce the effective number of parameters. Best regards, Dirk. Am 20.09.10 13:22, schrieb Ian Tickle: Hi Dirk First, constraints are just a special case of restraints in the limit of infinite weights, in fact one way of getting constraints is simply to use restraints with very large weights (though not too large that you get rounding problems). These 'pseudo-constraints' will be indistinguishable in effect from the 'real thing'. So why treat restraints and constraints differently as far as the statistics are concerned: the difference is purely one of implementation. Second, restraints are not interchangeable 1-for-1 with X-ray data as far as the statistics are concerned: N restraints cannot be considered as equivalent to N X-ray data, which would be the implication of adding together the number of restraints and the number of X-ray data. This can be seen in the estimation of the expected values of the residuals (chi-squared) for the working test sets, which are used to estimate the expected Rfree. If you take a look at our 1998 AC paper (D54, 547-557), Table 2 (p.551), the last row of the table (labelled 'RGfree/RG') shows the expected residuals for the working set (denominator) and test set (numerator) for the cases of no restraints, restrained and constrained refinement: No restraints (or constraints): Dwork = f - m Dfree = f + m Restrained: Dwork = f - (m - r + Drest) Dfree = f + (m - r + Drest) Constrained: Dwork = f - (m - r) Dfree = f + (m - r) where: Dwork = expected working set residual (chi-squared), Dfree = expected test set residual (chi-squared), f = no of reflections in working set, m = no of parameters, r = no of restraints and/or constraints, Drest = restraint residual (chi-squared). The constrained case is obviously just a special case of the restrained case with Drest = 0, i.e. in the constrained case the difference between the refined and target values is zero, and the 'no restraints' case is a special case of this with r = 0. We can generalise all of this by writing simply: Dwork = f - m' Dfree = f + m' where m' is the effective no of parameters corrected for restraints and/or constraints (m' = m - r + Drest); the effective no of parameters is reduced whether you're using restraints or constraints. In the case where you had both restraints and constraints r would be the total no of restraints + constraints, however constraints contribute nothing to Drest. The 'effectiveness' of a restraint depends on its contribution to Drest (Z^2), a smaller value means it's more effective. A contribution of Z^2 = 1 to Drest completely cancels the effect of increasing r by 1 by adding the restraint (i.e. the restraint has no effect). This incidentally shows that the effect of over-fitting (adding redundant effective parameters) is to reduce the working set and increase the test set residuals. If you consider the working set residual in the general case: Dwork = f - (m - r + Drest) = f + r - m - Drest it certainly appears from this that the number of X-ray data (f) and the number of restraints (r) are being added. However if you consider the test set residual: Dfree = f + (m - r + Drest) = f - r + m + Drest this is clearly not the case. All you can say is that the effective number of parameters is reduced by the number of restraints + constraints. Cheers -- Ian On Mon, Sep 20, 2010 at 9:20 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Hi Ian, Am 19.09.10 15:25, schrieb Ian Tickle: Hi Florian, Tight NCS restraints or NCS constraints (they are essentially the same thing in effect if not in implementation) both reduce the effective parameter count on a 1-for-1 basis. Restraints should not be considered as being added to the pool of X-ray observations in the calculation of the obs/param ratio, simply because restraints and X-ray observations can in no way be regarded as interchangeable (increasing the no of restraints by N is not equivalent to increasing the no of reflections by N). This becomes apparent when you try to compute the expected Rfree: the effective contribution of the restraints has to be subtracted from the parameter count, not added to the observation count. I always understood the difference between constraints and restraints such, that a constraint reduces the number of parameters by fixing certain parameters, whereas restraints are target values for parameters and as such can be counted as observations, similarly
Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio
Hi Ian, Am 19.09.10 15:25, schrieb Ian Tickle: Hi Florian, Tight NCS restraints or NCS constraints (they are essentially the same thing in effect if not in implementation) both reduce the effective parameter count on a 1-for-1 basis. Restraints should not be considered as being added to the pool of X-ray observations in the calculation of the obs/param ratio, simply because restraints and X-ray observations can in no way be regarded as interchangeable (increasing the no of restraints by N is not equivalent to increasing the no of reflections by N). This becomes apparent when you try to compute the expected Rfree: the effective contribution of the restraints has to be subtracted from the parameter count, not added to the observation count. I always understood the difference between constraints and restraints such, that a constraint reduces the number of parameters by fixing certain parameters, whereas restraints are target values for parameters and as such can be counted as observations, similarly to the Fobs, which are target values for the Fcalc (although with different weights). I don't see what is wrong with this view. Do I misunderstand something? Best regards, Dirk. The complication is that a 'weak' restraint is equivalent to less than 1 parameter (I call it the 'effective no of restraints': it can be calculated from the chi-squared for the restraint). Obviously no restraint is equivalent no parameter, so you can think of it as a continuous sliding scale from no restraint (effective contribution to be subtracted from parameter count = 0) through weak restraint (0 contribution 1) through tight restraint (count ~=1) to constraint (count = 1). Cheers -- Ian On Sat, Sep 18, 2010 at 9:23 PM, Florian Schmitzberger schmitzber...@crystal.harvard.edu wrote: Dear All, I would have a question regarding the effect of non-crystallographic symmetry (NCS) on the data:parameter ratio in refinement. I am working with X-ray data to a maximum resolution of 4.1-4.4 Angstroem, 79 % solvent content, in P6222 space group; with 22 300 unique reflections and expected 1132 amino acid residues in the asymmetric unit, proper 2-fold rotational NCS (SAD phased and no high-resolution molecular replacement or homology model available). Assuming refinement of x,y,z, B and a polyalanine model (i.e. ca. 5700 atoms), this would equal an observation:parameter ratio of roughly 1:1. This I think would be equivalent to a normal protein with 50 % solvent content, diffracting to better than 3 Angstroem resolution (from the statistics I could find, at that resolution a mean data:parameter ratio of ca. 0.9:1 can be expected for refinement of x,y,z, and individual isotropic B; ignoring bond angle/length geometrical restraints at the moment). My question is how I could factor in the 2-fold rotational NCS for the estimate of the observations, assuming tight NCS restraints (or even constraint). It is normally assumed NCS reduces the noise by a factor of the square root of the NCS order, but I would be more interested how much it adds on the observation side (used as a restraint) or reduction of the parameters (used as a constraint). I don't suppose it would be correct to assume that the 2-fold NCS would half the number of parameters to refine (assuming an NCS constraint)? Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Hi Pavel, Am 16.09.10 17:56, schrieb Pavel Afonine: Hi Dirk, so, wouldn't be the deposition of the final model's Fcalc, Phic (and their weights) along with the final coordinates be the best solution? The final Fcalc are our best model and can be used to reproduce the final statistics (which would remove the sfcheck annoyance) and to reproduce the final electron density maps, and the coordinates can be used for what ever purpose they are needed, irrespective of adding riding hydrogens or not. it is a great idea and if you look in PDB deposited structure factors there is a number of them (but certainly not the majority) that are accompanied by Fcalc. However, a few things to keep in mind: - Imagine a (not very uncommon, unfortunately) situation when someone obtains the final model and Fcalc, and then, right before the PDB deposition does a final check in Coot, and moves/removes a few atoms (a few waters, or instance) here and there. Or may be does a real-space fit of a residue. Or removes H, if present. Or renames a ligand by request of PDB staff and accidentally change an atom parameter(s). All this in turn will invalidate the R-factors and make previously calculated Fcalc inconsistent with such a manipulated model. So, the bottom-line is: having a model that you can use to reproduce the reported statistics is important (for validation and database sanity at least, if someones believe that such a minor things wouldn't impair the biological interpretation - ultimate goal of protein structures). but this is exactly what one shouldn't do: manipulate the structure after the final refinement! And if you manipulate it for a good reason, do a last final refinement after that, before depositing coordinates and structure factors. Then, there will be no problems, as far as I can see. Best regards, Dirk -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Dear Ian and contributors to this interesting thread, (please, scroll down a little bit) Am 15.09.10 23:34, schrieb Ian Tickle: I should just like to point out that the main source of the disagreement here seems to be that people have very different ideas about what a 'model' is or should be. Strictly a model is a purely mathematical construct, in this case it consists of the appropriate equation for the calculated structure factor and the best-fit values of the various parameters (scattering factors, atomic positions, occupancies, B factors, TLS parameters etc.) that appear in it. A mathematical model is inevitably going to be an imperfect representation of reality, but hopefully it's the best one we can come up with, in the sense of best explaining the data without significant overfitting. The problem arises because many users of the PDB, and I suspect many contributors to this BB, particularly non-crystallographers, don't see it like that, because they view a PDB file as a physical model, i.e. not as the best fit to the data (assuming that the non-crystallographers even know what the data are!), but the closest representation of reality. The difference between the N-H bond lengths that Ed referred to illustrates the distinction between the mathematical and the physical model. The mathematical model requires that the bond length is 0.86 Ang because that value gives the best fit of the assumed spherical scattering factor of H to the deformation density of the X-H covalent bond. The physical model requires that it be 1.00 Ang because that is the internuclear distance found by spectroscopic methods predicted by QM calculations. The same goes for B factors and TLS: to a large extent they are a mathematical construct whose purpose is to provide an optimal fit to the data. The connection of Bs TLS with reality is tenuous at best, nevertheless people obviously would like to have a physical interpretation such as rigid-body correlated motion. The fact that Bragg scattering provides no information about correlated motion (you need to measure the diffuse scattering for that) doesn't seem to deter them! I have no doubt in my mind that it is the mathematical model that should be published, because hopefully it's the best available interpretation of the data. Whether that involves publishing the riding H atoms explicitly, or alternatively the formulae and parameters that were used to calculate their positions I don't mind, as long as I can faithfully reproduce the Fcalcs to check the validity of the model. Then users of the PDB are free to *interpret* the mathematical models as physical models in a appropriate manner (e.g. by adjusting the bond lengths to H), and crystallographers have the untainted mathematical models needed to reproduce the Fcalcs. so, wouldn't be the deposition of the final model's Fcalc, Phic (and their weights) along with the final coordinates be the best solution? The final Fcalc are our best model and can be used to reproduce the final statistics (which would remove the sfcheck annoyance) and to reproduce the final electron density maps, and the coordinates can be used for what ever purpose they are needed, irrespective of adding riding hydrogens or not. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Molecular replacement question
Dear Paul Holland, I would spend some time in improving the search model, first. If there are more than one possible search molecules in the PDB, I usually do a structural alignment (ssm superposition) to get an idea about the flexibility of the search molecules. Then I remove all parts that I suspect to be flexible (usually N- and C-termini, long loops), until I get a very compact search model. You may try a model with no side-chain truncation, since in the hydrophobic core, there might be a similar isosteric packing of atoms. In addition, I would truncate the side chains either to the longest common chain (with ctruncate) if there is a good sequence alignment, or to poly-Ser or even poly-Ala. I would try these core-models as search models, with the idea that missing atoms lower the signal, but wrong atoms raise the noise and may produce wrong clashes. In case of several search models, where each individual model fails, you may try to run Phaser using all of them simultaneously as a search ensemble. This model-pruning together with a search-ensemble of several PDB entries worked recently in a project, where otherwise all molecular replacement trials failed. Good luck, Dirk. Am 13.09.10 16:52, schrieb Paul Holland: Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very high sequence similarity to the search model with several predicted flexible loop regions; however, all attempts at finding a solution have not produce very ideal starting solutions using Phaser and Molrep (CC = 0.3 and Z-score = 5). I am very confident that the unit cell parameters are C2 84.027 120.565 108.272 90.00 104.71 90.00, and there appears to be no evidence of twinning. The Matthews calculation predicts from anywhere from 2-4 monomers in the ASU, and calculation of the SRF in Molrep does not identify any peaks in higher order symmetry except for the expected crystallographic two-fold for C2. Below is the table from the calculated SRF in molrep. Any advice would be greatly appreciated. #thetaphichi alpha beta gamma Rf Rf/sigma Sol_RF 1 0.000.000.000.000.000.00 870.5 21.59 Sol_RF 258.61 -10.17 180.00 169.83 -117.23 10.17 162.5 4.03 Sol_RF 366.02 -0.00 180.00 180.00 -132.030.00 161.1 4.00 Sol_RF 458.42 -9.54 180.00 170.46 -116.859.54 159.8 3.96 Sol_RF 5 149.840.00 180.00 -180.00 60.320.00 156.0 3.87 Sol_RF 658.96 -5.52 180.00 174.48 -117.915.52 151.5 3.76 Sol_RF 765.59 20.95 180.00 20.95 131.18 159.05 143.9 3.57 Sol_RF 890.00 -98.96 180.000.00 180.00 17.92 142.9 3.55 Sol_RF 956.53 15.78 180.00 15.78 113.07 164.22 142.0 3.52 Sol_RF 1071.10 -19.94 180.00 160.06 -142.20 19.94 141.6 3.51 Sol_RF 1171.28 29.78 180.00 29.78 142.55 150.22 140.4 3.48 Sol_RF 1265.22 -15.88 180.00 164.12 -130.44 15.88 139.2 3.45 Sol_RF 1368.84 -0.00 180.00 180.00 -137.670.00 138.0 3.42 Sol_RF 1432.51 -180.00 180.00 -180.00 65.02 -0.00 137.9 3.42 Sol_RF 1575.02 -28.84 180.00 151.16 -150.04 28.84 134.7 3.34 Sol_RF 1671.69 -20.99 180.00 159.01 -143.37 20.99 133.0 3.30 Sol_RF 1792.13 101.46 179.93 102.35 -175.74 79.42 130.9 3.25 Sol_RF 18 107.89 144.73 179.79 145.06 -144.22 35.61 128.8 3.19 Sol_RF 1987.45 -78.19 180.00 101.81 -174.90 78.19 128.1 3.18 Sol_RF 2038.570.69 30.36 102.66 -18.79 -78.71 122.4 3.04 Sol_RF 2126.77 174.59 176.58 172.68 53.523.49 120.5 2.99 Sol_RF 22 116.66 178.08 175.143.49 126.48 187.32 120.5 2.99 Sol_RF 2375.56 -41.35 180.00 138.65 -151.12 41.35 119.8 2.97 Sol_RF 2466.12 36.35 180.00 36.35 132.24 143.65 116.6 2.89 Sol_RF 2583.87 71.62 180.00 71.62 167.74 108.38 114.7 2.85 Sol_RF 2669.24 -12.37 180.00 167.63 -138.48 12.37 112.3 2.79 Sol_RF 2759.75 15.26 172.297.64 119.07 157.12 112.2 2.78 Sol_RF 28 120.25 -164.74 172.29 22.88 119.07 172.36 112.2 2.78 Sol_RF 2996.68 -70.99 180.00 109.01 -166.63 70.99 110.9 2.75 Sol_RF 3063.23 -44.73 180.00 135.27 -126.47 44.73 108.9 2.70 Cheers, Paul Holland -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Practical MR advice
Hi Roger, personally, I would take the four dimers from Phaser, strip off all side chains (make a poly-ala/gly), do a ML refinement with tight NCS restraints. The resulting map could then be on-the-fly real-space-averaged with Coot. At your resolution, I would expect to see the real register of at least some side chains either in the 2mfodfc-map or in one of the real-space-averaged 2mfodfc-maps. Good luck, Dirk. Am 01.09.10 17:12, schrieb Roger Rowlett: I am trying to find a MR solution for a large unit cell (R3:H, 158x158x196) with a relatively poor, but I think workable search model (30% identity, 50% similarity). The data set is decent to 2.4 A. I might be able to get better if necessary. I submitted the sequence of the target to the Phyre server, and it returned a PDB file derived from what I had already identified as the most likely successful search model. Phaser finds a reasonable solution with four dimers (Z=9-15 depending on the data set) for which the unit cell packing looks good. Phaser even assembles what looks like correct biological tetramers in the ASU and across the symmetry interfaces. The main chain appears to be mostly traceable, but the side chains are not all well-resolved, and I suspect from the better-defined regions, that the chain is misregistered by a residue or two throughout most of the structure. Assuming that an MR solution is possible, what is a good approach from here? FWIW, Phaser does not correctly place a poly-Ala/Gly model, although it may place three chains similarly to the MR solution I have with the Phyre model. My first thought is to: 1. Chainsaw the currrent solution, and attempt to identify and build in the correct register of the side chains. after refinement. 2. Do a low resolution refinement of the poly-Ala/Gly model to better thread the main chain? 3. Try EPMR with the Phyre model or the poly-Ala/Gly model 4. Give up and get real phases (but I'm so close now!?) Thanks in advance. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu mailto:rrowl...@mail.colgate.edu -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] which software can calculate binding energy
Dear Min, in addition to what Greg Warren wrote, to my knowledge, there is still a big uncertainty in the calculation of desolvation energies. A colleague of mine, a theoretical physicist, when I was at Hoffmann-La Roche, tried to calulcate the desolvation energy contribution to the total binding energy of drug compounds to protein active sites, and estimated that the errors in the desolvation energies had about the same magnitude as the total net binding energy. So, this is another big source of inaccuracy, especially with very different drug compounds. Best regards, Dirk. Am 22.07.10 23:13, schrieb Greg Warren: Dear Min, There is no software that can accurately calculate the binding energy of a predicted (docking) or solved (X-ray structure) protein-ligand complex particularly for ligands that are different chemically -- not part of a congeneric series.While there are a number of publications on methods (LIE, FEP, MD, MMPB(GB)SA, QM/MM, even semi-empirical QM methods) for predicting binding energy, most of these publication show results for congeneric series compounds not chemically diverse ligands which is the result you will get from screening a chemical database with Autodock. There are publications by SP Brown J Chem Inf Model. 2007 Jul-Aug;47(4):1493-503, J Chem Inf Model. 2006 May-Jun;46(3):999-1005 using MMPBSA showing a correlation between predicted and measured binding energy of around 0.8. The 0.8 correlation may not be in the papers but might have only been shown in presentations given by Scott. If you are looking for accurate predictions a 0.8 correlation is not very accurate. If you were thinking about using docking scores, a publication that looked at using docking scores to predict binding energy is Warren et al. J Med Chem 2006, 49, 5912. The last third of this publication showed that using docking scores to predict binding energy was a very bad idea even for congeneric series. Regards, Greg *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *WEI MIN *Sent:* Thursday, July 22, 2010 1:51 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] which software can calculate binding energy Dear All I have been using the Autodock software for docking the drug candidate compounds into the receptor structures. I would like to calculate accurately the binding energy. Would anyone introduce me a software? Any help would be greatly appreciated. Best Min -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] differences Rfactor calculations
... yes, and this is the reason why sfcheck should be replaced by a more modern program at the Protein Data Bank! Best regards, Dirk. Am 13.07.10 22:15, schrieb Ethan Merritt: Should be in an FAQ somewhere: Q: Why does sfcheck not reproduce my original R factors? A: Because instead of using the Fc in your file, sfcheck tries to re-calculate Fc using only your atom names, coordinates and isotropic B factors. This is bad, because it ignores any contributions to your original Fc from things like F_partial, Anisotropic corrections, TLS models, scattering factor corrections, riding hydrogens, etc. My advice is to use sfcheck only to evaluate the Fobs file resulting from your data collection. It is not a suitable tool for validating a refined model. The same happened when I used this final model as starting model for a refinement with Refmac5. Again I got an Rfactor of 20.8%. Probably you failed to describe the full model to refmac. Refmac and phenix.refine can both handle all the contributing factors listed above, but it may take some work to pick a the correct corresponding set of options. Ethan As far as I know, Phenix uses different algorithms for the refinement than other programs, which in some cases can make Phenix gets better Rfactors. Could these differences be the reason for this large difference in the calculated Rfactors? Or I have to recheck my procedure for mistakes? Thanks a lot in advanced. Looking forward to hearing form you. Cheers, Ariel -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format
Hi James, I had similar problems with MRC maps. As a solution, a colleague of mine, working with EM, read the MRC map into SPIDER and saved it as a CCP4 map. That worked for me. Unfortunately, my colleague is absent for some time, and I'm still not familiar with EM software. But maybe, you find a colleague at your institute to help you with that. Good luck, Dirk. Am 13.07.10 14:32, schrieb James Whittle: Hi all- I'm trying to convert a cryoEM map from FREALIGN for use with various CCP4 programs, or with MAPMAN. Even though the MRC format is derived from the CCP4 map file format, every program I've tried fails to open it, (except for Chimera which displays the map but cannot save it to another format for lack of memory). For example, in MAPMASK I get the error: CCP4 library signal ccp4_map:No associated header (Error) raised in ccp4_cmap_open CCP4 library signal ccp4_map:Cannot open file (Error) raised in MRDHDS or with MAPMAN: **CCPOPN ERROR** FORMATTED OLD file open failure on unit 1 Logical name: DLP_100.map, File name: DLP_100.map Cannot send after transport endpoint shutdown ERROR --- While reading map header. Sorry ! ERROR --- While opening map file Is there a way to re-write the header to be compatible with CCP4? --James -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Question about R/Rfree value difference
Hi Tom, very nice tool! It would be good to get numerical values of the plotted distributions as well, like mean, median, standard deviation and so on. Best regards, Dirk. Am 08.07.10 15:20, schrieb Tom Oldfield: Sampath With regard to your question on what sort of statistics you should get within structure determination you might find this service at the PDBe useful : http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp You can view and manipulate distributions of R, Rfree and R-Rfree along within many other data distributions from Xray (also NMR/EM) during structure determination. There are also links (clicking the graph) that list all the depositions that have a particular value within the distribution. I agree with Pavel that from your quoted statistics that it would be un-wise to deposit the structure in the current state of refinement as there is clearly an issue. Regards Tom Oldfield Hi Sampath, this is how the distribution of Rwork, Rfree and Rfree-Rwork look like for 'all' PDB structures refined at around 2A resolution. The indicates where your structure stands with respect to this distribution. Histogram of Rwork for models in PDB at resolution 1.90-2.10 A: 0.093 - 0.118 : 2 0.118 - 0.143 : 35 0.143 - 0.168 : 390 0.168 - 0.193 : 1439 0.193 - 0.218 : 1802 your structure 0.218 - 0.242 : 785 0.242 - 0.267 : 159 0.267 - 0.292 : 14 0.292 - 0.317 : 1 0.317 - 0.342 : 1 Histogram of Rfree for models in PDB at resolution 1.90-2.10 A: 0.149 - 0.170 : 10 0.170 - 0.191 : 116 0.191 - 0.213 : 534 0.213 - 0.234 : 1166 0.234 - 0.255 : 1417 0.255 - 0.276 : 942 0.276 - 0.297 : 343 0.297 - 0.319 : 78 0.319 - 0.340 : 17 your structure 0.340 - 0.361 : 5 Histogram of Rfree-Rwork for all model in PDB at resolution 1.90-2.10 A: 0.001 - 0.011 : 41 0.011 - 0.021 : 230 0.021 - 0.031 : 724 0.031 - 0.041 : 1210 0.041 - 0.050 : 1206 0.050 - 0.060 : 654 0.060 - 0.070 : 318 0.070 - 0.080 : 160 0.080 - 0.090 : 56 0.090 - 0.100 : 29 So, it seems your case is the example of typical overfitting, which means the model parameterization or/and the refinement strategy is not good for your data and model. If you send me the data and model files then I will be able (hopefully) to suggest a better refinement strategy or explaine why it's not feasible with available tools. All files will be kept confidentially. The histograms above are obtained using this command from PHENIX family: phenix.r_factor_statistics 2.0 Good luck! Pavel. On 7/7/10 10:17 PM, Sampath Natarajan wrote: Dear all, I have a question about the R free value. I refined a structure with 2A resolution. After model building and restraint refinement using Refmac program, the average B factor was around 50 for all atoms. The R/Rfree were around 22/34. Then used the TLS refinement choosing entire molecule. Then R/Rfree reduced as 20/32. But the average B factor was reduced as 30. The R/Rfree difference is about 12% in final refinement. I feel it is significantly higher. Could any one suggest me to reduce the Rfree value more? or is it good to submit the data in the PDB database with this 12% difference? Thanks for the suggestions. Sincerely, Sampath N -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] R values are higher in SF-CHECK
Hello Rakesh, yes, you are right. In contrast to all modern refinement programs, sfcheck neither applies TLS nor the superior mask bulk solvent correction (it applies the Babinet bulk solvent correction by double-exponential scaling). As a result, the R-factors from sfcheck are higher than those from the refinement program. Annoyingly, I have to discuss/explain this discrepancy in R-factors every time when I want to deposit a refined X-ray structure with the Protein Data Bank ... Best regards, Dirk. Am 06.07.10 17:05, schrieb Rakesh Joshi: Hello, I refined my structures using REFMAC5 ( using TLS in combination ). When i used the SF-Check program, my R-values are ~5% higher than in those reported by refmac. Is this due to the fact that SF-check does bulk solvent calculations differently and does not account for TLS refinement? Also, when i used TLSANL to put in my total B factor in the pdb file I only get 3 sets of numbers instead of( what i expected) 6 sets(ie. last three entries have values=0). For example: ATOM246 C6 DA C 13 -29.692 15.902 14.379 1.00 36.42 C ANISOU 246 C6 DA C 13 3267 5459 5110 0 0 0 C Cheers Rakesh Graduate student Purdue University -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Wilson B and Mean B factors
Dear Murugan, at higher resolution, the Wilson plot captures mainly the contribution of atoms with lower B-factors which leads to a systematic underestimation of the true B-factor distribution. Accordingly, the average B-factor of refined structures tend to be higher then the Wilson B-factor, at least in my experience. In your case, it is the other way around. One possible problem could be, apart from the fit of the Wilson plot as James Holton suggested, that you have reflections at very low resolution with underestimated intensities due to cut overloads or measurement in the half-shadow of the beamstop. This would result in a too low overall B-factor for the model in order to try to fit the usually stronger low resolution reflections at the cost of the weaker high resolution data. One quick check of this hypothesis is to cut the low resolution at, say, 10 A instead of 50 A and run a test-refinement. If this results in more realistic model B-factors, you should have a closer look at the low resolution data and exclude the ill-measured ones. Best regards, Dirk. Am 30.06.10 19:31, schrieb Vandu Murugan: Dear all, If one could find a difference of more than 15 between Wilson B factor of the data ( 55) and Mean B factor of the structure, (30) what could be the possible reasons? I am seeing it in my structure. Could someone tell me why it could be?? Thanks in advance. Yours faithfully, Murugan -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] problem with coot
Dear Munan, this is a question that should better go to the Coot mailing list. Anyway - it is difficult to say what the problem is, without more informations. It could be an X11 problem or a Coot installation problem. Generally, on Mac OS X, you don't have to start X11 manually or at login - there is a launchd daemon that automatically starts X11 if it is required. Also, you must not set any DISPLAY variable in your .bashrc, .bash_proflie or elsewhere. The following works for me on Mac OS X: I've installed the precompiled Coot version for Mac OS X, kindly provided by Bill Scott (-Google), and I've installed the more up-to-date X11 from xquartz.macosforge.org (but this is not necessary). You may want to try this. Good luck, Dirk. Am 30.06.10 10:48, schrieb Md. Munan Shaik: Dear BB I have a problem with coot opening, i tried to open but its not opended. Then I found some other problem, X11 terminal is not opened on login (even its in the list on login items), if I open X11 and then tried to open coot still not working, I am using Macbook and the OS X is 10.6.1. (coot is install to Applications and not source to tcsh terminal, as i preferred not to open from terminal). if anybody have suggestion, please . thanking you all, === Md. Munan Shaik Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] measure of anamolous signal
Dear Murugan, Am 29.06.10 11:05, schrieb Vandu Murugan: Dear all, I have collected a 2.7 angstrom home source data with Cu-Kalpha source for a protein with 6 cysteines, with a multiplicity of around 23. I need to know, is there any significant anamolous signal present in the data set, since there is no good model for my protein. Can any one tell, which program to run, and what parameter to see? Thanks in advance. cheers, Murugan estimating the quality of the anomalous signal is not trivial, and several quality indicators have been discussed (see for example Fu, Rose Wang, Acta Cryst D60, 499-506 (2004), or Zwart, Acta Cryst D61, 1437-1444 (2005)). If you process your data with XDS, there are two quality indicators for the anomalous signal, given both in the CORRECT.LP and in the XSCALE.LP file. One is the correlation of anomalous differences between two randomly chosen subsets that should have the same anomalous difference due to crystallographic symmetry, called RANOM. The other describes the absolute anomalous difference divided by their standard deviation, called SIGANO. A typical rule of thumb (and the one that I use) is, that RANOM should be ~ 30%, and SIGANO should be ~ 1.2. However, these indicators might not be realistic (see references above) and therefore should be taken with a grain of salt. Good luck, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Snow leopard + NVidia quadro FX4500
Dear Deena, yes, I have a Mac Pro with an Nvidia FX 4500 running under 10.6.3. For me, all programs work more or less fine in hardware stereo (Pymol, Coot, Moloc, Chimera). I've done the following to get it working: 1. Connect the CRT monitor to the first DVI socket of the graphics card (the one further away from the 3-pin Mini-DIN) 2. Connect the TFT to the second DVI socket (in the middle) 3. Connect the emitter to the 3-pin Mini-DIN socket 4. Choose a resolution for the CRT that allows a refresh rate of 120 Hz 5. I've arranged the monitors such that the menu bar is on the TFT (you might want to change this, if you like) 6. Not necessary since 10.6, but I've installed the most recent X11 from xquartz.macosforge.org You can start MacPyMOL or PyMOLX11Hybrid with the parameters -X 1800 -Y 200 -S (you might want to play with the X,Y position) and switch pymol to stereo in the application (still required despite -S). For me, it is necessary to start pymol on the CRT monitor with suitable X,Y parameters, since dragging a X11 stereo window from the TFT to the CRT could lead to a crash of your whole session. Good luck, Dirk. Am 14.06.10 21:35, schrieb Deena Oren: Hi all, Does anyone have this combination of Nvidia FX4500 in a mac machine running 10.6 and if so is stereo working? I am getting a messed up screen when using either coot in hardware stereo or pymol -S even without invoking the stereo command. Yet ccp4mg is working fine in stereo. Thanks, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue, Box 295 New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] sigma cutoff for fitting waters in model
Dear Tassos, Am 19.04.10 17:31, schrieb Anastassis Perrakis: snip The sigma issue a bit more complicated. What we call usually sigma is the root mean square deviation (rmsd) of the map. Lets first recall, that the variation within the protein region is quite large, while the solvent is rather flat. Now, lets take an 'extreme' example, of a protein with 80% solvent. The rmsd for that will be quite low, since most of the AU is flat. Thus, I would argue that you might want to consider waters in relatively 'low sigma'levels. Of course 80% solvent will also mean that most likely this protein will only diffract to low resolution, so you should maybe not be putting any waters. The inverse case argument also applies. Similar issues, maybe more severe, come up for atom removal. /snip regarding fitting electron density maps: isn't it the other way around? Assume, that we have the same protein with the same absolute noise level (without F000/V) in the protein region and the same loop that's missing in the model with the same absolute density well above the protein region's noise level, and this protein crystallizes in two crystal forms, one with low solvent content and one with high solvent content. Let's also assume that the solvent regions are absolutely flat. Then, the rmsd of the total electron density in the unit cell will be lower for the crystal form with high solvent content and higher for the crystal form with low solvent content, as you said. However, if we want to interprete that missing loop above the noise level in the protein region, we would then have to contour the electron density map in the high solvent crystal form at a higher multiple of its rmsd value than in the low solvent crystal form to get to the same absolute electron density level. Is this true or did I misunderstand something? Best regards, Dirk. -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Hydrogen Bond Restraints
Dear Bradley, a recent refinement of a protein complex at 4.3 A was stabilized by using hydrogen bond restraints in secondary structures [1] (described in the supplementary material). Subjectively, the additional restraints had a small positive effect on the electron density interpretability of parts that were missing in the model. Irrespective of that, the hydrogen bonds stabilized the known/expected secondary structural elements during refinement and had a positive effect on the Ramachandran plot (which is not an independent quality control anymore, as with all restraints). Good luck, Dirk. [1] Nature 462, 323-330 (2009) Am 14.04.10 15:41, schrieb Bradley Hintze: I am looking for published examples where hydrogen bond restraints were helpful in refinement. Can anyone point me to some papers? -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] How to show electron density map for my ligand in pymol, which is bound in the active site..??/
Dear Hussain, in the electron density example of this tutorial, the parameter carve=1.6 is used, which means that density is only shown within a radius of 1.6 A around atoms. This is usually done for clarity, but may give an unrealistic impression of the density quality. Here, you should carefully choose a radius that shows the density similar as in a plot without any carve parameter, while cutting away the density from the surrounding atoms that you don't want to show. I've made good experiences choosing a radius similar to the maximum resolution of your data as a starting point. The carve-radius should then be reported in the figure. Good luck, Dirk. Am 13.04.10 15:40, schrieb Ed Pozharski: Hussain, http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html which is the top hit when you google pymol electron density. Using google (and not to appear biased, other available search engines) is the most valuable advice (per word) that you may possible get. On Tue, 2010-04-13 at 18:33 +0530, Hussain Bhukyagps wrote: Dear all, How can i show electron density map for my ligand in pymol, which is bound in the active site. i uploaded map as .xplor extension to the map file.. thank u Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Phasing statistics
Hi Tassos, my personal opinion is, that I would like to see the usual phasing statistics. At least to me, they provide hints how well the structure was determined, analogous to the R-factor/Free-R-factor providing hints how well the structure was refined. It would be good if SHELXE would print out those statistics before any density modification. Best regards, Dirk. Am 12.04.10 13:10, schrieb Anastassis Perrakis: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice the referee to read a bit about how SHELXE works ... or go to one of the nice courses that George teaches ... On Apr 12, 2010, at 10:37, Eleanor Dodson wrote: You can feed the SHELX sites into phaser_er or CRANK both of which will give this sort of information. Or mlphare if you know how to set it up.. Eleanor Harmer, Nicholas wrote: Dear CCP4ers, I've been asked by a referee to provide the phasing statistics for a SAD dataset that I used to solve a recent structure. Whilst I have been able to find a figure-of-merit for the data after phasing, I can't work out how to get any other statistics (e.g. phasing power or an equivalent or Rcullis). Does anyone know a good route to obtaining useful statistics to put in the paper for SAD data? The structure solution was carried out using SHELX C/D/E and then ARP/wARP. Thanks in advance, Nic Harmer = Dr. Nic Harmer School of Biosciences University of Exeter tel: +44 1392 725179 *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Phenix version 1.6.1 released
Dear Paul, this is very interesting! From the list of changes, it appears that in version 1.6.1, you use a similar idea to implement hydrogen bonds via DSSP during refinement that I used to stabilize the 4.3 A refinement of Pol II in complex with TFIIB [1]: CHANGE LOG for PHENIX distribution == Version 1.6.1 = snip - phenix.refine - much faster rotamer fixing - initial implementation of secondary structure restraints (hydrogen bonds) - automatic assignment of sec. str. using KSDSSP (from UCSF CGL) - proper treatment of charges on metal ions for scattering factors /snip Could you please give more details of how this is implemented? What are your hydrogen bond target distances and sigmas? Do you update this list during refinement? I used a simple list of additional 2.9 A target-bond-distances between N and O with a target sigma of 0.05 A. This list was determined with DSSP and a self-made Fortran95 program using a user-defined energy-threshold prior to refinement and was kept constant during refinement. Personally, I think, using secondary structure hydrogen bonds should be an option in every refinement program, especially at lower resolution!!! The BUSTER Wiki describes the procedure that I used. For REFMAC, I haven't seen anything similar, yet. Very exciting! Best regards, Dirk. [1] Nature 462, 323-330, (2009) Am 31.03.10 04:41, schrieb Paul Adams: The Phenix developers are pleased to announce that version 1.6.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.1) are: - Fast automated rotamer fixing in phenix.refine - Use of atomic charge in calculation of scattering factors - New Graphical User Interfaces for phenix.superpose_pdbs, phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, and phenix.fmodel - Consolidated validation tool in GUI - New map calculation tool, phenix.maps (also used in GUI) - Rapid loading of structures in GUI selection editor - Improved geometry restraints to maintain amino acid rotameric states - Alpha version of secondary structure restraints - Automated secondary structure analysis with KSDSSP (code from UCSF CGL) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] self rotation education
Dear Francis Reyes, from the self-rotation function at kappa=120 degrees, you can see that one threefold NCS axis is perpendicular to a crystallographic twofold axis. I haven't worked this out for your particular case, but the combination of a threefold (n-fold) NCS axis perpendicular to a crystallographic twofold axis creates three (n) NCS twofold axes (that can be viewed from both directions and in case of an uneven NCS axis appear twice). I've appended a schematic stereographic projection to make this a bit clearer (full dyad symbol crystallographic, open dyad and triangle symbols NCS, green circles positions above plane, red circles positions below plane created by crystallographic dyad, dashed lines help to visualize the NCS threefold, thick solid line crystallographic twofold, thin solid lines NCS twofolds). Good luck, Dirk. Am 18.03.10 16:03, schrieb Francis E Reyes: Hi all I have a solved structure that crystallizes as a trimer to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. The space group is P212121, calculating my self rotations from 50-3A, integration radius of 22 (the radius of my molecule is about 44). I can see the three fold NCS from my structure on the 120 slice, but I'm trying to rationalize apparent two folds in my kappa=180. A picture of both slices is enclosed. The non crystallographic peaks for kappa=180, P222 begin to appear at kappa=150 and are strongest on the 180 slice. My molecule looks close to a bagel (44A wide and 28A tall). The three fold NCS is down the axis of looking down on the bagel hole. I'm trying to find the two fold. I imagine it could be slicing the bagel in half (like to eat it for yourself) or slicing it vertically (like to share amongst kids) but I'm not exactly sure what's the best way to visualize this. Is there something easier than correlation maps with getax (since I have the rotation (polarrfn) and translation?). If you have an eye for spotting symmetry, Ill send the pdb in confidence. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** Combination-Crystallographic-NCS.pdf Description: Adobe PDF document
Re: [ccp4bb] self rotation education
... and here a slightly clearer version where I numbered the NCS-related positions 1,2,3 and their crystallographic equivalent positions 1',2',3', which makes the NCS dyads a bit easier to understand ... Sorry for sending two pictures. Best regards, Dirk. Am 19.03.10 10:31, schrieb Dirk Kostrewa: Dear Francis Reyes, from the self-rotation function at kappa=120 degrees, you can see that one threefold NCS axis is perpendicular to a crystallographic twofold axis. I haven't worked this out for your particular case, but the combination of a threefold (n-fold) NCS axis perpendicular to a crystallographic twofold axis creates three (n) NCS twofold axes (that can be viewed from both directions and in case of an uneven NCS axis appear twice). I've appended a schematic stereographic projection to make this a bit clearer (full dyad symbol crystallographic, open dyad and triangle symbols NCS, green circles positions above plane, red circles positions below plane created by crystallographic dyad, dashed lines help to visualize the NCS threefold, thick solid line crystallographic twofold, thin solid lines NCS twofolds). Good luck, Dirk. Am 18.03.10 16:03, schrieb Francis E Reyes: Hi all I have a solved structure that crystallizes as a trimer to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. The space group is P212121, calculating my self rotations from 50-3A, integration radius of 22 (the radius of my molecule is about 44). I can see the three fold NCS from my structure on the 120 slice, but I'm trying to rationalize apparent two folds in my kappa=180. A picture of both slices is enclosed. The non crystallographic peaks for kappa=180, P222 begin to appear at kappa=150 and are strongest on the 180 slice. My molecule looks close to a bagel (44A wide and 28A tall). The three fold NCS is down the axis of looking down on the bagel hole. I'm trying to find the two fold. I imagine it could be slicing the bagel in half (like to eat it for yourself) or slicing it vertically (like to share amongst kids) but I'm not exactly sure what's the best way to visualize this. Is there something easier than correlation maps with getax (since I have the rotation (polarrfn) and translation?). If you have an eye for spotting symmetry, Ill send the pdb in confidence. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** Combination-Crystallographic-NCS.pdf Description: Adobe PDF document
Re: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials
Could this be a long-standing bug in the ccp4i Refmac GUI? Some time ago, I sent a bug report to the ccp4 developers: if you did TLS refinement, you got an additional tab where you should set the B-factor to a uniform value. In the next round of refinement, where you read in the refined TLS parameters from the previous run, this tab vanished, but the B-factor was nevertheless still set to the same uniform value, which resulted in high starting R-factors for the first cycle! I haven't tested this recently, but if you display the actual Refmac command script from the GUI, it should be obvious whether this bug is still there or not. Best regards, Dirk. Am 25.02.10 17:54, schrieb Jan Schoepe: What I tried for instance was in refmac: 1.) 20 cycles TLS followed by 10 cycles restrained refinement which gave Rwork=24%/Rfree=33%. Afterwards I did 0-1 cycles restrained refinement with output from prev. run (pdb file, mtz file, tls file) as input for that. Result: 33%/44%. 2.) I omitted the restrained refinement, else same as above. Result was 26%/32% after TLS and 31%/38% after restrained refinement... --- gbirr...@bidmc.harvard.edu /gbirr...@bidmc.harvard.edu/ schrieb am *Do, 25.2.2010: * * Von: gbirr...@bidmc.harvard.edu gbirr...@bidmc.harvard.edu Betreff: RE: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials An: j.scho...@yahoo.de Datum: Donnerstag, 25. Februar, 2010 17:12 Uhr * * * *You can fix the TLS parameters as well. * *Zero cycles of Refmac and fixed TLS* *Will this work in your case?* * * * * * * *Gabriel Birrane** Beth Israel Deaconess Medical Center RN348 99 Brookline Ave Boston, MA 02215 * * * * * **From:* Jan Schoepe [mailto:j.scho...@yahoo.de] *Sent:* Thursday, February 25, 2010 11:06 AM *To:* Birrane,Gabriel (Bidmc-Research Fellow) *Subject:* RE: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials * In principle yes, but I doubt that this works properly, especially after TLS refinement. --- gbirr...@bidmc.harvard.edu /gbirr...@bidmc.harvard.edu/ schrieb am *Do, 25.2.2010: * * Von: gbirr...@bidmc.harvard.edu gbirr...@bidmc.harvard.edu Betreff: RE: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials An: j.scho...@yahoo.de Datum: Donnerstag, 25. Februar, 2010 16:04 Uhr * * You can do zero cycles of refinement in Refmac. This will just give you the statistics as Refmac calculates them without any refinement. Is this what you are looking for? From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jan Schoepe [j.scho...@yahoo.de] Sent: Thursday, February 25, 2010 9:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials Dear all, I do have a question about comparing Rfree and Rwork factors of different refinement trials whereas I always started with the same pdb file and structure factors (phasing by MR). Means I had a protein structure which was (not just by me) refined several times in different ways also with different programs and also accordingly got different R factors for each finally refined structure. Could anyone suggest if there is something like a standard run which makes all these R factors (or derivatives since this run should change the R factors) better comparable? (E.g. it did not work for me to do a 1 cycle rigid body refinement in refmac hoping that the R factors are measured well and the structure does not change much. In fact, the R factors increased dramatically, lets say Rfree from 30% to 40%.) Many thanks for your suggestions! Jan __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com * * __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com * __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail
[ccp4bb] Research Scientist / Postdoc Position at the Gene Center, University of Munich
Dear CCP4ers, on behalf of Patrick Cramer, I would like to draw your attention to the following open position at the Gene Center, University of Munich. Please, do not reply directly to me, but to the e-mail addresses given at the end of this job offer. Best regards, Dirk Kostrewa. --- Applications are invited for a RESEARCH SCIENTIST / POSTDOC (Multiprotein complex structure) in the lab of Patrick Cramer at the Gene Center Munich. Project: Crystal structure analysis of RNA polymerase I, the 14-subunit 600 kDa central enzyme that makes rRNA. Initial crystals are available. We study the mechanisms of transcription by an interdisciplinary structural, biochemical and genetic analysis of multi-component complexes. For details please visit: http://www.LMB.uni-muenchen.de/cramer/index.html We look for a collaborative person with a background in biochemistry and X-ray crystallography, documented by at least one significant first-author publication. We offer a stimulating environment on a leading European life science campus, and a longer-term perspective. There are possibilities to join ongoing projects of high scientific significance, to participate in networks of excellence at the national and international level, and to contribute to teaching. Applications including a one-page CV, list of publications, and email addresses of 2-3 referees should be sent to R. Menacher (menac...@lmb.uni-muenchen.de). Informal enquiries may be sent to P. Cramer (cra...@lmb.uni-muenchen.de). Deadline for applications is March 15, 2010.
Re: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials
Dear Jan, an initial increase in Rfree usually means, that either, in case of isomorphous crystal forms, the structure was refined before against a different test set, or, in case of completely different crystal forms, that you have a new test set. In both cases, Rwork and Rfree for the initial model start at very similar values and de-couple during refinement, resulting in decreasing Rwork and increasing Rfree values. If you have similar resolution ranges, you should define your own standard refinement protocol; for instance, rigid body - TLS - xyzB, such that the rmsd in bond lengths converge at similar values, and then compare the R-values afterwards. This can be done with all modern refinement programs, such as REFMAC, PHENIX, BUSTER and CNS. Good luck, Dirk. Am 25.02.10 15:38, schrieb Jan Schoepe: Dear all, I do have a question about comparing Rfree and Rwork factors of different refinement trials whereas I always started with the same pdb file and structure factors (phasing by MR). Means I had a protein structure which was (not just by me) refined several times in different ways also with different programs and also accordingly got different R factors for each finally refined structure. Could anyone suggest if there is something like a standard run which makes all these R factors (or derivatives since this run should change the R factors) better comparable? (E.g. it did not work for me to do a 1 cycle rigid body refinement in refmac hoping that the R factors are measured well and the structure does not change much. In fact, the R factors increased dramatically, lets say Rfree from 30% to 40%.) Many thanks for your suggestions! Jan __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] anomalous difference fourier maps
Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk. Am 19.02.10 15:04, schrieb Gerard Bricogne: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
