Re: [ccp4bb] CCP4 Wiki
On Friday 27 July 2007 16:48, Artem Evdokimov wrote: > I can turn it back on as easily as it was turned off - as I said, several > people had negative comments, so I decided to to turn it off for now. If > there's more positive than negative impact - I would be glad to turn it > back on. When you make an announcement, I'll add the "Unit Cell Volumes" page. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] CCP4 Wiki
Hi, I can turn it back on as easily as it was turned off - as I said, several people had negative comments, so I decided to to turn it off for now. If there's more positive than negative impact - I would be glad to turn it back on. Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis Sent: Friday, July 27, 2007 4:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Wiki Just to clarify, since I feel I got misunderstood, that what Artem writes below, is the only kind of 'validation' I would also suggest. Real names though, from real institutes or companies, no yahoo/gmail aliases, so people can check the sources of the articles. A. PS I actually think that Artem's wiki could had served as an invaluable testbed and repository of contributions until something else is up and running. I am a bit disappointed it went down when I decided to try starting the ARP/wARP wiki page ;-) On 27 Jul 2007, at 20:40, [EMAIL PROTECTED] wrote: For all it's worth, I generally agree with the proponents of the more "open" approach to wiki - such as articles could be written by anyone who has a 'real name registration'.
Re: [ccp4bb] Problem converting CNS cv file to mtz using f2mtz
What are you entering for the fortran format section and how many lines are
you skipping? Helps to know what you have tried and how. May also help to
attach your CNS cv header and first two-three reflections instead of
cut-pasting into the e-mail body since the formating, spacing tends to get
changed. Looks like you would use the following fortran format, does this
match what you have used?
'(6X,3F5.0,6X,F10.3,17X,F10.3,6X,F10.0)'
Number of lines to skip = 5
I've been converting files like crazy the last couple of days, I ran into the
"cannot read first reflection message" when the format was not set correctly.
Stuart Endo-Streeter
On Friday 27 July 2007 20:29, Ryan Watkins wrote:
> Hello Colleagues,
>
> I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
> Fobs and SigFs. Unfortunately, I cannot get f2mtz to work and am
> looking for some help. The program dies either with a "cannot read
> first reflection" or with a "child killed: bus error" error. Here are
> the 1st few lines of my file:
>
> NREFlection=140763
> ANOMalous=FALSe { equiv. to HERMitian=TRUE}
> DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
> DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
> DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
> INDE -4601 FOBS=63.800 0.000 SIGMA=33.060
> TEST= 0
> INDE -4602 FOBS= 168.800 0.000 SIGMA=19.440
> TEST= 0
> INDE -4603 FOBS= 331.700 0.000 SIGMA=13.850
> TEST= 0
> INDE -4611 FOBS= 210.000 0.000 SIGMA=13.400
> TEST= 0
> INDE -4612 FOBS= 297.800 0.000 SIGMA=11.830
> TEST= 0
> INDE -4501 FOBS= 559.100 0.000 SIGMA=18.030
> TEST= 1
> INDE -4502 FOBS= 500.400 0.000 SIGMA=16.800
> TEST= 0
>
> Thank you,
>
> Ryan
>
>
> Ryan Watkins
> Postdoctoral Fellow
> Brennan Lab
> MD Anderson Cancer Center
--
__
Stuart T. Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
[EMAIL PROTECTED]
Re: [ccp4bb] Problem converting CNS cv file to mtz using f2mtz
This is usually pretty easy with sftools. You need to feed in the cell
and space group interactively, and then it should give you the option to
write the output as mtz.
Ryan Watkins wrote:
> Hello Colleagues,
>
> I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
> Fobs and SigFs. Unfortunately, I cannot get f2mtz to work and am
> looking for some help. The program dies either with a "cannot read
> first reflection" or with a "child killed: bus error" error. Here are
> the 1st few lines of my file:
>
> NREFlection=140763
> ANOMalous=FALSe { equiv. to HERMitian=TRUE}
> DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
> DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
> DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
> INDE -4601 FOBS=63.800 0.000 SIGMA=33.060
> TEST= 0
> INDE -4602 FOBS= 168.800 0.000 SIGMA=19.440
> TEST= 0
> INDE -4603 FOBS= 331.700 0.000 SIGMA=13.850
> TEST= 0
> INDE -4611 FOBS= 210.000 0.000 SIGMA=13.400
> TEST= 0
> INDE -4612 FOBS= 297.800 0.000 SIGMA=11.830
> TEST= 0
> INDE -4501 FOBS= 559.100 0.000 SIGMA=18.030
> TEST= 1
> INDE -4502 FOBS= 500.400 0.000 SIGMA=16.800
> TEST= 0
>
> Thank you,
>
> Ryan
>
>
> Ryan Watkins
> Postdoctoral Fellow
> Brennan Lab
> MD Anderson Cancer Center
>
Re: [ccp4bb] CCP4 Wiki
Just to clarify, since I feel I got misunderstood, that what Artem writes below, is the only kind of 'validation' I would also suggest. Real names though, from real institutes or companies, no yahoo/gmail aliases, so people can check the sources of the articles. A. PS I actually think that Artem's wiki could had served as an invaluable testbed and repository of contributions until something else is up and running. I am a bit disappointed it went down when I decided to try starting the ARP/wARP wiki page ;-) On 27 Jul 2007, at 20:40, [EMAIL PROTECTED] wrote: For all it's worth, I generally agree with the proponents of the more "open" approach to wiki - such as articles could be written by anyone who has a 'real name registration'.
[ccp4bb] Problem converting CNS cv file to mtz using f2mtz
Hello Colleagues,
I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
Fobs and SigFs. Unfortunately, I cannot get f2mtz to work and am
looking for some help. The program dies either with a "cannot read
first reflection" or with a "child killed: bus error" error. Here are
the 1st few lines of my file:
NREFlection=140763
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
INDE -4601 FOBS=63.800 0.000 SIGMA=33.060
TEST= 0
INDE -4602 FOBS= 168.800 0.000 SIGMA=19.440
TEST= 0
INDE -4603 FOBS= 331.700 0.000 SIGMA=13.850
TEST= 0
INDE -4611 FOBS= 210.000 0.000 SIGMA=13.400
TEST= 0
INDE -4612 FOBS= 297.800 0.000 SIGMA=11.830
TEST= 0
INDE -4501 FOBS= 559.100 0.000 SIGMA=18.030
TEST= 1
INDE -4502 FOBS= 500.400 0.000 SIGMA=16.800
TEST= 0
Thank you,
Ryan
Ryan Watkins
Postdoctoral Fellow
Brennan Lab
MD Anderson Cancer Center
Re: [ccp4bb] CCP4 Wiki
On Friday 27 July 2007 06:10, Anastassis Perrakis wrote: > Being a small contributor to the Greek Wiki, which has far less > subscribers than the English one, > I can see that the dynamics do not work well. People can sneak in > loads of crap, that are unlikely to be read > and corrected by an expert, due to the smaller number of contributors. The dynamics of over-restriction are in some cases worse. Consider this google search: "volume triclinic cell". Note the relevant equation on the top hit (http://webmineral.com/help/CellDimensions.shtml) page. I sent three emails to the maintainer of that page to correct the equation, but they never got it right and in the end simply ignored me. Previously this equation was just-plain-wrong, but now the parentheses aren't balanced. Were that a wiki, I would have fixed it up in three seconds.* From the wikipedia article on wikis: "Wikis are generally designed with the philosophy of making it easy to correct mistakes, rather than making it difficult to make them." I think that if you ignored this philosophy, you probably wouldn't want to call it a wiki and instead call it something else entirely. For a crystallography wiki, I'd be surprised if registration that requires a valid institutional email address verified by an auto-responder, some vital stats like first and last names, and a CAPTCHA wouldn't be sufficient to thwart most vandalism. The pymol wiki was a bit on the restrictive side when I registered as I was required to send an email to the maintainer. Now it appears that they have moved to an automated CAPTCHA. Given its excellent and reliable content, it appears that it could serve as a model. James *Apologies to those who run that particular site, but your incorrect equation is a liability to everyone who tries to use it--I did try real hard to help. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] CCP4 Wiki
Hi, I personally am not concerned as much (as I should be?) with the security - Wiki's tend to get attacked but as you point out the databases contain all the old articles and can be backed up on a regular basis. There has been enough concern expressed to me by different folks that I took down the xtals.org/wiki, in order to avoid confusion. I would guess the biggest advantage of a truly commercial solution for this wiki is the fact that it would be managed and backed up by someone who is paid for their services. For all it's worth, I generally agree with the proponents of the more "open" approach to wiki - such as articles could be written by anyone who has a 'real name registration'. Any kind of rigorous procedure designed to select 'worthy' contributors goes against the spirit of the whole enterprise, in my opinion :) Artem > Kevin Cowtan schrieb: >> Yes, that is our intention. CCP4 would probably be at the third level of >> a hierarchy including: >> >> Macromolecular crystallographic techniques >> Structure solution, analysis and visualisation software >> The CCP4 suite > > Kevin, > > why does/will/should the CCP4 Wiki have a hierarchy at all? I thought > that the structure of the Wiki emerges from the links between the > articles. > As far as I know the MediaWiki software does not even support a > hierarchy (but of course I may be wrong, and other software might > support it). > > And why are you concerned about security? In what sense? Breakins into > the computer that runs the software, or vandalism of articles? I believe > the first point is best dealt with by setting up a virtual machine > dedicated to the Wiki, and running an OS that gets automatic security > updates for a number of years. The "vandalism" thing is probably less of > an issue than it is in Wikipedia - but even at the Wikipedia scale it > can be handled well, it seems. > > One other thing that I thought about has to do with permissions. Let me > explain. The easiest way to come up with useful articles would probably > be to just write summaries citing people's emails to the CPP4BB. Citing > Eleanor's postings alone would certainly produce a great Wiki! But - is > it appropriate/allowed to cite people's old emails to the CCP4BB on the > Wiki, without their consent? I for one would certainly give permission > to cite my earlier CCP4BB postings, provided they are cited in the > proper context. > > And finally: why is there a concern by some people about the "premature" > setup of a Wiki, like the one that was set up by Artem? If the articles > in a Wiki are good they can just be copied over to the "CCP4 Wiki" when > it exists. At least that is my understanding concerning Wikipedia > articles - you can just use them under the GNU Free Documentation License. > > thanks, > > Kay > >> >> So there would be room for other software packages at the same level as >> CCP4, and things like purification and crystallisation off of the top >> level. >> >> James Stroud wrote: >>> Would a "CCP4 wiki" be different from a general crystallography wiki? >>> Would it reflect, for instance, the breadth of topics on the CCP4BB? >>> >>> >>> On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote: Contributions from volunteers to establish and maintain the CCP4 wiki will be definitely appreciated. >>> >>> > >
Re: [ccp4bb] CCP4 Wiki
Actually, if one follows Bill's public appearances closely, one may notice that each time a different person appears under that name. I've done some digging, and apparently "William Scott" is a bot. Apparently, some bioinformatics grad students were trying to determine if crystallography could be done entirely by AI. Given "Bill's" publication record, it appears that it could. (Also explains how those Coot builds get packaged at 4 a.m. Pacific Standard Time.) -- William Scott On Jul 27, 2007, at 7:26 AM, Oganesyan, Vaheh wrote: Isn't this e-mail's topic and it's appearance contradict each other? It comes from William Scott's e-mail account, but signed as coming from Paul Emsley. How do we figure out who actually wrote this e-mail with or without control access. The easiest way is to assume that it is coming from Bill, he just decided to sign as a Paul to disprove his own point. On the other way, it is only 7:30 am in Santa Cruz, then it is unlikely to be Bill, which means that e-mail was sent by Paul. Worth looking at this http://en.wikipedia.org/wiki/Sherlock_Holmes Wiki page, isn't it? Vaheh Oganesyan -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of William Scott Sent: Friday, July 27, 2007 10:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Wiki Most of us register on the CCP4 bb with our own names. If we say something stupid, it damages our reputation in front of our peers. A similar approach can be used for the Wiki. Control access, and limit it only to people who register with their own name and who are registered to the ccp4 bb. -- Paul Emsley Kay Diederichs wrote: Anastassis Perrakis schrieb: Kay - disagreeing once was enough ... so: I share your thoughts about the wiki ! However, the dynamics of Wikipedia are an interesting issue and relate to 'vandalism'.
Re: [ccp4bb] CCP4 Wiki
Isn't this e-mail's topic and it's appearance contradict each other? It comes from William Scott's e-mail account, but signed as coming from Paul Emsley. How do we figure out who actually wrote this e-mail with or without control access. The easiest way is to assume that it is coming from Bill, he just decided to sign as a Paul to disprove his own point. On the other way, it is only 7:30 am in Santa Cruz, then it is unlikely to be Bill, which means that e-mail was sent by Paul. Worth looking at this http://en.wikipedia.org/wiki/Sherlock_Holmes Wiki page, isn't it? Vaheh Oganesyan -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of William Scott Sent: Friday, July 27, 2007 10:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Wiki Most of us register on the CCP4 bb with our own names. If we say something stupid, it damages our reputation in front of our peers. A similar approach can be used for the Wiki. Control access, and limit it only to people who register with their own name and who are registered to the ccp4 bb. -- Paul Emsley Kay Diederichs wrote: > Anastassis Perrakis schrieb: >> Kay - disagreeing once was enough ... so: >> >> I share your thoughts about the wiki ! >> >> However, the dynamics of Wikipedia are an interesting issue and relate >> to 'vandalism'.
Re: [ccp4bb] CCP4 Wiki
Most of us register on the CCP4 bb with our own names. If we say something stupid, it damages our reputation in front of our peers. A similar approach can be used for the Wiki. Control access, and limit it only to people who register with their own name and who are registered to the ccp4 bb. -- Paul Emsley Kay Diederichs wrote: > Anastassis Perrakis schrieb: >> Kay - disagreeing once was enough ... so: >> >> I share your thoughts about the wiki ! >> >> However, the dynamics of Wikipedia are an interesting issue and relate >> to 'vandalism'.
Re: [ccp4bb] CCP4 Wiki
Hi- I just wanted to point you to a nice example of using Wikipedia in a very simple way: http://en.wikipedia.org/wiki/Software_tools_for_molecular_microscopy This is a web page listing the programs used in EM. It was started by one person, Bridget Carragher at Scripps, in relation with a JSB special issue, and has grown into a well-maintained collection of nearly all the software tools in the field. If you look at the history, the updates are done by the groups publishing the programs themselves, and there is very little problem with vandalism. Of course, a much smaller project than a full CCP4 wiki, but I think quite encouraging in the usefulness and robustness of the Wiki approack. -Christoph -- | Christoph Best <[EMAIL PROTECTED]> http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634
Re: [ccp4bb] CCP4 Wiki
Anastassis Perrakis schrieb: Kay - disagreeing once was enough ... so: I share your thoughts about the wiki ! However, the dynamics of Wikipedia are an interesting issue and relate to 'vandalism'. Being a small contributor to the Greek Wiki, which has far less subscribers than the English one, I can see that the dynamics do not work well. People can sneak in loads of crap, that are unlikely to be read and corrected by an expert, due to the smaller number of contributors. Since there are less crystallographers that Greeks, I would conclude, that the English Wiki dynamics can not be taken for granted. So, some thought might need be given not to 'security' but if you prefer 'access rights'. People at CCP4 should (I guess are) thinking for moderation, access rights to types of articles etc. I agree that it is good to think about possible problems before they occur. On the other hand there is a proverb that I don't quite remember, something to the effect of "fear is a bad advisor". What this means to me is a) the "vandalism damage" is moderate (the MediaWiki software even stores older versions of each article), and what the "risk of vandalism" is we actually don't know (even given your experience with the Greek Wiki). b) why not just start and see how the Wiki develops? Maybe a bigger risk than that of vandalism is that no-one contributes if the hurdles are too high! c) I see this as a community effort. Having only a few selected persons contribute is against this idea, and reduces the potential benefit. Kay For hierarchies, parallel efforts, GPL, I agree. ;-) Tassos PS Kay, your digital signature has some trouble for me - cant read it - you may want to know. On Jul 27, 2007, at 11:14, Kay Diederichs wrote: Kevin Cowtan schrieb: Yes, that is our intention. CCP4 would probably be at the third level of a hierarchy including: Macromolecular crystallographic techniques Structure solution, analysis and visualisation software The CCP4 suite Kevin, why does/will/should the CCP4 Wiki have a hierarchy at all? I thought that the structure of the Wiki emerges from the links between the articles. As far as I know the MediaWiki software does not even support a hierarchy (but of course I may be wrong, and other software might support it). And why are you concerned about security? In what sense? Breakins into the computer that runs the software, or vandalism of articles? I believe the first point is best dealt with by setting up a virtual machine dedicated to the Wiki, and running an OS that gets automatic security updates for a number of years. The "vandalism" thing is probably less of an issue than it is in Wikipedia - but even at the Wikipedia scale it can be handled well, it seems. One other thing that I thought about has to do with permissions. Let me explain. The easiest way to come up with useful articles would probably be to just write summaries citing people's emails to the CPP4BB. Citing Eleanor's postings alone would certainly produce a great Wiki! But - is it appropriate/allowed to cite people's old emails to the CCP4BB on the Wiki, without their consent? I for one would certainly give permission to cite my earlier CCP4BB postings, provided they are cited in the proper context. And finally: why is there a concern by some people about the "premature" setup of a Wiki, like the one that was set up by Artem? If the articles in a Wiki are good they can just be copied over to the "CCP4 Wiki" when it exists. At least that is my understanding concerning Wikipedia articles - you can just use them under the GNU Free Documentation License. thanks, Kay So there would be room for other software packages at the same level as CCP4, and things like purification and crystallisation off of the top level. James Stroud wrote: Would a "CCP4 wiki" be different from a general crystallography wiki? Would it reflect, for instance, the breadth of topics on the CCP4BB? On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote: Contributions from volunteers to establish and maintain the CCP4 wiki will be definitely appreciated. -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] CCP4 Wiki
Kay - disagreeing once was enough ... so: I share your thoughts about the wiki ! However, the dynamics of Wikipedia are an interesting issue and relate to 'vandalism'. Being a small contributor to the Greek Wiki, which has far less subscribers than the English one, I can see that the dynamics do not work well. People can sneak in loads of crap, that are unlikely to be read and corrected by an expert, due to the smaller number of contributors. Since there are less crystallographers that Greeks, I would conclude, that the English Wiki dynamics can not be taken for granted. So, some thought might need be given not to 'security' but if you prefer 'access rights'. People at CCP4 should (I guess are) thinking for moderation, access rights to types of articles etc. For hierarchies, parallel efforts, GPL, I agree. ;-) Tassos PS Kay, your digital signature has some trouble for me - cant read it - you may want to know. On Jul 27, 2007, at 11:14, Kay Diederichs wrote: Kevin Cowtan schrieb: Yes, that is our intention. CCP4 would probably be at the third level of a hierarchy including: Macromolecular crystallographic techniques Structure solution, analysis and visualisation software The CCP4 suite Kevin, why does/will/should the CCP4 Wiki have a hierarchy at all? I thought that the structure of the Wiki emerges from the links between the articles. As far as I know the MediaWiki software does not even support a hierarchy (but of course I may be wrong, and other software might support it). And why are you concerned about security? In what sense? Breakins into the computer that runs the software, or vandalism of articles? I believe the first point is best dealt with by setting up a virtual machine dedicated to the Wiki, and running an OS that gets automatic security updates for a number of years. The "vandalism" thing is probably less of an issue than it is in Wikipedia - but even at the Wikipedia scale it can be handled well, it seems. One other thing that I thought about has to do with permissions. Let me explain. The easiest way to come up with useful articles would probably be to just write summaries citing people's emails to the CPP4BB. Citing Eleanor's postings alone would certainly produce a great Wiki! But - is it appropriate/allowed to cite people's old emails to the CCP4BB on the Wiki, without their consent? I for one would certainly give permission to cite my earlier CCP4BB postings, provided they are cited in the proper context. And finally: why is there a concern by some people about the "premature" setup of a Wiki, like the one that was set up by Artem? If the articles in a Wiki are good they can just be copied over to the "CCP4 Wiki" when it exists. At least that is my understanding concerning Wikipedia articles - you can just use them under the GNU Free Documentation License. thanks, Kay So there would be room for other software packages at the same level as CCP4, and things like purification and crystallisation off of the top level. James Stroud wrote: Would a "CCP4 wiki" be different from a general crystallography wiki? Would it reflect, for instance, the breadth of topics on the CCP4BB? On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote: Contributions from volunteers to establish and maintain the CCP4 wiki will be definitely appreciated.
Re: [ccp4bb] initial model built in Fo map not refining
Hi Eleanor,
On Fri, Jul 27, 2007 at 12:56:07PM +0100, Eleanor Dodson wrote:
> Phasing tasks) , worrying a lot if they are not! then using the 2.3A
> data for phase extension from the 2.7A exptl phases. DM with averaging
> and phase extension will improve your map a lot, and maybe you can build
> the other 30%
> Eleanor
>
> PS - as a crystallographic educator I am a bit upset that this isnt the
> norm for experimental phasing - phase extension is brilliant!! and not
> using it is rather reminiscent of self flagelation..
It is the default/norm - at least for SHARP/autoSHARP (and most likely
for all other modern program suites). Ok, the NCS-averaging part
hasn't been automated (yet) completely, but the phase-extension is:
all reflections of all datasets will be used within our SOLOMON
density-modification approach.
It works really well for me - at least if there is meaningful
experimental phase information to a certain resolution. 2.7 to 2.3 is
easy ... the tricky ones are when you have poor 6A phases and some
really borderline 3.5A dataset ... which seems the norm for the kind
of datasets coming my way these days ... sigh.
Cheers
Clemens
>
> Anastassis Perrakis wrote:
> >Hi -
> >
> >Its not clear to me if the 2.3 A dataset is from a different crystal,
> >if it has the same space group as the 2.7 A dataset and if it is
> >isomorphous, and how the 'jump' from the 2.7 A dataset to the 2.3 A
> >dataset has been done. I can think of quite a few ways to do that
> >transition, and each way can carry its own problems.
> >
> >Maybe its worth clarifying these in more detail.
> >
> >I also have to say that (for once!) I dont agree with Kay. I have
> >tried in the past to refine against datasets processed with different
> >programs, and I know people that do that a lot; the differences are
> >minor at best (1-2 % Rfree, mostly differences are in the anomalous
> >signal quality). Thus I dont think its processing but a mistake in the
> >settings or somewhere else something that went clearly wrong
> >(different origin ?). Anyway, i am not sure about that either, since
> >Satinder says that the model does fit the density (which density
> >though ? Also not clear).
> >
> >BTW, assuming that the two datasets are from different non-isomorpous
> >crystals, thats what I would be tempted to try and do:
> >
> >1. Use 'phaser' to do a molecular replacement of the 70% complete
> >model to the 2.3 A dataset
> >2. Use 'cad' to combine the output mtz file of 'phaser' with phases
> >and weights, with you SAD phases and weights, plus Fobs of both datasets.
> >3. Use dmmulti to do 'multi-crystal averaging' using the molecular
> >replacement phases of the 2.3 A dataset and the 2.7 A SAD phases. Also
> >use the NCS. That must result to a good 2.3 A map.
> >4. Use ARP/wARP to autotrace the 2.3 A map with the 2.3 A fobs.
> >
> >I should also add that if I had a 2.3 A native and a 2.7 A SAD map in
> >NON-isomorphous crystals in the first place, I would use DM-multi
> >directly,
> >even without phases for the 2.3 A map. That has worked beautifully for
> >me in the past. Anyway - too late for that now since you have a model.
> >
> >Last but not least if the 2.3 A dataset and the 2.7 A dataset are
> >isomorphous, I would most definitely have tried phasing using both of them
> >Especially if one had eg Se and one did not (the best SAD experiment
> >will give you 6 to 7 e to use; Se-S has 18 e. why not use them if you
> >can ??
> >yes, SAD might sometimes be the best map as many people have shown
> >over the last few years,
> >but also sometimes the Se-derivative - Native has lots and lots of
> >info and using all info can give better maps when non-isomorphism is
> >not a problem.)
> >
> >May I also assume that when you are sure of the space group that means
> >you put it through x-triage and its not a disguised P21 twin,
> >as many P21212 cases I have seen.
> >
> >Tassos
> >
> >On Jul 27, 2007, at 2:19, Satinder K. Singh wrote:
> >
> >>Hello,
> >>
> >>I have a SAD data set to 2.9A and a native data set on the same
> >>protein to 2.3A. I have built 70% of the model (polyalanine) into the
> >>SAD experimental map that has been subjected to 2-fold NCS averaging
> >>and phase-extended to 2.3 A. From the maps, the model looks like it
> >>fits the density fine, but when I try to refine (either rigid-body or
> >>positional refinement in REFMAC or simulated annealing in CNS), I get
> >>an R-factor of ~60%, worse than random. Similarly, a SigmaA run
> >>("combine isomorphous phase with partial structure") on the model
> >>yields an R-factor of ~60%. However, when I run DM on the
> >>original phase-combined file (before NCS averaging and phase
> >>extension) in omit mode, I get an R-free of 34.6%, which suggests
> >>that the map files itself is okay.
> >>
> >>I also checked the space group of the processed data, and it is
> >>definitely P21212.
> >>
> >>Does anyone have any suggestions of what I m
Re: [ccp4bb] Crystallography short courses?
The Rapidata course held at Brookhaven every year is a five-day course precisely for what you are talking about. I benefited much from attending the course. Check the link: http://www.px.nsls.bnl.gov/courses/rr_course_2007/ Hope that helps. Raji -Included Message-- >I am looking for information on short courses on data collection, >processing, and refinement. > >Thanks, >Kendall >-- >Kendall W. Nettles, PhD >Assistant Professor >Department of Cancer Biology >The Scripps Research Institute >5353 Parkside Dr. >Jupiter Fl 33458 > >office 561-799-8851 >fax 561-799-8805 >cell 561-306-7566 > > > > > > -End of Included Message--
Re: [ccp4bb] initial model built in Fo map not refining
The new pointless which is the underlying program for the "Test
Alternate Indexing" task from the CCP4-6.0.2 GUI works brilliantly for
matching 2 data sets.
However in P21212 if a not-equal b not-equal c it is hard to confuse them..
Like Tassos I think you should start your experiment by merging all
data sets with CAD - checking they are isomorphous with SCALEIT ( Exptl
Phasing tasks) , worrying a lot if they are not! then using the 2.3A
data for phase extension from the 2.7A exptl phases. DM with averaging
and phase extension will improve your map a lot, and maybe you can build
the other 30%
Eleanor
PS - as a crystallographic educator I am a bit upset that this isnt the
norm for experimental phasing - phase extension is brilliant!! and not
using it is rather reminiscent of self flagelation..
Anastassis Perrakis wrote:
Hi -
Its not clear to me if the 2.3 A dataset is from a different crystal,
if it has the same space group as the 2.7 A dataset and if it is
isomorphous, and how the 'jump' from the 2.7 A dataset to the 2.3 A
dataset has been done. I can think of quite a few ways to do that
transition, and each way can carry its own problems.
Maybe its worth clarifying these in more detail.
I also have to say that (for once!) I dont agree with Kay. I have
tried in the past to refine against datasets processed with different
programs, and I know people that do that a lot; the differences are
minor at best (1-2 % Rfree, mostly differences are in the anomalous
signal quality). Thus I dont think its processing but a mistake in the
settings or somewhere else something that went clearly wrong
(different origin ?). Anyway, i am not sure about that either, since
Satinder says that the model does fit the density (which density
though ? Also not clear).
BTW, assuming that the two datasets are from different non-isomorpous
crystals, thats what I would be tempted to try and do:
1. Use 'phaser' to do a molecular replacement of the 70% complete
model to the 2.3 A dataset
2. Use 'cad' to combine the output mtz file of 'phaser' with phases
and weights, with you SAD phases and weights, plus Fobs of both datasets.
3. Use dmmulti to do 'multi-crystal averaging' using the molecular
replacement phases of the 2.3 A dataset and the 2.7 A SAD phases. Also
use the NCS. That must result to a good 2.3 A map.
4. Use ARP/wARP to autotrace the 2.3 A map with the 2.3 A fobs.
I should also add that if I had a 2.3 A native and a 2.7 A SAD map in
NON-isomorphous crystals in the first place, I would use DM-multi
directly,
even without phases for the 2.3 A map. That has worked beautifully for
me in the past. Anyway - too late for that now since you have a model.
Last but not least if the 2.3 A dataset and the 2.7 A dataset are
isomorphous, I would most definitely have tried phasing using both of them
Especially if one had eg Se and one did not (the best SAD experiment
will give you 6 to 7 e to use; Se-S has 18 e. why not use them if you
can ??
yes, SAD might sometimes be the best map as many people have shown
over the last few years,
but also sometimes the Se-derivative - Native has lots and lots of
info and using all info can give better maps when non-isomorphism is
not a problem.)
May I also assume that when you are sure of the space group that means
you put it through x-triage and its not a disguised P21 twin,
as many P21212 cases I have seen.
Tassos
On Jul 27, 2007, at 2:19, Satinder K. Singh wrote:
Hello,
I have a SAD data set to 2.9A and a native data set on the same
protein to 2.3A. I have built 70% of the model (polyalanine) into the
SAD experimental map that has been subjected to 2-fold NCS averaging
and phase-extended to 2.3 A. From the maps, the model looks like it
fits the density fine, but when I try to refine (either rigid-body or
positional refinement in REFMAC or simulated annealing in CNS), I get
an R-factor of ~60%, worse than random. Similarly, a SigmaA run
("combine isomorphous phase with partial structure") on the model
yields an R-factor of ~60%. However, when I run DM on the
original phase-combined file (before NCS averaging and phase
extension) in omit mode, I get an R-free of 34.6%, which suggests
that the map files itself is okay.
I also checked the space group of the processed data, and it is
definitely P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
[ccp4bb] Problem reading syminfo.lib
All- I've written a program which reads all the space-group info in syminfo.lib (in order to generate Cheshire groups - currently syminfo.lib only contains the limits of the Cheshire cell - it doesn't list the elements of the group which is what I need). However I'm running into a problem: s/r MSYMLB3 chokes on this line for SG 2005: basisop y,-1/2*x+z,1/2*x The SG 2005 entry 'A 2 1 1' doesn't make any sense because it is A centred with unique axis A & there's no such space group in IT (the symop.lib entry also appears to be garbage). IMO the current entry in syminfo for 'A 1 2 1' should be changed to 'symbol ccp4 2005' and the current entry for 'A 2 1 1' (ccp4 2005) deleted. The SG 2005 'A 2 1 1' in symop should be changed accordingly, i.e. to 'A 1 2 1'. A search of the PDB for SG 'A 2' reveals only 2 structures: 1MBS and 1BM3 (both of which are actually 'A 1 2 1' - which I think proves my point!). Cheers -- Ian Ian J. Tickle, DPhil. Director of X-ray Technology Astex Therapeutics Ltd 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226214 Fax: +44(0)1223 226201 www.astex-therapeutics.com Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] struggling with molecular replacement
Does your cell show pseudo symmetry or NCS translations? Eleanor Wu, Mousheng wrote: hi, everyone! I am struggling with my crystal structure in a very big unit cell. my protein is about 16KDa. probably there are about 20 molecules in the asymmetric unit. I tried to use molecular replacement to solve the structure. However, there is only one NMR structure available for me. The second trouble is there are so many molecules in the ASU. I tried use NMR structure as a model to solve it. MolRep gave me 4 solutions. I refined it first and see the map. The map looks quite reasonable. some parts of the model fit the density and some do not . i tried to trace one molecule first. you can image how hard it is. Does anyone have such experience? how can i find so many solutions with NMR model? your suggestions are much appreciated! Mousheng Wu
Re: [ccp4bb] initial model built in Fo map not refining
Does the mtz file you are using for refinement have the correct
spacegroup in it? Sometimes it gets left as the pointgroup P222 and
causes disasters
(you just need to run
mtzutils hklin1 now.mtz hklout x.mtz
SYMM P21212
end
Eleanor
Satinder K. Singh wrote:
Hello,
I have a SAD data set to 2.9A and a native data set on the same
protein to 2.3A. I have built 70% of the model (polyalanine) into the
SAD experimental map that has been subjected to 2-fold NCS averaging
and phase-extended to 2.3 A. From the maps, the model looks like it
fits the density fine, but when I try to refine (either rigid-body or
positional refinement in REFMAC or simulated annealing in CNS), I get
an R-factor of ~60%, worse than random. Similarly, a SigmaA run
("combine isomorphous phase with partial structure") on the model
yields an R-factor of ~60%. However, when I run DM on the
original phase-combined file (before NCS averaging and phase
extension) in omit mode, I get an R-free of 34.6%, which suggests that
the map files itself is okay.
I also checked the space group of the processed data, and it is
definitely P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
Re: [ccp4bb] initial model built in Fo map not refining
Anastassis Perrakis schrieb: I also have to say that (for once!) I dont agree with Kay. I have tried in the past to refine against datasets processed with different programs, and I know people that do that a lot; the differences are minor at best (1-2 % Rfree, mostly differences are in the anomalous if the datasets are unproblematic I agree completely with you. The fact that Satinder got a SAD map at all indicates that the data are likely to be unproblematic. It could well be that by suspecting overloads as the culprits I'm "barking up the wrong tree". But it is a possibility - and different programs treat overloads differently, and more important: they give different hints about what other things could go wrong - like the possibility of several settings. best, Kay smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] CCP4 Wiki
Kevin Cowtan schrieb: Yes, that is our intention. CCP4 would probably be at the third level of a hierarchy including: Macromolecular crystallographic techniques Structure solution, analysis and visualisation software The CCP4 suite Kevin, why does/will/should the CCP4 Wiki have a hierarchy at all? I thought that the structure of the Wiki emerges from the links between the articles. As far as I know the MediaWiki software does not even support a hierarchy (but of course I may be wrong, and other software might support it). And why are you concerned about security? In what sense? Breakins into the computer that runs the software, or vandalism of articles? I believe the first point is best dealt with by setting up a virtual machine dedicated to the Wiki, and running an OS that gets automatic security updates for a number of years. The "vandalism" thing is probably less of an issue than it is in Wikipedia - but even at the Wikipedia scale it can be handled well, it seems. One other thing that I thought about has to do with permissions. Let me explain. The easiest way to come up with useful articles would probably be to just write summaries citing people's emails to the CPP4BB. Citing Eleanor's postings alone would certainly produce a great Wiki! But - is it appropriate/allowed to cite people's old emails to the CCP4BB on the Wiki, without their consent? I for one would certainly give permission to cite my earlier CCP4BB postings, provided they are cited in the proper context. And finally: why is there a concern by some people about the "premature" setup of a Wiki, like the one that was set up by Artem? If the articles in a Wiki are good they can just be copied over to the "CCP4 Wiki" when it exists. At least that is my understanding concerning Wikipedia articles - you can just use them under the GNU Free Documentation License. thanks, Kay So there would be room for other software packages at the same level as CCP4, and things like purification and crystallisation off of the top level. James Stroud wrote: Would a "CCP4 wiki" be different from a general crystallography wiki? Would it reflect, for instance, the breadth of topics on the CCP4BB? On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote: Contributions from volunteers to establish and maintain the CCP4 wiki will be definitely appreciated. smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] initial model built in Fo map not refining
Hi -
Its not clear to me if the 2.3 A dataset is from a different crystal,
if it has the same space group as the 2.7 A dataset and if it is
isomorphous, and how the 'jump' from the 2.7 A dataset to the 2.3 A
dataset has been done. I can think of quite a few ways to do that
transition, and each way can carry its own problems.
Maybe its worth clarifying these in more detail.
I also have to say that (for once!) I dont agree with Kay. I have
tried in the past to refine against datasets processed with different
programs, and I know people that do that a lot; the differences are
minor at best (1-2 % Rfree, mostly differences are in the anomalous
signal quality). Thus I dont think its processing but a mistake in
the settings or somewhere else something that went clearly wrong
(different origin ?). Anyway, i am not sure about that either, since
Satinder says that the model does fit the density (which density
though ? Also not clear).
BTW, assuming that the two datasets are from different non-isomorpous
crystals, thats what I would be tempted to try and do:
1. Use 'phaser' to do a molecular replacement of the 70% complete
model to the 2.3 A dataset
2. Use 'cad' to combine the output mtz file of 'phaser' with phases
and weights, with you SAD phases and weights, plus Fobs of both
datasets.
3. Use dmmulti to do 'multi-crystal averaging' using the molecular
replacement phases of the 2.3 A dataset and the 2.7 A SAD phases.
Also use the NCS. That must result to a good 2.3 A map.
4. Use ARP/wARP to autotrace the 2.3 A map with the 2.3 A fobs.
I should also add that if I had a 2.3 A native and a 2.7 A SAD map in
NON-isomorphous crystals in the first place, I would use DM-multi
directly,
even without phases for the 2.3 A map. That has worked beautifully
for me in the past. Anyway - too late for that now since you have a
model.
Last but not least if the 2.3 A dataset and the 2.7 A dataset are
isomorphous, I would most definitely have tried phasing using both of
them
Especially if one had eg Se and one did not (the best SAD experiment
will give you 6 to 7 e to use; Se-S has 18 e. why not use them if you
can ??
yes, SAD might sometimes be the best map as many people have shown
over the last few years,
but also sometimes the Se-derivative - Native has lots and lots of
info and using all info can give better maps when non-isomorphism is
not a problem.)
May I also assume that when you are sure of the space group that
means you put it through x-triage and its not a disguised P21 twin,
as many P21212 cases I have seen.
Tassos
On Jul 27, 2007, at 2:19, Satinder K. Singh wrote:
Hello,
I have a SAD data set to 2.9A and a native data set on the same
protein to 2.3A. I have built 70% of the model (polyalanine) into
the SAD experimental map that has been subjected to 2-fold NCS
averaging and phase-extended to 2.3 A. From the maps, the model
looks like it fits the density fine, but when I try to refine
(either rigid-body or positional refinement in REFMAC or simulated
annealing in CNS), I get an R-factor of ~60%, worse than random.
Similarly, a SigmaA run ("combine isomorphous phase with partial
structure") on the model yields an R-factor of ~60%. However, when
I run DM on the original phase-combined file (before NCS averaging
and phase extension) in omit mode, I get an R-free of 34.6%, which
suggests that the map files itself is okay.
I also checked the space group of the processed data, and it is
definitely P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
