Re: [ccp4bb] Off-topic: Best Scripting Language
I'd just use a decent shell scripting language (like zsh) in conjunction with a unix tool like awk. But the gnuplot option sounds ideal. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Sep 12, 2012, at 7:32 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear List, since this probably comes up a lot in manipulation of pdb/reflection files and so on, I was curious what people thought would be the best language for the following: I have some huge (100s MB) tables of tab-delimited data on which I would like to do some math (averaging, sigmas, simple arithmetic, etc) as well as some sorting and rejecting. It can be done in Excel, but this is exceedingly slow even in 64-bit, so I am looking to do it through some scripting. Just as an example, a sort which takes 10 min in Excel takes ~10 sec max with the unix command sort (seems crazy, no?). Any suggestions? Thanks, and sorry for being off-topic, Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Ligand geometry obs. vs. ideal
In case it helps… After you've done unrestrained refinement, you can use prosmart to generate external self-restraints to the current conformation (using the -self_restrain keyword). This is flexible - you can specify residue ranges, and it works for protein, ligand, DNA/RNA, waters, etc. These external restraints will attempt to maintain the original relative conformation throughout refinement. If you want any help doing this, feel free to email me off-board. Cheers, Rob On 12 Sep 2012, at 21:11, Edwin Pozharski wrote: You can do unrestrained refinement in refmac, at your resolution it may be OK. If you want to keep protein restrained, you can either use harmonic restraints or come up with a special cif-file for your ligand with large esd targets. There is no direct way to tell refmac to exclude specific residue from restraints, at least to my knowledge. Cheers, Ed. On 09/12/2012 02:44 PM, Yuri Pompeu wrote: What is the best way to refine the ligand unrestrained and then generate measurements?
Re: [ccp4bb] Aimless and Pointless
It is possible to force Pointless to select a particular solution, using the Find or match Laue group option in CCP4i. The default option here is Determine Laue group but if you select the Choose a previous solution checkbox you can specify the solution you want Pointless to select, by Space group name, Laue group name or Laue group solution number (from a previous run). You can do the same with the Symmetry, Scale, Merge (Aimless) if you check the tickbox Customise symmetry determination and then Choose a previous solution. In cases of pseudosymmetry it is sometimes necessary to override the solution Pointless thinks is best. Andrew On 12 Sep 2012, at 23:41, Cosmo Z Buffalo wrote: Hi all, I am currently trying to perform a quickscale in iMosflm 7.0.9 after I integrate in an R 32 space group. Unfortunately, both Pointless and Aimless are both giving me a best solution space group of P 43 3 2. After analyzing the statistics, this cannot be correct. Other programs such as HKL2000 have confirmed this to be true. So my question: is it possible to force Aimless and Pointless to generate statistics in a space group other than the one it predicts? And if so, how would I do this? -Cosmo
Re: [ccp4bb] Ligand geometry obs. vs. ideal
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yuri, at 1.18A resolution you can also refine using shelxl. It's basically your choice on a per-atom-basis what properties you wish to restrain and which to leave unrestrained. With L.S. refinement and given enough RAM it can print esds of your coordinates to its log file from which you can calculate all properties you mention - some of these might already be in the log-file itself. Cheers, Tim On 09/12/2012 08:44 PM, Yuri Pompeu wrote: Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQUak9UxlJ7aRr7hoRApdnAJ0SvhnucqonoCCrwaYMXaNeYlRPXACeJdyz qxDduM1vcxPCMYOmtkIOtkY= =Wt7O -END PGP SIGNATURE-
Re: [ccp4bb] Ligand geometry obs. vs. ideal
Hi Yuri, If you have access to mogul you can get an understanding of what your geometry should be based on the small molecule database. Of course not everything is well represented so if your ligand is unusual this will flag up in lower statistical significance. Mogul will allow you to understand how far you are from ideal. Not really sure if this is what you might be after Joe P -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: 12 September 2012 19:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ligand geometry obs. vs. ideal Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
Re: [ccp4bb] Off-topic: Best Scripting Language
After this religious debate concludes, I propose we return to the old standby - vi versus emacs. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Thursday, September 13, 2012 5:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Best Scripting Language -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I don't read blaming in George's words, just reasoning for a personal decision. Maybe I suffer from similar prejudice: I have the impression that python programmers spend a lot of effort in trying to convince others that python is a good choice. Why bother rather than let people make their own decision? Cheers, Tim On 09/12/2012 09:49 PM, James Stroud wrote: On Sep 12, 2012, at 1:00 PM, George Sheldrick wrote: It is the lack of compatibility between different versions mentioned by Ethan that really put me off learning PYTHON. Python is backwards compatible. I have reams of code I wrote in python 2.3 that still works in 2.7 without modification. Also, python (aka python 2) and python 3000 (aka python 3) are considered two different languages. It's not reasonable to consider them one language and then complain that they are incompatible. Python 3 was created as a new language (and should be treated as such) precisely because it breaks compatibility with python 2. That was the intent of the language authors. You blame the authors for recognizing limitations of a language and inventing a new one to overcome those limitations. If the FORTRAN authors would have done that about 30 years ago, we all might be programming in FORTRAN. James - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQUaZRUxlJ7aRr7hoRAimoAJwPAw1o0VqugVERQcYN0RBR424mYgCgu8mF cwGd1+0swzfudjmf0pgu0ek= =NIVw -END PGP SIGNATURE- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Off Topic: Maltose Binding Protein Purification
CCP4, I will be doing some MBP fusion purification in the near future and I was wondering if anyone knew what the most cost effective MBP trapping resin to use. So, far I have seen the following two products, are there any others I should consider? GE* Healthcare MBPTrap HP ColumnsNew England Amylose Resin High Flow Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
[ccp4bb] Postdoc Position in Grenoble, France
Dear Colleagues, Please find attached announcement about a postdoc position at the UVHCI, Grenoble.Could You please communicate to anybody who might be interested? Thanks in advance! Best regards, Patricia *Patricia Renesto, PhD UVHCI UMI 3265 CNRS-UJF-EMBL 6, rue Jules Horowitz 38042 Grenoble, France 04 76 20 94 04* POSTDOCTORAL POSITION_UVHCI.pdf Description: Adobe PDF document
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote: I have the impression that python programmers spend a lot of effort in trying to convince others that python is a good choice. Why bother rather than let people make their own decision? Someone asked. Plus, python programmers put no more effort than any other programmer. It's just that python has more advocates (for good reason) so the apparent effort is amplified. Don't hate us because our preferred programming language is beautiful. James -- James Stroud http://www.jamesstroud.com
Re: [ccp4bb] Off-topic: Best Scripting Language
Like most computer users and many scientists I don't write scripts to organize or analyse my data unless I get desperate. I've used both Python and Perl a few years ago, but it would take quite a lot of time and effort and staring at on-line tutorials to get back into either of them right now. So I end up using massive Excel files that kind of work, but are a pain. I've noticed that quite a few structural biologists have the same problem. I've never understood why there can't be a simple programming language that is completely self-explanatory bercause it uses English sentences. Our robot scripting language uses syntax like Dispense 0.5 * DropVol ul to TargetWells using ProteinSyringe That is pretty obvious. So why can't I have a language where I can write Carry_out_a_sequence_where x is 1 to 10 with_step_size 1 : if age of person(x) is_greater_than 50 then print name of person(x) is an old man (or woman) . Repeat_for_next x . ? I don't care if it's efficient (anything is efficient compared to Excel) or if it's easy to write big programs in. All I care about is that it's easy to get going. Later on I can learn to write simply Sequence instead of Carry_out_a_sequence_where. I could click a button that would make the replacement to make my code more compact and readable to a trained eye. And of course is_greater_than could be written as . Any intelligent school-child could understand it too, which would be fantastic here in the UK where kids aren't taught to program any more. Does such a language exist? On 13 September 2012 17:08, James Stroud xtald...@gmail.com wrote: On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote: I have the impression that python programmers spend a lot of effort in trying to convince others that python is a good choice. Why bother rather than let people make their own decision? Someone asked. Plus, python programmers put no more effort than any other programmer. It's just that python has more advocates (for good reason) so the apparent effort is amplified. Don't hate us because our preferred programming language is beautiful. James -- James Stroud http://www.jamesstroud.com -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic: Best Scripting Language
In my opinion, the Python equivalent of your pseudo-code is fairly close to how you would write the instructions logically. But then maybe not everyone thinks in the same way that I do :-) for x in range(1, 10): if age_of_person(x) 50: print name_of_person(x), is an old man (or woman) Of course you would have to define the functions age_of_person() and name_of_person() in order for this to work, or you could write it in a more object-oriented method so you have a Person object which has attributes name, age, gender, etc. and the code would be even more readable. for person in list_of_people: if person.age 50: print person.name, is an old , person.gender Disclaimer: I mainly write in Python, so obviously am naturally biased towards Python, however I have yet to see another widely used language that is as readable or intuitive to learn (to me). Cheers, Richard -- Richard Gildea Software Developer Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd Mail Stop 64R0121 Berkeley CA 94720-8118 On 13 September 2012 10:02, Patrick Shaw Stewart patr...@douglas.co.ukwrote: Like most computer users and many scientists I don't write scripts to organize or analyse my data unless I get desperate. I've used both Python and Perl a few years ago, but it would take quite a lot of time and effort and staring at on-line tutorials to get back into either of them right now. So I end up using massive Excel files that kind of work, but are a pain. I've noticed that quite a few structural biologists have the same problem. I've never understood why there can't be a simple programming language that is completely self-explanatory bercause it uses English sentences. Our robot scripting language uses syntax like Dispense 0.5 * DropVol ul to TargetWells using ProteinSyringe That is pretty obvious. So why can't I have a language where I can write Carry_out_a_sequence_where x is 1 to 10 with_step_size 1 : if age of person(x) is_greater_than 50 then print name of person(x) is an old man (or woman) . Repeat_for_next x . ? I don't care if it's efficient (anything is efficient compared to Excel) or if it's easy to write big programs in. All I care about is that it's easy to get going. Later on I can learn to write simply Sequence instead of Carry_out_a_sequence_where. I could click a button that would make the replacement to make my code more compact and readable to a trained eye. And of course is_greater_than could be written as . Any intelligent school-child could understand it too, which would be fantastic here in the UK where kids aren't taught to program any more. Does such a language exist? On 13 September 2012 17:08, James Stroud xtald...@gmail.com wrote: On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote: I have the impression that python programmers spend a lot of effort in trying to convince others that python is a good choice. Why bother rather than let people make their own decision? Someone asked. Plus, python programmers put no more effort than any other programmer. It's just that python has more advocates (for good reason) so the apparent effort is amplified. Don't hate us because our preferred programming language is beautiful. James -- James Stroud http://www.jamesstroud.com -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 13, 2012, at 11:02 AM, Patrick Shaw Stewart wrote: Like most computer users and many scientists I don't write scripts to organize or analyse my data unless I get desperate. I've used both Python and Perl a few years ago, but it would take quite a lot of time and effort and staring at on-line tutorials to get back into either of them right now. So I end up using massive Excel files that kind of work, but are a pain. I've noticed that quite a few structural biologists have the same problem. I've never understood why there can't be a simple programming language that is completely self-explanatory bercause it uses English sentences. Yeah. They tried that. It's called AppleScript and is a complete disaster for programmers simply because of its vague resemblance to natural language. There are essays on this issue [1, 2], but other than the message stay away from programming languages that try to be natural languages, these essays are mostly academic. It turns out that the syntax and semantics of all reasonable programming languages are very similar, or fall into only a few classes (e.g. C-like, S-expressions, etc.), so once you are fluent in one from a class, it's easy to pick up the others. This can't be said of natural languages, which are full of idioms and grammatical exceptions, even in closely related dialects. James [1] http://www.codinghorror.com/blog/2006/08/computer-languages-arent-human-languages.html [2] http://daringfireball.net/2005/09/englishlikeness_monster
Re: [ccp4bb] Off-topic: Best Scripting Language
It turns out that the syntax and semantics of all reasonable programming languages are very similar, or fall into only a few classes (e.g. C-like, S-expressions, etc.), so once you are fluent in one from a class, it's easy to pick up the others. This can't be said of natural languages, which are full of idioms and grammatical exceptions, even in closely related dialects. This is more opinions than I can shake a stick at! Don't we all have other fish to fry (or for the French, other cats to whip? Other national equivalents?) Anyway, I was nervous as a long-tailed cat in a room full of rocking chairs to ask this question, and look at the Pandora's box that this has opened! Java anyone?! I've actually noticed a bit of a dearth of Java in the crystallography world, with some exceptions... Thanks everybody for your suggestions--I will mull them over, since you all make such good arguments (not meant in the programming sense, but probably that's true too!), Jacob James [1] http://www.codinghorror.com/blog/2006/08/computer-languages-arent-human-languages.html [2] http://daringfireball.net/2005/09/englishlikeness_monster -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] Series termination effect calculation.
Dear Colleagues,
I am trying to repeat a series termination effect calculation displayed as
figure 2 in a publihsed paper
(http://www.ncbi.nlm.nih.gov/pubmed/12215645). Formula
(1) was used to implement this calculation. Since f(s) is not defined in
detail in this paper, I used formula and parameters listed in another
paper (http://scripts.iucr.org/cgi-bin/paper?a05896) to calculate it.
However, the result I got is not consistent with figure 2 of the first
paper. I am not sure if the formulas I used are right or not. Or if there
is any problem in the MatLab code, which I list below:
###
clear all;clc;format compact;format long;
% matrix of a, b, c coefficients:
% rows: Fe, S, Fe1, Mo
% columns: A1; B1; A2; B2; A3; B3; A4; B4; C
fM = ...
[11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 1.40818;...
7.18742 1.43280 5.88671 0.02865 5.15858 22.1101 1.64403 55.4651
-3.87732;...
11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339 1.40818;...
19.3885 0.97877 11.8308 10.0885 3.75919 31.9738 1.46772 117.932 5.55047];
%%% store radius data:
% distance from: origin
% columns: Fe, S, Fe, Mo
R_el = [2.0 3.3 3.5 3.5];
RHO_t = zeros(4,400);
for numel = 1:4
EL = numel;
RHO = zeros(1,400);
dmax = zeros(1,400);
for iter = 1:400
dmax(iter) = iter/100; % in angstroms
% numerical integration
int_fun = @(s) 4*pi*(s.^2).* ...
(fM(EL,1).*exp(-fM(EL,2).*(s.^2)*0.25) + ...
fM(EL,3).*exp(-fM(EL,4).*(s.^2)*0.25) + ...
fM(EL,5).*exp(-fM(EL,6).*(s.^2)*0.25) + ...
fM(EL,7).*exp(-fM(EL,8).*(s.^2)*0.25) + fM(EL,9)).* ...
sin(2*pi*s*R_el(EL))./(2*pi*s*R_el(EL));
RHO(iter) = quad(int_fun,0,1/dmax(iter));
clc;display(iter);display(numel);
end
RHO_t(numel,:) = RHO;
end
RHO_t(1,:)= 6*RHO_t(1,:);
RHO_t(2,:)= 9*RHO_t(2,:);
figure;
axis([0.5 3.5 -10 10]); hold on;
plot(dmax,RHO_t(1,:),...
dmax,RHO_t(2,:),...
dmax,RHO_t(3,:),...
dmax,RHO_t(4,:),...
dmax,sum(RHO_t,1));
title('Electron Density Profile');
legend('Fe','S','Fe1','Mo','Sum');
xlabel('d_m_a_x'); ylabel('Rho(r)');
set(gca,'XDir','reverse');
##
Any suggestions will be appreciated. Thanks!
Niu
Re: [ccp4bb] Series termination effect calculation.
Hi,
pointers listed here may be of help:
1) CCP4 Newsletterhttp://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) https://www.phenix-online.org/presentations/latest/pavel_maps.pdf
3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16 Å
Resolution: A.
Oliver Einsle, et al. Science, 1696 (2002) 297
4) Page 267 Figure 4:
On the possibility of the observation of valence electron density for
individual
bonds in proteins in conventional difference maps
P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev
Acta Cryst. (2004). D60, 260-274
Pavel
On Thu, Sep 13, 2012 at 2:09 PM, Niu Tou niutou2...@gmail.com wrote:
Dear Colleagues,
I am trying to repeat a series termination effect calculation displayed as
figure 2 in a publihsed paper (http://www.ncbi.nlm.nih.gov/pubmed/12215645).
Formula
(1) was used to implement this calculation. Since f(s) is not defined in
detail in this paper, I used formula and parameters listed in another
paper (http://scripts.iucr.org/cgi-bin/paper?a05896) to calculate it.
However, the result I got is not consistent with figure 2 of the first
paper. I am not sure if the formulas I used are right or not. Or if there
is any problem in the MatLab code, which I list below:
###
clear all;clc;format compact;format long;
% matrix of a, b, c coefficients:
% rows: Fe, S, Fe1, Mo
% columns: A1; B1; A2; B2; A3; B3; A4; B4; C
fM = ...
[11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339
1.40818;...
7.18742 1.43280 5.88671 0.02865 5.15858 22.1101 1.64403 55.4651
-3.87732;...
11.9185 4.87394 7.04848 0.34023 3.34326 15.9330 2.27228 79.0339
1.40818;...
19.3885 0.97877 11.8308 10.0885 3.75919 31.9738 1.46772 117.932 5.55047];
%%% store radius data:
% distance from: origin
% columns: Fe, S, Fe, Mo
R_el = [2.0 3.3 3.5 3.5];
RHO_t = zeros(4,400);
for numel = 1:4
EL = numel;
RHO = zeros(1,400);
dmax = zeros(1,400);
for iter = 1:400
dmax(iter) = iter/100; % in angstroms
% numerical integration
int_fun = @(s) 4*pi*(s.^2).* ...
(fM(EL,1).*exp(-fM(EL,2).*(s.^2)*0.25) + ...
fM(EL,3).*exp(-fM(EL,4).*(s.^2)*0.25) + ...
fM(EL,5).*exp(-fM(EL,6).*(s.^2)*0.25) + ...
fM(EL,7).*exp(-fM(EL,8).*(s.^2)*0.25) + fM(EL,9)).* ...
sin(2*pi*s*R_el(EL))./(2*pi*s*R_el(EL));
RHO(iter) = quad(int_fun,0,1/dmax(iter));
clc;display(iter);display(numel);
end
RHO_t(numel,:) = RHO;
end
RHO_t(1,:)= 6*RHO_t(1,:);
RHO_t(2,:)= 9*RHO_t(2,:);
figure;
axis([0.5 3.5 -10 10]); hold on;
plot(dmax,RHO_t(1,:),...
dmax,RHO_t(2,:),...
dmax,RHO_t(3,:),...
dmax,RHO_t(4,:),...
dmax,sum(RHO_t,1));
title('Electron Density Profile');
legend('Fe','S','Fe1','Mo','Sum');
xlabel('d_m_a_x'); ylabel('Rho(r)');
set(gca,'XDir','reverse');
##
Any suggestions will be appreciated. Thanks!
Niu
Re: [ccp4bb] Off-topic: Best Scripting Language
Another option that could be cheap or free (if your university offers license deals, as mine does) is SPSS. It has a lot of the quick and dirty spreadsheet functionality of Excel, is much faster than Excel with large tables, has lots of good analysis tools, has its own scripting language, and is compatible with R and Python. Eric On Thu, Sep 13, 2012 at 2:21 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: It turns out that the syntax and semantics of all reasonable programming languages are very similar, or fall into only a few classes (e.g. C-like, S-expressions, etc.), so once you are fluent in one from a class, it's easy to pick up the others. This can't be said of natural languages, which are full of idioms and grammatical exceptions, even in closely related dialects. This is more opinions than I can shake a stick at! Don't we all have other fish to fry (or for the French, other cats to whip? Other national equivalents?) Anyway, I was nervous as a long-tailed cat in a room full of rocking chairs to ask this question, and look at the Pandora's box that this has opened! Java anyone?! I've actually noticed a bit of a dearth of Java in the crystallography world, with some exceptions... Thanks everybody for your suggestions--I will mull them over, since you all make such good arguments (not meant in the programming sense, but probably that's true too!), Jacob James [1] http://www.codinghorror.com/blog/2006/08/computer-languages-arent-human-languages.html [2] http://daringfireball.net/2005/09/englishlikeness_monster -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Ligand geometry obs. vs. ideal
I second Tim Gruene's suggestion of SHELXL; it's perfect for this. However, there is a steep learning curve, so I strongly urge you to pay close attention to the SHELXL (and SHELXPRO) manuals. On Wed, Sep 12, 2012 at 11:44 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 12, 2012, at 2:28 PM, Ethan Merritt wrote: Why are you dis-ing python? Seems everybody loves it... I'm sure you can google for many reasons I hate Python lists. Mine would start 1) sensitive to white space == fail 2) dynamic typing makes it nearly impossible to verify program correctness, and very hard to debug problems that arise from unexpected input or a mismatch between caller and callee. 3) the language developers don't care about backward compatibility; it seems version 2.n+1 always breaks code written for version 2.n, and let's not even talk about version 3 4) slw unless you use it simply as a wrapper for C++, in which case why not just use C++ or C to begin with? 5) not thread-safe you did ask... Ethan While I agree generally with your points and try to avoid python if at all possible, I'm not sure about what you mean with point 5, since it's certainly possible to write threaded python scripts. Another point that is purely personal taste is the language philosophy that there is one official way to do something in Python, as contrasted with Perl (which is my choice) where the language philosophy is that there are many ways of doing any given task and the language is not designed to force you into a particular way of doing it. Ed adds: While indeed 1/3=0 (but so it will be in C), I think it's a bit of an overstatement that python code execution is nearly impossible to verify. Another goal of python is to accelerate implementation, and dynamic/duck typing supposedly helps that. The argument is simply that weak typing favours strong testing, which should be a good thing. Actually it's a bit of a hindrance. In Perl I can call the int function on anything and get a sensible answer. In python if you call int on a string that contains a floating point number the default behavior is that it will crash: [woz:~] bennette% cat pytest.py example_string = 10.3 number = int(example_string) [woz:~] bennette% /Library/Frameworks/Python.framework/Versions/2.6/bin/python pytest.py Traceback (most recent call last): File pytest.py, line 2, in module number = int(example_string) ValueError: invalid literal for int() with base 10: '10.3' That's brain dead. IMHO of course. Cheers, Eric
