Assuming that your homology model is that of a dimer, you could put it in a
large unit cell (just add CRYST1 record). The only interface you will get from
pisa will be your dimer interface.
If your homology model is a monomer, then pisa will not help, of course, and
you would need to pred
I suspect the question might be about converting intensities to anplitudes. If
so ctruncate is your friend.
Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5
Original message
From: Eleanor Dodson
Date:01/03/2015 3:42 PM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Sub
Why? Merging waters like that in coot is a user error, and it does not happen
too often. I realize you are talking about changeable settings, but it would
be really annoying if a refinement program kept removing water molecules that
were placed manually because it does not fit some internal sta
Edit the ATOM records?
Sent on a Sprint Samsung Galaxy S® III
Original message From: luzuok
Date:10/23/2014 6:51 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Merge PDB
chains
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
Yes, having different crystal forms in the same crystallization conditions is,
while clearly uncommon, not unheard of. I had a case once where at least four
different crystal forms were observed in crystals harvested from identically
prepared drops. It may be that there is some major set of con
Try refining your model both ways (with and without covalent link) and see if
electron density maps give you an indication. At this resolution there will be
some model bias, so be critical.
Sent on a Sprint Samsung Galaxy S® III
Original message From: rohit kumar
Date:08/1
Same here. Ultimately, the KD test must be used in the end to finalize the
resolution (keeping in mind recently discussed issues of effective resolution
given data completeness). I just want to add that at least some versions of
aimless report overestimated resolution based on CC1/2 cutoff whe
Probably the only way is to take unmerged scalepack output to aimless.
Sent on a Sprint Samsung Galaxy S® III
Original message From: Faisal Tarique
Date:08/15/2014 9:40 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cc1/2 value
in hkl2000
Hello everyone
Can a
By all means, try it both ways and see whether the R-Rfree gap narrows with
random vs thin shell selection. Depending on resolution and data quality, you
may also consider imposing NCS restraints.
Sent on a Sprint Samsung Galaxy S® III
Original message From: Xianchi Dong
Dat
You may need to
1) modify _chem_comp.group to be "DNA" in the cif-file
2) import the resulting cif-file in coot
Cheers
Sent on a Sprint Samsung Galaxy S® III
Original message From: "Wang, Wei"
Date:07/15/2014 5:14 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb]
Try to put your crystal into oil drop?
Sent on a Sprint Samsung Galaxy S® III
Original message From: Frank von Delft
Date:07/07/2014 12:32 PM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency
substitute for RT loop cover?
Hi all
Pretend you were stuck ha
Roger,
Given that PAK value is the number of clashing residues I doubt that in this
case it is a loop clash etc.
As a general comment though you are absolutely correct.
Cheers,
Ed
Sent on a Sprint Samsung Galaxy S® III
Original message From: Roger Rowlett
Date:06/17/20
There is no actual requirement to use Kabat numbering, you can avoid it
alrogether. Some argue that L27A is actually 28th amino acid in the protein
sequence, and labeling it as L27A is simply incorrect. I would suggest doing
refinement with plain numbering (no insertion codes) and changing it
Or, if for whatever reason sphere refine isn't an option, fix the metal and all
of its ligands
Sent on a Sprint Samsung Galaxy S® III
Original message From: Paul Emsley
Date:06/05/2014 3:51 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] metal ion
dominatin
Would a no-space symlink resolve this?
Sent on a Sprint Samsung Galaxy S® III
Original message From: Mark J van Raaij
Date:06/03/2014 8:03 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage:
no tables were found in this file
completely agree with avoi
This may not work if a program implements its own algorithm for parsing command
line parameters
Sent on a Sprint Samsung Galaxy S® III
Original message From: Tim Gruene
Date:06/03/2014 8:27 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage:
no tables
My suggestion is to ignore Rmerge when making decisions about resolution
cutoff. While cc1/2 may still perhaps qualify for the "recent discussion" tag
(is two years recent?), deeply flawed nature of the Rmerge concept is over a
decade old.
Sent on a Sprint Samsung Galaxy S® III
Orig
Try refining without disulfide bond - from the way density looks it might work.
Whether this is what happens in vivo is a different question entirely.
Sent on a Sprint Samsung Galaxy S® III
Original message From: Eze Chivi
Date:06/02/2014 1:08 AM (GMT-05:00)
To: CCP4BB@J
ffinities from crystal soaks is, hmm, not very good pratice, simply
> because there are other dedicated methods to do it that suffer less
> from side effects. Including the docking approach.
>
> Kind regards, Baerbel
>
>
> Quoting Ed Pozharski :
>
> > If I under
rent concentrations nor B-factor
> analysis are solid methods to determine some sort of relative
> affinities. I'd suggest to design mutants for either binding site and
> ITC measurements with the mutant proteins. This might also tell you if
> some sort of co-op exists between b
IMHO, while explaining binding affinity from a structure is fun, it does
not prove anything. Assuming that I understand your situation
correctly, you can (relatively) easily find out from experiment which
pocket has higher affinity. Just do soaks with different ligand
concentrations - the expecta
Dear Kay,
I wonder what is your opinion of the following proposition.
"None of the data quality indicators derived from data alone matter too
much".
Let me explain what I mean by this.
Ultimately, I truly don't care what value of Rmerge, Rpim, or even CC1/2
data processing produces from the set
http://www.ccp4.ac.uk/html/watertidy.html
On 10/29/2013 04:43 PM, Elise B wrote:
Hello,
I am working on a project with several (separate) structures of the
same protein. I would like to be able to compare the solvent molecules
between the structures, and it would be best if the waters that e
It's definitely possible to rig, say, autodock to run the same small
molecule over every protein in the PDB. Results, of course, should be
taken with a grain of salt.
On Mon, 2013-10-14 at 20:53 +0900, L wrote:
> Hi all,
>
>
> I'm looking for a way to find/predict protein partner(s) for our
> l
Florian,
B-factors will likely correlate with any property that changes depending
on the distance from protein surface. Whether such correlation means
causation is always difficult to prove.
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
> May I ask a question?
>
This is a catch-22 situation. If you ask permission to ask a question,
you are already asking a question. Answering this with no would
probably create a wormhole. I'd also like to see a bulletin board where
asking questions requires separate permission.
> When we pre
On Thu, 2013-08-22 at 14:22 -0400, Bosch, Juergen wrote:
> But when it sits and crystallizes it is cleaner - unless some
> opportunistic fungal contamination helps you trim off those nasty
> loops that you would have omitted anyhow from your model.
Jurgen,
Good point and admittedly I never consi
On Thu, 2013-08-22 at 13:58 -0400, Bosch, Juergen wrote:
> well if we hit the timer after lysis, say via cell disruptor then I
> have my eluted protein in less than 1 hour, including 40 minutes batch
> binding.
then proceeds to wait six weeks for crystals to appear... :)
Cheers,
Ed.
PS. There
On Thu, 2013-08-22 at 10:07 -0400, Bosch, Juergen wrote:
> Yes, I'm also surprised why people run gradients for the capturing
> step ?
Because we can. Joking aside, I've seen some examples where protein
eluted at relatively low imidazole and upon running the gradient there
remains some (minimal)
According to Qiagen
> Since imidazole absorbs UV radiation at 280 nm, an elution profile
> measured at 280 nm while purifying a 6xHis tagged protein by FPLC will
> show an increase in absorbance above the background signal allowing
> quantitation of your protein. The absorbance of imidazole can v
On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset
or many other tools. Writing code for this should only be necessary
if you're processing large numbers of models, or have a spectacularly
misformatted PDB file. Again, I'll repeat wh
James,
On 08/07/2013 05:36 PM, James Stroud wrote:
Anyone can learn Python in an hour and a half.
Isn't this a bit of an exaggeration? Python is designed to be easy to
learn, but we probably talking about different definitions of "learning"
and "anyone".
I.e. programs would look like thi
On 08/07/2013 03:54 PM, James Stroud wrote:
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its inspiration
from SQL
For this to work, a particular interface must monopolize access to
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its inspiration
from SQL
For this to work, a particular interface must monopolize access to
structural data. Then maintainers of that victorious interface could
change the underlying fo
This question may be better suited for more small-angle-oriented forum,
e.g.
http://www.saxier.org/forum/
On 08/07/2013 11:22 AM, Remec, Mark wrote:
Dear CCP4bb,
I have a few questions concerning SANS data recently collected that
I'm having trouble analyzing. The data was collected at 2 dif
Douglas,
Observed intensities are the best estimates that we can come up with in an
experiment.
I also agree with this, and this is the clincher. You are arguing that Ispot-Iback=Iobs is
the best estimate we can come up with. I claim that is absurd. How are you quantifying
"best"? Usually
On 06/21/2013 10:19 AM, Ian Tickle wrote:
If you observe the symptoms of translational NCS in the diffraction
pattern (i.e. systematically weak zones of reflections) you must take
it into account when calculating the averages, i.e. if you do it
properly parity groups should be normalised separa
On 06/20/2013 06:20 AM, Eleanor Dodson wrote:
But you say you took the Balbes model into phaser? and I think Balbes
automatically runs cycles of refinement so any comment on R factors
may not mean much.
I have seen a model coming out of Balbes pipeline hitting extremely high
marks when fed in
On 06/20/2013 01:07 PM, Douglas Theobald wrote:
How can there be nothing "wrong" with something that is unphysical?
Intensities cannot be negative.
I think you are confusing two things - the true intensities and observed
intensities.
True intensities represent the number of photons that di
Dear Kay and Jeff,
frankly, I do not see much justification for any rejection based on
h-cutoff.
French&Wilson only talk about I/sigI cutoff, which also warrants further
scrutiny. It probably could be argued that reflections with I/sigI<-4
are still more likely to be weak than strong so F~0 se
and don't have
a copy of F&W here at home, but I can have a look in the morning when
I get into the lab and let you know.
Jeff
On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski <mailto:epozh...@umaryland.edu>> wrote:
I noticed something strange when processing a dataset w
I noticed something strange when processing a dataset with imosflm. The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to French&Wilson. Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97% complet
The only thing that seems to make sense is bonds rmsd - but you should
ask the annotator for specifics directly. If it is bonds rmsd, this has
been discussed many times - just google "rmsd bonds ccp4bb" and look for
most recent entries.
On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote:
> D
On 06/14/2013 07:00 AM, John R Helliwell wrote:
Alternatively, at poorer resolutions than that, you can monitor if the
Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as
more data are steadily added to your model refinements.
Dear John,
unfortunately the behavior of DPIfree
t 2. This
is based predominantly on Scala/Aimless.
Cheers,
Ed.
On Thu, 2013-06-13 at 18:20 +0200, Tim Gruene wrote:
>
> On 06/13/2013 06:16 PM, Ed Pozharski wrote:
> > [...] With that said, I am pretty sure that in vast majority of
> > cases structural conclusions derived wi
On Thu, 2013-06-13 at 08:44 -0700, Andrea Edwards wrote:
> In this case, the author should report a correlation coefficient along
> with the other standard statistics (I/sigI, Rmerg, Completeness,
> redundancy, ect.)?
Won't hurt.
> What about Rpim instead of Rmerg? and if Rpim is reported, wha
On Thu, 2013-06-06 at 14:41 +1000, Nat Echols wrote:
> You should resist the temptation to write your own PDB parser; that
> way lies pain and suffering. There are multiple free libraries for
> Python that can be used for this task - I recommend either CCTBX or
> BioPython (probably the latter if
ATOM records have fixed format so you can (and should) use string
slicing instead, like so (one-liner)
serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = line[6:11], line[12:16], line[16], line[17:20], line[21],
line[22:26], line[26], line[30:38], line[38:46], line[46:
> I am wondering whether there is a function I could use to build the
> missing bases in one strand of the DNA to base pair with the other
> strand of DNA which is complete...
Calculate->Other modeling tools-> Base pair...
--
Coot verendus est
On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote:
> In this particular case you can see the website was registered in
> September of 2012, which is a good indication that it was set up just
> to scam people.
Just curious - why registration date indicates unsavory nature of
"Jieke"?
--
A
On 05/27/2013 12:14 PM, Kavyashree Manjunath wrote:
Later I tried with 0.8, 0.99 for which the map was normal
and also validation did not report it as short contact.
Is it ok if I give 0.99 occupancy?
"Validation" most likely will not report any short contacts if occupancy
is <1. If the distanc
On 05/27/2013 11:27 AM, ka...@ssl.serc.iisc.in wrote:
Sir,
Ok. It is an acetate ion which interacts with its symmetry
equivalent ion only one of its oxygen atoms is closer to
its symmetry equivalent and not the entire ion. So do I
need to give lower occupancy for this ion?
Thank you
Regards
Kav
It is probably a wrong question to ask here. Pretty much everything is
"tolerated" by PDB during deposition, the report you get is an advice,
not instruction. I wonder whether anyone has an example of the
RCSB/PDBe/PDBj ever turning down submitted structure.
The right question is whether the
Matt,
with this technique, how do you prevent crystal from drying up (other
than "doing it fast")? I know Thorne's group does this trick under oil.
If you take no extra precautions, do you have an estimate of how often
diffraction is destroyed by this?
On the other hand, it's quite possible th
ably the number of people
> spending time trying to find and give a helpful answer.
>
> Regards,
> Tim
>
> On 05/22/2013 07:55 PM, Ed Pozharski wrote:
> > On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
> >> the answers you received were correct with respect t
On Wed, 2013-05-22 at 18:09 +0200, Tim Gruene wrote:
> the answers you received were correct with respect to the question you
> asked. If they are not satisfactory, you have not given sufficient
> information.
>
Tim,
Not sure when I expressed any dissatisfaction with replies I received.
I asked w
e 2008) from buster 2.10. Which
> version of pdbvconv are you using?
> Best,
> Tim
>
>
> On 05/21/2013 10:40 PM, Ed Pozharski wrote:
> > On 05/21/2013 04:35 PM, Francis Reyes wrote:
> >> Since you're using buster, have you tried global phasing's own
On 05/21/2013 04:35 PM, Francis Reyes wrote:
Since you're using buster, have you tried global phasing's own pdbvconv tool?
Naturally, but it leaves file unchanged.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, K
Does anyone have a script to convert pdb file with DNA atom records from
v3 back to v2? I can certainly right my own and asking only if you
already have it written. Strictly speaking, this is not ccp4-related -
apparently, buster expects the old format.
Cheers,
Ed.
--
Oh, suddenly throwing
At this point you do have the scalepack2mtz output file (BTW,
imosflm/aimless is wholeheartedly recommended by this convert), and you
can easily extract all the info from there. There is mtzdmp, of course,
but it's easier to parse the actual mtz file (hey, the records are
actually text). Like so:
Don't believe such program/server does exist. Notice that you are asking for
something that *can* predict Kd. One can *try* making such predictions and
they may even be routinely in the ballpark, assuming that you are satisfied
with being routinely off by, say, an order of magnitude.
One ca
Protein-DNA complex crystal with channels too small for the dye is *extremely*
unlikely, imho.
Original message
From: Ulrike Demmer
Date: 04/15/2013 8:48 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] salt or not?
Dear Careina,
altough your crystals doe
On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
mailto:bshaa...@exchange.bgu.ac.il>> wrote:
Whichever way the input file for the run is prepared (via GUI or
command line), anybody who doesn't inspect the log file at the end
of the run is doome
Doesn't lsqkab work? It just needs proper atom matching.
Coot definitely does superimpose DNA. One problem is that simple-lsq works on
a single chain, but you can trick it by changing chain id and renumbering the
other strand.
As for helix rotation, you can derive it from rotation reported by
On 04/04/2013 04:51 PM, 李翔 wrote:
Hi everyone,
I met a problem when trying to build ideal DNA model in Coot. The
calculated DNA looks less than 10.5 bp/ turn, probably is about 10 bp/
turn. Is there a way for me to change the pitch to make it 10.5
bp/turn in Coot?
Thanks for your kind help!
On 04/04/2013 04:29 AM, Tim Gruene wrote:
Dear --,
Are we, the "ccp4bb community", recently on the hunt to find new and
exciting ways to make sure people stop asking questions? Gentleman from
Moscow has clearly disclosed his full name and affiliation, but perhaps
I am wrong and subtle critici
On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote:
> I think this is a good time to end the discussion.
As a general comment, discussions on boards like ccp4bb often digress
and take direction different from you original intent. I may understand
your desire to try to control the situatio
This might have changed, but in the past file formats were different.
Microcal files are text, while TA's are binary. I do have the actual
description of TA's format if anyone is interested, but it must be easier to
use native text export than write a converter.
Original message --
As I recall, number of reflections set aside for cross-validation also affects
stability of sigmaA estimates. With 500 reflections and 20 resolution shells
you are down to 25 reflections per shell, which may be a bit too low.
Original message
From: Robbie Joosten
Date:
To:
On 03/23/2013 09:59 AM, Wei Feng wrote:
Can you help me to check out why these maps can not be converted by
sftools?
sftools is not for manipulating map files. Mapman from uppsala software
factory would be a good choice. xdlmapman, a gui frontend to it, used
to be part of ccp4.
--
Oh, sudde
Jacob,
So you'd have to explain why the codon convention is so
intolerant/invariant relative to the other features--it seems to me
that either it is at an optimum or there is some big barrier holding
it in place.
Because altering codon convention will result in massive translation errors.
Ho
On 03/19/2013 02:41 PM, Jacob Keller wrote:
I don't understand this argument, as it would apply equally to all
features of the theoretical LUCA
No it won't. Different features would have different tolerance levels
to modifications.
Philosophically, one is wrong to expect that living organism
Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri, 2013-03-15
Ian,
On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote:
> So I don't see there's a question of wilfully choosing to ignore. or
> not sampling certain factors: if the experiment is properly calibrated
> to get the SD estimate you can't ignore it.
>
So perhaps I can explain better by using the s
> OK. Other words, what is potentially removable error is always
> statistical error, whether it is sampled or not.
Clarification - what I meant is potentially removable by proper sampling
and reducing standard error to zero with infinite number of
measurements. Not removable by better calibrati
in a much more concise way!
> This random (uncontrollable) error then gets propagated through the
> sequence of steps in the experiment along with all the other
> uncontrollable errors.
>
> Cheers
>
>
> -- Ian
>
>
>
> On 11 March 2013 19:04, Ed Po
Kay,
> the latter is _not_ a systematic error; rather, you are sampling (once!) a
> statistical error component.
OK. Other words, what is potentially removable error is always
statistical error, whether it is sampled or not.
So is it fair to say that if there are some factors that I either d
Adam,
OK, seems like you are going with "it's always statistical error we just
don't yet know what it is" option.
Ed.
On Tue, 2013-03-12 at 16:15 +, Adam Ralph wrote:
> Hi Ed,
>
>
> You can have both types of error in a single experiment, however
> you cannot determine
> statistical
Pete,
> Actually, I was trying to say the opposite - that the decision to
> include something in the model (or not) could change the nature of the
> error.
Duly noted
> Pete
>
> PS - IIUC := ?
>
IIUC - If I Understand Correctly
--
Bullseye! Excellent shot, Maurice.
By the way, am I the only one who gets this thing with every post? If
anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his
mailbox or unsubscribe, that would be truly appreciated. Delete button
is easy and fun to use, but this has been going on for quite some time.
On Tue, 20
Pete,
On Mon, 2013-03-11 at 13:42 -0500, Pete Meyer wrote:
> My take on it is slightly different - the difference seems to be more
> on
> how the source of error is modeled (although that may dictate changes
> to
> the experiment) rather than essentially depending on how the
> experiment
> was
Ian,
thanks for the quick suggestion.
On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote:
> Personally I tend to avoid the systematic vs random error distinction
> and think instead in terms of controllable and uncontrollable errors:
> systematic errors are potentially under your control (given
Tim,
On Mon, 2013-03-11 at 18:51 +0100, Tim Gruene wrote:
> I don't share your opinion about a single measurement translating into
> a systematic error. I would call it a poorly designed experiment in
> case you were actually iterested in how accurately you determined the
> protein concentration.
Salve,
I would like to solicit opinions on a certain question about the
relationship between statistical and systematic error. Please read and
consider the following in its entirety before commenting.
Statistical error (experiment precision) is determined by the degree to
which experimental measu
Is there some way of opening a log file (specifically, the
pointandscale.log that imosflm bridge to scala generates) with qtrview
from command line?
I tried, of course, this
qtrview pointandscale.log
but it opens empty, no log-file. I tried qtrview -h and qtrview --help
and man qtrview but there
is worth checking by running the tests provided
with the suite. Aggressive optimization can be a source of bugs.
Best regards
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Monday, March 04, 2013 8:55 AM
To
On 03/04/2013 10:02 AM, Marcin Wojdyr wrote:
It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get after compiling refmac?
My numbers are not as impressive, but I also get quite detectable
improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
> Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
>
Numbers are almost too impressive to believe :)
How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free)
Indeed, the problem goes away when -static flag is omitted.
Interestingly, the resulting binary dependencies do not include any
ccp4-related libraries. For those interested, I was able to track the
segfault down to the close() operator - so basically it fails when
closing a file opened with ccpdpn
Adam,
On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote:
> One of the first routines called by CCP4
> progs is "ccp4fyp". This initialises the CCP4 environment.
I think you might have missed in my original post that I get an error
when I *do* source ccp4 environment.
>
> Does the error occur
Adam,
I am not compiling CCP4, just refmac. IIUC, all that sourcing
ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c
and libccp4f. And presumably lapack and libblas, but that's a separate
issue.
On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote:
> Hi Ed,
>
>
>It loo
I am trying to compile refmac from source on a machine running Ubuntu
12.04. In a nutshell, after some troubleshooting I end up with
executable that generates a segmentation fault. Log-file states that
>> CCP4 library signal ccp4_parser:Failed to open external command
file (Success)
We might have just found a new recurring discussion - what to do with insertion
codes! I am sure the opinion split is close to 50/50.
Personally, I don't think insertion codes make sense in the first place. Are
catalytic triad residues always the same distance from the N-terminus? No. The
resid
There should be many ways to do this. You can split the file, renumber with
pdbset, and then reassemble it. This may be useful
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Useful_scripts_(aka_smart_piece_of_code)
Cheers,
Ed
Original message
From: Amar Joshi
D
Maybe you can try different energies hoping that damage is wavelength
dependent. It must be dose dependent though, so you may consider merging short
sweeps from multiple crystals.
Original message
From: Uma Ratu
Date:
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] S-nitrosyl
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote:
> This is a 'compatability' option in Refmac that internally renames
> atoms. If you comment out 'MMA .C7 CM' in your
> mon_lib_list.cif file, the problem will disappear.
>
Robbie,
thanks a lot - this fixes it.
Is th
I see a strange issue with a model that includes O1-methyl-mannose
(three letter code MMA). Basically, refmac fails and says that C7 is
missing in the model while "CM" is absent from the library. The problem
is that there is no CM atom in the pdb file, while C7 is right there.
This happens wi
ry & Molecular Biology
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On Fri, 2013-02-08 at 09:57 -0500, Jacob Keller wrote:
> do you have a reference quickly on hand
http://www.ncbi.nlm.nih.gov/pubmed/8129868
and references therein
http://www.sciencedirect.com/science/article/pii/S0022024801010922
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300955/
The last r
On Fri, 2013-02-08 at 14:53 +0400, Evgeny Osipov wrote:
> Protein crystals behave rather as gelatine and not as solid
I'd have to disagree on that. Protein crystals are fragile but not
soft. If your crystals are like gelatine it's unusual. It has been
demonstrated that elastic properties of pro
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