Re: [ccp4bb] AI and cis-peptides

[Leiman, Petr G.]

> On Jul 13, 2023, at 8:12 AM, Randy John Read  wrote:
>
>
> External Email Warning: Do not click links or open attachments unless you 
> recognize the sender and expect the content. UTMB Email Phishing 
> Awareness
>
> I’m not sure about other methods, but AlphaFold does predict peptides in both 
> cis and trans configurations. In a recent paper, Osnat Herzberg and John 
> Moult show that it was pretty successful in predicting proline cis-peptides, 
> among the novel structures in the CASP15 set of targets 
> (https://www.pnas.org/doi/10.1073/pnas.2221745120).
>

Indeed, back in late 2020, at the CASP14 conference, Osnat showed that the 
AF-predicted model of her protein containing a cis-proline fit the X-ray map 
way better than the model that she built de novo with a trans-proline. 
Considering that these days many (most?) of us are working with 3A+ resolution 
cryoEM maps in which the conformation of the main chain is uncertain (main 
chain oxygen bumps are invisible), the question of trans/cis-prolines is 
omnipresent. Sometimes (most often?) it can be answered with the help of an AF 
model.

> For non-proline cis-peptides, I’m not aware of published work but Tristan 
> Croll has shown me examples of correctly-predicted non-proline cis-peptides, 
> including cases where some of the related structures in the PDB have an 
> incorrect trans configuration. This implies that AlphaFold is not slavishly 
> reproducing what it has seen during training.

Thank you for this note. This is another confirmation that these days we need 
to carefully examine all discrepancies between our de-novo built structures and 
AF models.

Petr Leiman


>
> Best wishes,
>
> Randy Read
>
>> On 13 Jul 2023, at 13:56, Oliviero Carugo  
>> wrote:
>>
>> Does anybody know if cis-peptides are predicted by the AI tools (AlphaFold2, 
>> ColabFold, or ESM-2)?
>>
>> 
>>
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>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road   E-mail: 
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.  
> www-structmed.cimr.cam.ac.uk
>
>
> 
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Re: [ccp4bb] iMosflm execution error

[Leiman Petr]

Dear Andy,

We have seen this error since forever on our Ubuntu boxes (I believe starting 
from ubuntu ver. 8.04). This is what the latest version of imosflm outputs on 
startup:
lbbspc2 ~  imosflm 
MOSFLM_EXEC set to /usr/local/lbbs/ccp4/current/bin/ipmosflm
[: 180: =: unexpected operator
testing MOSFLM_WISH (/usr/local/lbbs/ccp4/tcltk++/bin/wish)

but (!) this error never manifested itself in any program malfunction. 
imosflm seems to run just fine.

Sincerely,

Petr 


On Jan 28, 2011, at 8:44 PM, Andrew T. Torelli wrote:

 To the CCP4bb,
  
 I am working on installing the latest version of iMosflm (version 
 1.0.5) on my computer (running Ubuntu 10.10 (Meerkat).  I've followed the 
 installation instructions at the following link.  I also have CCP4 ver. 6.1 
 and ActiveTcl ver. 8.4.19.3 installed and working (as far as I know) as per 
 the instructions:
  
 http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver105/installation.html
 
 The only problem I encountered is that I had to correct pointers set 
 up by my CCP4 installation to the CCP4-packaged Tcl/Tk and iMosflm 
 components.  I believe I have corrected those problems and I am able to get 
 iMosflm loaded with no errors *as reported by the program*.  However, after 
 running the iMosflm executable, the following text is produced before the 
 iMosflm GUI is loaded:
  
 snip
  
 VM%  /usr/local/imosflm1.0.5/src/imosflm
 MOSFLM_EXEC set to /usr/local/imosflm1.0.5/bin/mosflm
 [: 180: =: unexpected operator
 testing MOSFLM_WISH (/usr/local/ActiveTcl8.4.19.3/bin/wish8.4)
  
 /snip
  
 I can't figure out what is generating this 'unexpected operator' 
 error or how to correct it.  I haven't recognized anything on the internet or 
 in the documentation to help me identify the source of the problem.  Can 
 anyone provide insight on how to trace its origin or what it means? I will 
 also test/confirm the ability to actually process data with the program later 
 tonight, but I'm just puzzled by this error.
  
 Thanks for your help and insight,
 -Andy
  
  
 =
 Andrew T. Torelli, Ph.D.
 Department of Chemistry  Chemical Biology
 Baker Laboratory, Cornell University
 Ithaca, NY 14853-1301
 =
  
  
  

Re: [ccp4bb] Strange spots

[Leiman Petr]

I think this is a poly-crystalline incommensurately modulated crystal, i.e.
incommensurately modulated crystal, which fractured upon freezing, resulting
in averaging of satellite spots.

Fig. 3b from here:
http://www.princeton.edu/~actin/documents/Proteincrystalscanbeincommensurate
lymodulated.pdf

Petr



On 10/29/10 6:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk
wrote:

 Dear All,
 
 Does anyone have any insight into what the circles around the spots
 might be?
 
 cheers
 
 Dave

Re: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

[Leiman Petr]

Dear Ed,

This libg2c:
http://dl.dropbox.com/u/3579334/libg2c.tgz
works with older scalepack versions requiring it. It is a 32 bit library and 
should run on 64 bit and 32 bit systems.

I have not tried the 699m version of HKL2000, but 699a and 699k2 segfault on my 
standard 64 bit Ubuntu (10.04.1) running on a 2 year old Dell Optiplex 960. 

Petr  


From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] on behalf of Edward A. Berry 
[ber...@upstate.edu]
Sent: Wednesday, October 20, 2010 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] what package provides libg2c.so.0 on Ubuntu ?

I'm helping set up crystallography programs on a ubuntu system, and we're
stuck because one program (scalepack) needs the library libg2c.so.0 .

I understand this is absent from modern distributions because gcc discontinued
support for g77 and f2c in recent releases. However on fedora there are
compatibility packages like compat-libf2c which allow running old executables
compiled with g77. Is something like this available for ubuntu? Or is there
some other trick to get scalepack running?
I understand ubuntu is used by many crystallographers, and while I'm sure
most of them use mosflm or XDS, I'm sure someone has tried setting up 
denzo/scalepack.

the system:
Linux x 2.6.31-22-generic #65-Ubuntu SMP Thu Sep 16 15:48:58 UTC 2010 i686 
GNU/Linux
gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1

Thanks,
eab

[ccp4bb] Fluorometers

[Leiman Petr]

Dear all,

Not a CCP4-related question, but there is no better informed group of people
out there.

We would like to buy a fluorometer equipped with a Peltier controlled sample
cell. We will measure Trp/Tyr fluorescence, but other groups will be using
the instrument for measuring fluorescence of DNA and various small molecule
fluorophores. 

There are basically three instruments (in about the same price range) we are
aware of: Fluoromax-4 (Horiba),  RF-5301 (Shimatzu),  FP-6300 (Jasco).

Any opinions on the above or related instruments are very welcome. On paper
the machines are very similar with Fluoromax-4 being the most sensitive and
the most expensive...

Please forward your opinions to me and if there is enough responses I will
post a summary.

Thank you very much,

Petr

---

Petr Leiman
EPFL
IPSB-LBBS
CH-1015, Lausanne
Suisse

Re: [ccp4bb] Coot cannot read mtz or pdb files

[Leiman Petr]

Many thanks to everybody who quickly replied to my cry for help. It is a
locale definition problem as the laptop in question is set up with the
French Swiss locale.

Cheers,

Petr

Re: [ccp4bb] Coot cannot read mtz or pdb files

[Leiman Petr]

Again, many thanks to all who responded. The simplest fix is to include this
line in your .profile file:

export LC_NUMERIC=C

Cheers,

Petr

[ccp4bb] ARP/wARP 7.1; ccp 6.1.13 and Mac OSX 10.6 (64bit fink)

[Leiman Petr]

Dear All,

My new Mac is affected by a bizarre software bug (or a feature), which has
been reported on this board earlier. In fact, it has been more than a year
since this problem was first reported, but it has not been resolved yet as
far as I can tell. Namely, it is not possible to add the ARP/wARP interface
into the CCP4I GUI of a ccp4 package compiled with 64bit fink (the /sw64
installation).  
The problem was described in detail by Klaas Max here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg10117.html
The problem came up again not so long ago:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17241.html

Well, the workaround is not pretty, but it does exist. One has to copy the
missing files from the installation in which the ARP/wARP CCP4I tasks are
installed properly.

One can install the 32bit version of fink (the /sw branch) and download
Bill Scott's precompiled CCP4 binaries (this will take some disk space, but
not much time). Switch to the 32bit environment (source /sw/bin/init.sh in a
new terminal window). Install ARP/wARP, apply the patch. Make sure that the
ARP/wARP tasks work in the CCP4I interface. Modify the .profile file to
source the ARP/wARP env variables.
 
Switch to the 64bit environment (source /sw64/bin/init.sh in a new terminal
window). Install ARP/wARP while in this terminal (not sure if this is needed
actually, probably not).

Then copy all the files from these directories:
/sw/share/xtal/ccp4-6.1.13/ccp4i/templates
/sw/share/xtal/ccp4-6.1.13/ccp4i/tasks
/sw/share/xtal/ccp4-6.1.13/ccp4i/scripts
to their 64bit equivalents /sw64/...

Then copy /sw/share/xtal/ccp4-6.1.13/ccp4i/etc/UNIX/modules.def to /sw64/...

That's it. Start ccp4i and the CCP4I GUI is supposed to show all the
ARP/wARP buttons at this point.

On a side note, the CCP4I DBviewer button does not work in the current CCP4I
interface because the directory with the DB is not where the button is
pointing. One has to make this symlink
ln -s $CCP4/share/dbccp4i $CCP4/share/mrbump/include/.
to restore the functionality of the CCP4I DBviewer button.

Cheers,

Petr

--
Petr Leiman
LBBS
EPFL
Cubotron/BSP-415
CH-1015, Lausanne
Switzerland

Re: [ccp4bb] Fitting high resolution structures to low resolution map

[Leiman Petr]

If it is a _true_ 4.5 A resolution map, you should be able to build 
alpha-helices and beta strands (can buccaneer do that automatically in at 
4.5A?) and then use these secondary structure elements to find your known 
structures.

Foldhunter from EMAN should be able to build helices and strands automatically. 
UCSF Chimera either comes with EMAN extensions or they can be added and one can 
run hunter directly in Chimera: http://ncmi.bcm.tmc.edu/software/AIRS

You can also try Situs: http://situs.biomachina.org/  If the map is good, Situs 
works like a charm.

Cheers,

Petr

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Peter Grey
Sent: Tuesday, March 30, 2010 12:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fitting high resolution structures to low resolution map

Dear All,

I have a crystal (not EM) density map of a very large complex at 4.5A 
resolution. I have pdb files for homologs of a few of the subunits of this huge 
complex. I would like to fit these homologs into the density. I have tried 
without success so far programs that handle phased molecular replacement - 
MOLREP, ESSENS and  FFFEAR.
Could you please suggest other programs or servers that can tackle this problem 
?

Many thanks,

Peter

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

[Leiman Petr]

 
 thanks so far for sharing your experience with Butanediol. But is it
 important to use a specific enantiomer ? Are you all only using 2R3R-
 Butanediol which is quite expensive ?

Sigma Cat. # 18970 
2,3-Butanediol puriss., mixture of racemic and meso forms, ≥99.0% (GC) (Fluka)  
works well and freezes clear.
And it's cheap!

We've used it recently to collect 1.6 A resolution data from a crystal with 
2000+ residues in the asymmetric unit.

Petr

Re: [ccp4bb] Projection of map?

[Leiman Petr]

 Dear CCP4ers,
 
 I want to calculate projections of an electron density map covering a
 molecule along arbitrary directions. Please note: I don't want to
 calculate the usual centric zone projections by using (h0l) zones and
 alike, but really work on the map. Which program can I use for that?

Use one of the 3D EM software packages such as EMAN or Spider (both read in 
CCP4 maps, and EMAN even maintains pixel size and other parameters)

EMAN:
http://blake.bcm.tmc.edu/eman/eman1/progs/project3d.html

Spider:
http://www.wadsworth.org/spider_doc/spider/docs/man/pj3q.html

Best,

Petr

---
Petr Leiman
Head of the Laboratory of Structural Biology and Biophysics
Institut de physique des systèmes biologiques 
École Polytechnique Fédérale de Lausanne (EPFL)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland
Phone: +41 21 69 30441
Mobile: +41 79 538 7647
Fax:+41 21 69 30422




 
 Best regards,
 
 Dirk.
 
 --
 
 ***
 Dirk Kostrewa
 Gene Center, A 5.07
 Ludwig-Maximilians-University
 Feodor-Lynen-Str. 25
 81377 Munich
 Germany
 Phone:+49-89-2180-76845
 Fax:  +49-89-2180-76999
 E-mail:   kostr...@genzentrum.lmu.de
 WWW:  www.genzentrum.lmu.de
 ***

Re: [ccp4bb] low UV reading on AKTA prime

[Leiman Petr]

Apologies for coming late with this comment, but this A280 filter clouding 
problem appears to be a common feature of the AKTA machines. The UV unit on 
these AKTAs is the same as on the old FPLC machines and the filters are 
interchangeable. The filters from the 10-20 year old FPLC machines fit 
perfectly into the AKTA UV unit and have a much longer life (15+ years) than 
the new GE-made filters.

Best,

Petr

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Patrick 
Loll
Sent: Wednesday, July 01, 2009 11:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] low UV reading on AKTA prime

I second Scott's post.  About the only problem we've had with our Akta 
instruments is this type of degradation of the filter. I'm not sure what the 
mechanism is, but the filters do seem to crap out after a while, at least in 
the cold room (oxidation? I have no idea of what the filter is made of...).

Pat

On 1 Jul 2009, at 5:07 PM, Scott Walsh wrote:


Hi Matt,

Check to make sure the A280 filter is clean.  Ours was filthy.  You might need 
to replace this (~$350).  We were experiencing the same thing you mentioned and 
just had the GE technician out today.  Also, make sure the A280 dial is set 
correctly on the lamp.  Please check the manual for guidance.

Best,

Scott

- Original Message -
From: Matt Colins matt.colins2...@yahoo.commailto:matt.colins2...@yahoo.com
Date: Wednesday, July 1, 2009 4:40 pm
Subject: [ccp4bb] low UV reading on AKTA prime
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK

 Hi all,

 We recently got low UV reading on our AKTA prime. We contacted
 GE healthcare, but was told that the UV reading on AKTA prime
 should be 20% of the spectrometer reading, because the path
 length of the flow cell of AKTA prime is only 2 mm (20% of the
 pathlength of a spectrometer cuvette).

 I am not sure whether that is the case, but we used to get much
 higher UV readings on the same AKTA prime (almost the same as
 the spectrometer reading). The UV reading just keeps dropping
 over time in the past several months.

 Here I have two questions. First,  should the UV reading on
 AKTA prime be 20% of the spectrometer reading? Second, what
 could go wrong with our AKTA prime? (I know it is not the lamp,
 because we put in a new lamp and it didn't solve the problem)

 Thanks a lot!
 Matt






---

Patrick J. Loll, Ph. D.

Professor of Biochemistry  Molecular Biology

Director, Biochemistry Graduate Program

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA  19102-1192  USA



(215) 762-7706

pat.l...@drexelmed.edumailto:pat.l...@drexelmed.edu

Re: [ccp4bb] phasing with se-met at low resolution

[Leiman Petr]

Dear Engin Ozkan,

You have told us how bad your crystals are, but you did not mention how good 
your anomalous signal is:
1. To what resolution does your anomalous signal extend and what statistic is 
used for this estimate?
2. Do your dispersive and Bijvoet Pattersons look similar and what is the 
measure of similarity?

This structure
http://www.pdb.org/pdb/explore/explore.do?structureId=1K28
which contains ~1100 residues in the asymmetric unit (and ~3500 in the entire 
complex),
was solved using a chimerical SeMet derivative, in which one protein was SeMet 
labeled (17 Se per a.u.) and the other was native.
The Semet dataset had a detectable anomalous signal to 4 A resolution (at 
most). The diffraction extended to 2.9A resolution.

Sincerely,

Petr


---
Petr Leiman
Institut de physique des systèmes biologiques 
École Polytechnique Fédérale de Lausanne (EPFL)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland




 -Original Message-
 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
 Engin Ozkan
 Sent: Sunday, May 10, 2009 11:01 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] phasing with se-met at low resolution
 
 Hi everyone,
 
 I thought I start a new thread while it is unusually quiet on the bb. I
 am pondering over the practical limitations to MAD and SAD phasing with
 Se-Met at low resolution. What is the lowest resolution at which people
 have solved structures only using phases from selenium in a
 realistic case? Let me further qualify my question:  My *realistic*
 *low* resolution case is where
 1.  Rmerge over all resolution bins is 6-10% (i.e. your crystals are
 lousy).
 2.  Resolution limit is worse than 3.5 Angstroms, where I/sigma in
 the last resolution bin is between 1 and 3 (i.e. your crystals are
 really lousy).
 3.  Assuming good selenium occupancy (~85%; I work with eukaryotic
 expression systems, so 100% is not usually achieavable),
 4.  The number of selenium atoms are enough many that the Crick-Magdoff
 equation would give you *at least* an average 5% change in intensities
 (assuming 6 electrons contributed per selenium, based on both
 absorptive
 and dispersive differences being at about 6 e- at the absorption edge).
 5.  and specifically, no other phases and molecular replacement
 solutions are available.
 
 Obviously, I have a case very similar to what's described above, and
 three years of failure with heavy atom derivatization (I am still
 trying). I would be happy to hear about Se-Met cases, and data
 collection strategies (2wl vs. 3wl MAD vs. SAD, etc.) and phasing
 methods used in these cases, or references of them. Again, no other
 partial phases, and no data cut off at 3.6 A with an I/s of 15 in the
 last resolution bin. Are there any examples out there? Searching the
 RCSB and PubMed did not point out to me many successful cases.
 
 Thanks,
 
 Engin
 
 P.S. I would also appreciate the specific query type for searching the
 PDB on the web for phasing method (MR, MAD, SAD, MIR, etc.).  They seem
 to have everything under the sun searchable, but I cannot find this
 one.

Re: [ccp4bb] Calculation of angle between two helix of different subunits

[Leiman Petr]

Every other week this question comes up!

This is Geometry 101 or beginner's geometry!!!
http://www.euclideanspace.com/maths/algebra/vectors/angleBetween/index.htm

I am not sure if it possible to understand _anything_ in crystallography if it 
is not clear how to calculate an angle between two vectors! 

Honestly,

Petr


From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of peter hudson 
[peter.hudson.pe...@gmail.com]
Sent: Wednesday, April 15, 2009 6:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of angle between two helix of different subunits

Hello all

I am interested to know about any programme which can calculate the angle 
between the helices of different subunit not the consecutive helices. I know 
about helixang which is a ccp4 supported programme but, i am not sure that does 
it calculate the relative angle between the two helix of different subunit in 
different orientation. Suggestiona would be appreciated.

Thnaks in advance
Peter