Re: [ccp4bb] NCS axis detrmination

[Zhijie Li]

Hi Vandna,

Assuming you have two copies, chain A and B.

In UCSF chimera:

1) open two copies of the pdb (model #0 and #1)
2) in command line, type:

match   #1:.B@CA   #0:.A@CA showMatrix true

Besides moving model #1 chain B to model #0 chain A, the match command 
also outputs the rotation and translation matrices and angles, axes in 
Favorite-> Reply Log.


Note that you might need to specify residue number range for the two 
chains if the number of CAs in them are not equal - just to make the 
match working. The match command does not guess the range of residues to 
align as the MatchMaker does. Alt confs involving CAs also count. You 
may run:


del @CA.B

to delete all alt conf B CA atoms before the match command to make it 
working



If you wish to draw the rotation axis in Chimera, you need to make a 
bild file  that draws an arrow from the "Axis point" with direction 
specified by the Axis vector. Assuming the "Axis" is "Ax Ay Az" and the 
"Axis point" is "x y z", you need to calculate X1=x+Ax*20,  Y1=y+Ay*20, 
Z1=z+Az*20, then put this  in the arrow.bld file:


.arrow x y z X1 Y1 Z1

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html


COOT also outputs the matrices in the terminal window. But COOT does not 
seem to directly show the more human friendly "rotation angle" and 
"shift along axis".


Zhijie



On 29/06/2017 3:16 PM, Vands wrote:

Hi  every one ,
I am looking for a tool to perfectly determine 
the NCS axis. I have two forms of crystals where diamer is with NCS 
but on a comparison of both forms, it looks like NCS axis is little 
off when i superpose two forms, i would like to measure rotation or 
translation between axes .



--
Vandna Kukshal
Senior Scientist
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

[Jared Sampson]

Thanks to Dave, Tristan and David for the suggestions.  

The code Tristan posted is similar to what I had been thinking about doing, and 
probably will do in the future, although not being familiar with ChimeraX, I'll 
likely end up using Biopython.  

For this particular round, for expediency (and since it's been a while since I 
really used Biopython), I just went through the file residue-by-residue, in 
brute-force fashion using grep and Vim.  It wasn't as bad as I initially 
thought.

First I got a list of the side chain hydrogens in question:

grep -E "HD1 HIS|HE2 HIS" my_structure.pdb > his.txt

Then for each His residue, I checked the text file to se whether HD1 or HE2 or 
both were present, and modified the residue code with a substitution in Vim:

:%s /HIS A 251/HIP A 251/
etc.

It only took me about 15 minutes to do this for His/Asp/Glu for 2 PDBs, which 
is somewhat faster than I could have re-learned how to do it in one of the 
(clearly more appropriate) scripting languages.  Not exactly elegant, but it 
got the job done.  Of course, if it looks like I'll have to do this more 
frequently in the future, I'll likely go the scripting route next time.

Thanks everyone!

Cheers,
Jared

 

> On Jun 29, 2017, at 4:46 AM, Tristan Croll  wrote:
> 
> This can be done in a few lines of script in any structural biology package 
> that provides a Python (or other) shell. Here's how I'd do it in ChimeraX, 
> for example:
> 
> Assuming your model is the only one loaded and atom names are all standard:
> 
> m = session.models.list()[0]
> histidines = m.residues.filter(m.residues.names == 'HIS')
> for his in histidines:
>names = his.atoms.names
>he2 = 'HE2' in names
>hd1 = 'HD1' in names
>if hd1 and not he2:
>his.name = 'HID'
>elif he2 and not hd1:
>his.name = 'HIE'
>elif hd1 and he2:
>his.name = 'HIP'
>else:
>raise RuntimeError('HIS {}:{} is missing both hydrogens!'.format(
>h.chain_id, h.number))
> 
> Cheers,
> 
> Tristan
> 
> On 2017-06-29 07:09, Briggs, David C wrote:
>> I believe the ProPka or Pdb2pqr webservers can do this.
>> ProPka.org 
>> http:// [1]nbcr [1]-222.ucsd.edu/pdb2pqr_2.0.0/ 
>>  [1]
>> HTH,
>> Dave
>> --
>> Dr David C Briggs
>> Hohenester Lab
>> Department of Life Sciences
>> Imperial College London
>> UK
>> http://about.me/david_briggs  [2]
>> -
>> FROM: CCP4 bulletin board  on behalf of
>> Sampson, Jared 
>> SENT: Wednesday, June 28, 2017 11:34:05 PM
>> TO: CCP4BB@JISCMAIL.AC.UK
>> SUBJECT: [ccp4bb] Correcting 3-letter codes based on protonation
>> states in a PDB file
>> Dear all -
>> I'm working with a PDB file with explicit hydrogens where many of the
>> histidines are in protonated form due to crystallization at low pH.
>> Unfortunately, although the additional protons are present in the
>> model for the positively charged histidines, the residues in question
>> are indicated in both the SEQRES and the ATOM records as 3-letter code
>> `HIS` regardless of protonation state (i.e. instead of `HIP` for
>> positively charged, and `HID` or `HIE` for the neutral tautomers).
>> Are there existing tools available to determine the proper 3-letter
>> residue code for titratable amino acid residues based on which
>> hydrogens are present, and output a corrected PDB file?
>> Thank you in advance for your suggestions.
>> Cheers,
>> Jared Sampson
>> Ph.D. Candidate
>> Columbia University
>> Links:
>> --
>> [1] http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ 
>> 
>> [2] http://about.me/david_briggs 

[ccp4bb] Postdoctoral Position in Biophysical Studies of Neuronal Membrane Proteins at Yale University

[Singh, Satinder Kaur]

JOB DESCRIPTION
A postdoctoral position at Yale University School of Medicine is available 
immediately for highly motivated, creative individuals with a strong interest 
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biology (macromolecular crystallography and cryoEM) and HDX-MS 
(hydrogen-deuterium exchange mass spectrometry) in nanoscale lipid bilayers.

The laboratory is located in renovated space in the Department of Cellular and 
Molecular Physiology in a highly collaborative environment. We have 
state-of-the art facilities for expression, purification, reconstitution, and 
functional characterization of membrane proteins. The lab also has regular 
access to Waters Synapt G2 Q-TOF mass spectrometers equipped with an 
HDX-enabled NANO UPC.


JOB REQUIREMENTS
Candidates must hold (or soon expect to hold) a recent Ph.D. (less than 1 year) 
in biochemistry, biophysics, or related field with at least some expertise in 
HDX-MS (as evidenced by publications in the field), and have an excellent 
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protein expression, purification, and biochemical/biophysical characterization 
is required. Applicants with experience in membrane proteins, nanodiscs, some 
structural biology, and HDX-MS are preferred. A creative approach to developing 
new functional assays and an ability to troubleshoot experimental obstacles are 
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collaborative team.

The candidate must have an excellent command of oral and written English. In 
addition to compiling and analyzing data, s/he will be responsible for 
providing assistance in preparation of materials for publications and grant 
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For more information, please contact me via email.
Additional contact information is given below:

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Associate Professor of Cellular and Molecular Physiology
Yale University School of Medicine
333 Cedar Street, SHM B147
Lab room # SHM BE11/17
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Office #: 203-737-6477
Fax#: 203-785-4951

Website: https://medicine.yale.edu/physiology/faculty/satinder_k_singh-2.profile

Thank you.

Kind regards,
Satinder

[ccp4bb] NCS axis detrmination

[Vands]

Hi  every one ,
I am looking for a tool to perfectly determine the
NCS axis. I have two forms of crystals where diamer is with NCS but on a
comparison of both forms, it looks like NCS axis is little off when
i superpose two forms, i would like to measure rotation or translation
between axes .


-- 
Vandna Kukshal
Senior Scientist
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

[Robbie Joosten]

Hi Pavel,

Similar results in PDB-REDO https://pdb-redo.eu/db/5xql, nothing wrong but 
clear room for improvement. That said, I would hope that the epositors set the 
record straight on the data completeness or conjur up the missing reflection 
data.

Cheers,
Robbie

Sent from my Windows 10 phone

Van: Pavel Afonine
Verzonden: donderdag 29 juni 2017 20:23
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] Questionable Data collection and refinement statistics 
for 5XQL

I agree with Dominika, I can't see major problems with this entry (I also did 
some quick refinement and briefly looked at maps). Reported R factors match 
re-calculated values using data from PDB, which is good.

Smaller issues I see are:
- no solvent (water) in the model, while density suggests some;
- maps don't look like 2.5A resolution, which is perfectly expectable given 
data completeness (overall 81%):

  ResolutionCompl
35.051-13.721   89.38
13.660-11.061   95.19
11.024-8.85898.41
 8.848-7.119   100.00
 7.115-5.723   100.00
 5.714-4.596   100.00
 4.595-3.692   100.00
 3.692-2.96795.92
 2.966-2.49456.98

and effective resolution along axes a,b,c:  2.453  2.453  3.167 A.

- model contains 4% of rotamer outliers, some of them can be trivially fixed.
- Xtriage shows three yellow "traffic lights".

I'm sure many PDB entries (especially older ones) would have something that you 
could do better or fix using modern tools.

Pavel

On Thu, Jun 29, 2017 at 10:48 AM, Dominika Borek 
> wrote:
Dear C-Daddy,

Did you look at the maps? Do you see any astonishing misinterpretations there?
Do you think that the completeness in the last resolution shell would affect 
the maps and the model? If so, why?

There are many possible reasons for the discrepancy you pointed out. In I422 
a=b, alpha=90.00, so typos in the table are the most probable reason. I did 
look at the maps after running a quick refinement. Both the structure and the 
ligand are fine. I would probably add solvent molecules myself, but some 
conservative crystallographers prefer not to do it, even at 2.5 A.

In other words, there is nothing wrong with this deposit. I would even say that 
the level of sloppiness is below the average for this one.

D.




On 2017-06-29 11:07 AM, CDaddy wrote:
Dear colleagues,

I am really astonished by a recently released structure 5XQL. This
structure was just published in BBRC with a super fast process
(accepted overnight). Significant inconsistences were observed when I
compared the Data collection and refinement statistics in the paper
and at PDB website. The paper shows the crystal belong to  I 4 2 2
with  a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is
2.5Å with  completeness of 99.7 (99.1). However when I checked the
released structure I got  a= b=135.94, c=95.13 (Å) ; α=90.0. The
resolution is 2.5Å with  completeness of 81.5 (44.0). The
completeness of the highest resolution shell is so low that 2.5Å
seems unreasonable. At first I thought that the authors could be
rookies in structural biology. But the molecular replacement in this
paper could be very difficult due to very low sequence identity
between the search model and the final structure. It was unlikely that
two new hands could solve it easily. Is there anyone who has this kind
of experience and know why?

With best wishes,
Richard

--
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

[Pavel Afonine]

I agree with Dominika, I can't see major problems with this entry (I also
did some quick refinement and briefly looked at maps). Reported R factors
match re-calculated values using data from PDB, which is good.

Smaller issues I see are:
- no solvent (water) in the model, while density suggests some;
- maps don't look like 2.5A resolution, which is perfectly expectable given
data completeness (overall 81%):

  ResolutionCompl
35.051-13.721   89.38
13.660-11.061   95.19
11.024-8.85898.41
 8.848-7.119   100.00
 7.115-5.723   100.00
 5.714-4.596   100.00
 4.595-3.692   100.00
 3.692-2.96795.92
 2.966-2.49456.98

and effective resolution along axes a,b,c:  2.453  2.453  3.167 A.

- model contains 4% of rotamer outliers, some of them can be trivially
fixed.
- Xtriage shows three yellow "traffic lights".

I'm sure many PDB entries (especially older ones) would have something that
you could do better or fix using modern tools.

Pavel

On Thu, Jun 29, 2017 at 10:48 AM, Dominika Borek 
wrote:

> Dear C-Daddy,
>
> Did you look at the maps? Do you see any astonishing misinterpretations
> there?
> Do you think that the completeness in the last resolution shell would
> affect the maps and the model? If so, why?
>
> There are many possible reasons for the discrepancy you pointed out. In
> I422 a=b, alpha=90.00, so typos in the table are the most probable reason.
> I did look at the maps after running a quick refinement. Both the structure
> and the ligand are fine. I would probably add solvent molecules myself, but
> some conservative crystallographers prefer not to do it, even at 2.5 A.
>
> In other words, there is nothing wrong with this deposit. I would even say
> that the level of sloppiness is below the average for this one.
>
> D.
>
>
>
>
> On 2017-06-29 11:07 AM, CDaddy wrote:
>
>> Dear colleagues,
>>
>> I am really astonished by a recently released structure 5XQL. This
>> structure was just published in BBRC with a super fast process
>> (accepted overnight). Significant inconsistences were observed when I
>> compared the Data collection and refinement statistics in the paper
>> and at PDB website. The paper shows the crystal belong to  I 4 2 2
>> with  a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is
>> 2.5Å with  completeness of 99.7 (99.1). However when I checked the
>> released structure I got  a= b=135.94, c=95.13 (Å) ; α=90.0. The
>> resolution is 2.5Å with  completeness of 81.5 (44.0). The
>> completeness of the highest resolution shell is so low that 2.5Å
>> seems unreasonable. At first I thought that the authors could be
>> rookies in structural biology. But the molecular replacement in this
>> paper could be very difficult due to very low sequence identity
>> between the search model and the final structure. It was unlikely that
>> two new hands could solve it easily. Is there anyone who has this kind
>> of experience and know why?
>>
>> With best wishes,
>> Richard
>>
>
> --
> Dominika Borek, Ph.D. *** UT Southwestern Medical Center
> 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
> 214-645-9577 (phone) *** 214-645-6353 (fax)
>

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

[Dominika Borek]

Dear C-Daddy,

Did you look at the maps? Do you see any astonishing misinterpretations 
there?
Do you think that the completeness in the last resolution shell would 
affect the maps and the model? If so, why?


There are many possible reasons for the discrepancy you pointed out. In 
I422 a=b, alpha=90.00, so typos in the table are the most probable 
reason. I did look at the maps after running a quick refinement. Both 
the structure and the ligand are fine. I would probably add solvent 
molecules myself, but some conservative crystallographers prefer not to 
do it, even at 2.5 A.


In other words, there is nothing wrong with this deposit. I would even 
say that the level of sloppiness is below the average for this one.


D.



On 2017-06-29 11:07 AM, CDaddy wrote:

Dear colleagues,

I am really astonished by a recently released structure 5XQL. This
structure was just published in BBRC with a super fast process
(accepted overnight). Significant inconsistences were observed when I
compared the Data collection and refinement statistics in the paper
and at PDB website. The paper shows the crystal belong to  I 4 2 2
with  a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is
2.5Å with  completeness of 99.7 (99.1). However when I checked the
released structure I got  a= b=135.94, c=95.13 (Å) ; α=90.0. The
resolution is 2.5Å with  completeness of 81.5 (44.0). The
completeness of the highest resolution shell is so low that 2.5Å
seems unreasonable. At first I thought that the authors could be
rookies in structural biology. But the molecular replacement in this
paper could be very difficult due to very low sequence identity
between the search model and the final structure. It was unlikely that
two new hands could solve it easily. Is there anyone who has this kind
of experience and know why?

With best wishes,
Richard


--
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)

[ccp4bb] Questionable Data collection and refinement statistics for 5XQL

[CDaddy]

Dear colleagues,


I am really astonished by a recently released structure 5XQL. This structure 
was just published in BBRC with a super fast process (accepted overnight). 
Significant inconsistences were observed when I compared the Data collection 
and refinement statistics in the paper and at PDB website. The paper shows the 
crystal belong to  I 4 2 2 with  a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The 
resolution is 2.5Å with  completeness of 99.7 (99.1). However when I checked 
the released structure I got  a= b=135.94, c=95.13 (Å) ; α=90.0. The resolution 
is 2.5Å with  completeness of 81.5 (44.0). The completeness of the highest 
resolution shell is so low that 2.5Å seems unreasonable. At first I thought 
that the authors could be rookies in structural biology. But the molecular 
replacement in this paper could be very difficult due to very low sequence 
identity between the search model and the final structure. It was unlikely that 
two new hands could solve it easily. Is there anyone who has this kind of 
experience and know why?


With best wishes,
Richard

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

[Tristan Croll]

This can be done in a few lines of script in any structural biology 
package that provides a Python (or other) shell. Here's how I'd do it in 
ChimeraX, for example:


Assuming your model is the only one loaded and atom names are all 
standard:


m = session.models.list()[0]
histidines = m.residues.filter(m.residues.names == 'HIS')
for his in histidines:
names = his.atoms.names
he2 = 'HE2' in names
hd1 = 'HD1' in names
if hd1 and not he2:
his.name = 'HID'
elif he2 and not hd1:
his.name = 'HIE'
elif hd1 and he2:
his.name = 'HIP'
else:
raise RuntimeError('HIS {}:{} is missing both 
hydrogens!'.format(

h.chain_id, h.number))

Cheers,

Tristan

On 2017-06-29 07:09, Briggs, David C wrote:

I believe the ProPka or Pdb2pqr webservers can do this.

 ProPka.org

 http:// [1]nbcr [1]-222.ucsd.edu/pdb2pqr_2.0.0/ [1]

 HTH,

 Dave

 --

 Dr David C Briggs

 Hohenester Lab

 Department of Life Sciences

 Imperial College London

 UK

 http://about.me/david_briggs [2]

-

FROM: CCP4 bulletin board  on behalf of
Sampson, Jared 
 SENT: Wednesday, June 28, 2017 11:34:05 PM
 TO: CCP4BB@JISCMAIL.AC.UK
 SUBJECT: [ccp4bb] Correcting 3-letter codes based on protonation
states in a PDB file

Dear all -

 I'm working with a PDB file with explicit hydrogens where many of the
histidines are in protonated form due to crystallization at low pH.
Unfortunately, although the additional protons are present in the
model for the positively charged histidines, the residues in question
are indicated in both the SEQRES and the ATOM records as 3-letter code
`HIS` regardless of protonation state (i.e. instead of `HIP` for
positively charged, and `HID` or `HIE` for the neutral tautomers).

 Are there existing tools available to determine the proper 3-letter
residue code for titratable amino acid residues based on which
hydrogens are present, and output a corrected PDB file?

 Thank you in advance for your suggestions.

 Cheers,

 Jared Sampson
 Ph.D. Candidate
 Columbia University

Links:
--
[1] http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
[2] http://about.me/david_briggs

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

[Briggs, David C]

I believe the ProPka or Pdb2pqr webservers can do this.

ProPka.org

http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

HTH,

Dave

--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs


From: CCP4 bulletin board  on behalf of Sampson, Jared 

Sent: Wednesday, June 28, 2017 11:34:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Correcting 3-letter codes based on protonation states in a 
PDB file

Dear all -

I'm working with a PDB file with explicit hydrogens where many of the 
histidines are in protonated form due to crystallization at low pH.  
Unfortunately, although the additional protons are present in the model for the 
positively charged histidines, the residues in question are indicated in both 
the SEQRES and the ATOM records as 3-letter code `HIS` regardless of 
protonation state (i.e. instead of `HIP` for positively charged, and `HID` or 
`HIE` for the neutral tautomers).

Are there existing tools available to determine the proper 3-letter residue 
code for titratable amino acid residues based on which hydrogens are present, 
and output a corrected PDB file?

Thank you in advance for your suggestions.

Cheers,

Jared Sampson
Ph.D. Candidate
Columbia University