Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-28 Thread Eleanor Dodson 
I am locked down and dont have access easily to the lsqkab code. Remind me
- if/when we are able to go to the University again! to check this..
I am sure you are right - lsqkab certainly predates TER records..
All the best Eleanor

On Tue, 28 Apr 2020 at 14:18, benjamin bax  wrote:

>
> Hi Eleanor,
>Thanks for fix.
>
> Sometimes I just superpose three atoms (making sure they are not in a
> straight line).
> But my atom superposition lsqkab script (below) - suggests that lsqkab has
> a different atom count than used ‘standardly’.
> Has anyone else found this problematic?
>
> Thanks, Ben
>
>
> cat lsq_compound_new.com
> #!/bin/sh
>
> set -e
> #
> # nb xyzin1 is reference structure - not moving.
> lsqkab xyzin2 ABITIO-p-nh-p-nometal.pdb xyzin1 1S16-on_mola_ndom.pdb \
> XYZOUT abit_nomet_on_1s16.pdb  \
> RMSTAB sub_suba_rms.tab  < # BE CAREFUL - USES OWN INTERNAL ATOM COUNT.
> # IN THIS EXAMPLE IT IS ONE OUT.
> # I THINK THIS IS BECAUSE TER RECORD IN PDB FILE
> # HAS AN ATOM NUMBER RECORD.
> # LSQ DOES NOT COUNT THIS AS AN ATOM - SO EVERYTHING
> # AFTER THIS IS ONE NUMBER OUT.
> #FIT ATOM 2 TO 2
> #MATCH ATOM 2957 TO 2957
> FIT ATOM 5 TO 5
> MATCH ATOM 2953 TO 2953
> FIT ATOM 6 TO 6
> MATCH ATOM 2954 TO 2954
> #FIT ATOM 9 TO 9
> # M#ATCH ATOM 2960 TO 2960
> FIT ATOM 3 TO 3
> MATCH ATOM 2955 TO 2955
> OUTPUT  RMS# ! output file RMSTAB with differences
> OUTPUT  XYZ# ! output file RMSTAB with differences
> END
> EOF
>
>
>
> On 28 Apr 2020, at 11:54, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote:
>
> I MEANT to upgrade lsqkab to accept DNA, and there is a small possibility
> that I did!
> Cheers Eleanor
>
> On Tue, 28 Apr 2020 at 11:52, Carter, Charlie  wrote:
>
>> In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think
>> Eleanor once told me I needed a different alternative for nucleic acids. If
>> this is no longer true, I’m happy to learn of it.
>>
>> Charlie
>>
>> On Apr 28, 2020, at 6:40 AM, benjamin bax > > wrote:
>>
>>
>> HI Fred,
>>
>>   I still use command line version of lsqkab to do this kind of DNA
>> fitting - script below only uses mainchain atoms (not bases) which helps if
>> you have different DNAs.
>> Chain E and F are DNA.
>>
>>Ben
>>
>> ./lsq-hinge-6fqv-bin-EV-B.com  >
>> lsq-hinge-6fqv-bin-EV-B.log
>>
>>
>> cat lsq-hinge-6fqv-bin-EV-B.com 
>> #!/bin/sh
>>
>> set -e
>> # Obtain NCS rotation/translation relating CHAIN R to CHAIN S
>> #
>> # nb xyzin1 is reference structure - not moving.
>> lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \
>> XYZOUT binaryB-on-3-6E-15-18F.pdb  \
>> RMSTAB test1.tab  <> #
>> #  DNA fit two strands - trying for just backbone.
>> #
>> FIT RESIDUE MAIN 3 TO 6 CHAIN E
>> MATCH RESIDUE MAIN 3 TO 6 CHAIN E
>> FIT RESIDUE MAIN 15 TO 18 CHAIN F
>> MATCH RESIDUE MAIN 15 TO 18 CHAIN F
>> OUTPUT  RMS# ! output file RMSTAB with differences
>> OUTPUT  XYZ# ! output file RMSTAB with differences
>> END
>> EOF
>>
>> On 24 Apr 2020, at 12:08, Fred. Vellieux > > wrote:
>>
>> Hi folks,
>>
>> Some of you may have had to do this already. Either in the lab or more
>> recently perhaps from home.
>>
>> I have two structures that I wish to superpose (two protein:dsDNA
>> complexes). Not using the protein part, but superposition through the dsDNA.
>>
>> I'm not quite certain what is the "best" way of doing this.
>>
>> Your suggestions will be appreciated, thanks.
>>
>> Fred. Vellieux
>>
>> --
>> MedChem, 1st F. Medicine, Charles University
>> BIOCEV, Vestec, Czech Republic
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
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>>
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>
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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-28 Thread benjamin bax 

Hi Eleanor,
   Thanks for fix.

Sometimes I just superpose three atoms (making sure they are not in a straight 
line).
But my atom superposition lsqkab script (below) - suggests that lsqkab has a 
different atom count than used ‘standardly’. 
Has anyone else found this problematic?

Thanks, Ben 
  

cat lsq_compound_new.com 
#!/bin/sh 

set -e
# 
# nb xyzin1 is reference structure - not moving. 
lsqkab xyzin2 ABITIO-p-nh-p-nometal.pdb xyzin1 1S16-on_mola_ndom.pdb \
XYZOUT abit_nomet_on_1s16.pdb  \
RMSTAB sub_suba_rms.tab  < wrote:

I MEANT to upgrade lsqkab to accept DNA, and there is a small possibility that 
I did!
Cheers Eleanor

On Tue, 28 Apr 2020 at 11:52, Carter, Charlie mailto:car...@med.unc.edu>> wrote:
In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think 
Eleanor once told me I needed a different alternative for nucleic acids. If 
this is no longer true, I’m happy to learn of it.

Charlie
> On Apr 28, 2020, at 6:40 AM, benjamin bax  > wrote:
> 
> 
> HI Fred, 
> 
>   I still use command line version of lsqkab to do this kind of DNA fitting - 
> script below only uses mainchain atoms (not bases) which helps if you have 
> different DNAs.
> Chain E and F are DNA. 
> 
>Ben 
> 
> ./lsq-hinge-6fqv-bin-EV-B.com  > 
> lsq-hinge-6fqv-bin-EV-B.log
> 
> 
> cat lsq-hinge-6fqv-bin-EV-B.com  
> #!/bin/sh 
> 
> set -e
> # Obtain NCS rotation/translation relating CHAIN R to CHAIN S
> # 
> # nb xyzin1 is reference structure - not moving. 
> lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \
> XYZOUT binaryB-on-3-6E-15-18F.pdb  \
> RMSTAB test1.tab  < # 
> #  DNA fit two strands - trying for just backbone. 
> # 
> FIT RESIDUE MAIN 3 TO 6 CHAIN E
> MATCH RESIDUE MAIN 3 TO 6 CHAIN E
> FIT RESIDUE MAIN 15 TO 18 CHAIN F
> MATCH RESIDUE MAIN 15 TO 18 CHAIN F
> OUTPUT  RMS# ! output file RMSTAB with differences
> OUTPUT  XYZ# ! output file RMSTAB with differences
> END
> EOF
> 
> On 24 Apr 2020, at 12:08, Fred. Vellieux  > wrote:
> 
> Hi folks,
> 
> Some of you may have had to do this already. Either in the lab or more 
> recently perhaps from home.
> 
> I have two structures that I wish to superpose (two protein:dsDNA complexes). 
> Not using the protein part, but superposition through the dsDNA.
> 
> I'm not quite certain what is the "best" way of doing this.
> 
> Your suggestions will be appreciated, thanks.
> 
> Fred. Vellieux
> 
> -- 
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
> 
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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-28 Thread Eleanor Dodson 
I MEANT to upgrade lsqkab to accept DNA, and there is a small possibility
that I did!
Cheers Eleanor

On Tue, 28 Apr 2020 at 11:52, Carter, Charlie  wrote:

> In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think
> Eleanor once told me I needed a different alternative for nucleic acids. If
> this is no longer true, I’m happy to learn of it.
>
> Charlie
>
> On Apr 28, 2020, at 6:40 AM, benjamin bax  > wrote:
>
>
> HI Fred,
>
>   I still use command line version of lsqkab to do this kind of DNA
> fitting - script below only uses mainchain atoms (not bases) which helps if
> you have different DNAs.
> Chain E and F are DNA.
>
>Ben
>
> ./lsq-hinge-6fqv-bin-EV-B.com  >
> lsq-hinge-6fqv-bin-EV-B.log
>
>
> cat lsq-hinge-6fqv-bin-EV-B.com 
> #!/bin/sh
>
> set -e
> # Obtain NCS rotation/translation relating CHAIN R to CHAIN S
> #
> # nb xyzin1 is reference structure - not moving.
> lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \
> XYZOUT binaryB-on-3-6E-15-18F.pdb  \
> RMSTAB test1.tab  < #
> #  DNA fit two strands - trying for just backbone.
> #
> FIT RESIDUE MAIN 3 TO 6 CHAIN E
> MATCH RESIDUE MAIN 3 TO 6 CHAIN E
> FIT RESIDUE MAIN 15 TO 18 CHAIN F
> MATCH RESIDUE MAIN 15 TO 18 CHAIN F
> OUTPUT  RMS# ! output file RMSTAB with differences
> OUTPUT  XYZ# ! output file RMSTAB with differences
> END
> EOF
>
> On 24 Apr 2020, at 12:08, Fred. Vellieux  > wrote:
>
> Hi folks,
>
> Some of you may have had to do this already. Either in the lab or more
> recently perhaps from home.
>
> I have two structures that I wish to superpose (two protein:dsDNA
> complexes). Not using the protein part, but superposition through the dsDNA.
>
> I'm not quite certain what is the "best" way of doing this.
>
> Your suggestions will be appreciated, thanks.
>
> Fred. Vellieux
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
> --
>
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>
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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-28 Thread Carter, Charlie 
In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think 
Eleanor once told me I needed a different alternative for nucleic acids. If 
this is no longer true, I’m happy to learn of it.

Charlie
On Apr 28, 2020, at 6:40 AM, benjamin bax 
mailto:ben.d.v@gmail.com>> wrote:


HI Fred,

  I still use command line version of lsqkab to do this kind of DNA fitting - 
script below only uses mainchain atoms (not bases) which helps if you have 
different DNAs.
Chain E and F are DNA.

   Ben

./lsq-hinge-6fqv-bin-EV-B.com > 
lsq-hinge-6fqv-bin-EV-B.log


cat lsq-hinge-6fqv-bin-EV-B.com
#!/bin/sh

set -e
# Obtain NCS rotation/translation relating CHAIN R to CHAIN S
#
# nb xyzin1 is reference structure - not moving.
lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \
XYZOUT binaryB-on-3-6E-15-18F.pdb  \
RMSTAB test1.tab  > wrote:

Hi folks,

Some of you may have had to do this already. Either in the lab or more recently 
perhaps from home.

I have two structures that I wish to superpose (two protein:dsDNA complexes). 
Not using the protein part, but superposition through the dsDNA.

I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-28 Thread benjamin bax 

HI Fred, 

  I still use command line version of lsqkab to do this kind of DNA fitting - 
script below only uses mainchain atoms (not bases) which helps if you have 
different DNAs.
Chain E and F are DNA. 

   Ben 

./lsq-hinge-6fqv-bin-EV-B.com > lsq-hinge-6fqv-bin-EV-B.log


cat lsq-hinge-6fqv-bin-EV-B.com 
#!/bin/sh 

set -e
# Obtain NCS rotation/translation relating CHAIN R to CHAIN S
# 
# nb xyzin1 is reference structure - not moving. 
lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \
XYZOUT binaryB-on-3-6E-15-18F.pdb  \
RMSTAB test1.tab  < wrote:

Hi folks,

Some of you may have had to do this already. Either in the lab or more recently 
perhaps from home.

I have two structures that I wish to superpose (two protein:dsDNA complexes). 
Not using the protein part, but superposition through the dsDNA.

I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

-- 
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Paul Emsley 
@Tim: The infrastructure is already in place. Use user-defined-click 
with 6 clicks, then use add-lsq-atom-pair for each atom extracted from 
the clicks, then apply-lsq-matches. 10 lines of code or thereabouts.  
Exercise for the reader :-)


user-define-click is used in the acedrg-link interface if you want to 
see it in use.


To answer Fred's question, I think he was after the equivalent of gesamt 
for DNA. I don't think that that exists, so I don't know a better way 
than using LSQ. Worthy of mention though is lsq-improve - that might be 
what Fred wants, I've not tried it on DNA.



Paul.


On 24/04/2020 13:33, Tim Gruene wrote:

Hallo Fred,

lsqman (Uppsala software factory) is another option. With lsqman you
can give explicit atom names, so that it works e.g. even for small
molecule structures that do not follow PDB conventions.

@Paul Emsley: a graphical option that let's you e.g. click on 2x3
corresponding atoms in Coot would come very handy ;-)

Best,
Tim

On Fri, 24 Apr 2020 13:08:26 +0200
"Fred. Vellieux"  wrote:


Hi folks,

Some of you may have had to do this already. Either in the lab or
more recently perhaps from home.

I have two structures that I wish to superpose (two protein:dsDNA
complexes). Not using the protein part, but superposition through the
dsDNA.

I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux








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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Tim Gruene 
Hallo Fred,

lsqman (Uppsala software factory) is another option. With lsqman you
can give explicit atom names, so that it works e.g. even for small
molecule structures that do not follow PDB conventions.

@Paul Emsley: a graphical option that let's you e.g. click on 2x3
corresponding atoms in Coot would come very handy ;-)

Best,
Tim

On Fri, 24 Apr 2020 13:08:26 +0200
"Fred. Vellieux"  wrote:

> Hi folks,
> 
> Some of you may have had to do this already. Either in the lab or
> more recently perhaps from home.
> 
> I have two structures that I wish to superpose (two protein:dsDNA 
> complexes). Not using the protein part, but superposition through the 
> dsDNA.
> 
> I'm not quite certain what is the "best" way of doing this.
> 
> Your suggestions will be appreciated, thanks.
> 
> Fred. Vellieux
> 



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Anat Bashan 
Hi Fred,


Quite the same as Chimera, can be done in COOT.

Calculate ->  LSQ superimpose. Specify for each PDB files to be superimposed 
the chains and residue range you wish to superimpose.


Hope this helps,

Anat.

 =

Anat Bashan , Ph.D  Tel:972-8-9344289

@The Ribosome Group

The Weizmann Institute of Science   Fax:972-8-9344154

The Department of Structural BiologyMobile:972-52-3347229

Rehovot7610001  
 e-mail: anat.bas...@weizmann.ac.il<mailto:anat.bas...@weizmann.ac.il>

<mailto:anat.bas...@weizmann.ac.il>Israel

=











From: CCP4 bulletin board  on behalf of Barone, Matthias 

Sent: Friday, April 24, 2020 2:27:53 PM
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] superimposition of 3D structures with the DNA part only


Hi Fred

Chimera let's you choose to selectively superpose chains of one entry onto a 
selective chain of the second. The easiest way is to assign the dsDNA into a 
separate chain before loading the pdb (if this is not already the case).

If you want to selectively superpose only certain atoms of one with the other 
pdb, I use a program called moloc to do a rigid body match. It's not too 
intuitive to work with but has a lot of advantages when moving and comparing 
complex structures.

Best, Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Fred. Vellieux 

Sent: Friday, April 24, 2020 1:08:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] superimposition of 3D structures with the DNA part only

Hi folks,

Some of you may have had to do this already. Either in the lab or more
recently perhaps from home.

I have two structures that I wish to superpose (two protein:dsDNA
complexes). Not using the protein part, but superposition through the
dsDNA.

I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Barone, Matthias 
Hi Fred

Chimera let's you choose to selectively superpose chains of one entry onto a 
selective chain of the second. The easiest way is to assign the dsDNA into a 
separate chain before loading the pdb (if this is not already the case).

If you want to selectively superpose only certain atoms of one with the other 
pdb, I use a program called moloc to do a rigid body match. It's not too 
intuitive to work with but has a lot of advantages when moving and comparing 
complex structures.

Best, Matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Fred. Vellieux 

Sent: Friday, April 24, 2020 1:08:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] superimposition of 3D structures with the DNA part only

Hi folks,

Some of you may have had to do this already. Either in the lab or more
recently perhaps from home.

I have two structures that I wish to superpose (two protein:dsDNA
complexes). Not using the protein part, but superposition through the
dsDNA.

I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Fred. Vellieux 

Hi folks,

Some of you may have had to do this already. Either in the lab or more 
recently perhaps from home.


I have two structures that I wish to superpose (two protein:dsDNA 
complexes). Not using the protein part, but superposition through the 
dsDNA.


I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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