Re: [ccp4bb] MrBUMP in CCP4I2

[Christian Roth]

HI Derek,
I don't know which options you need, but there is the interactive task of
model preparation with mrbump and ccp4mg in the bioinformatic tasks, which
might allow what you want to do.

Cheers
Christian

On Thu, Oct 15, 2020 at 11:02 PM Derek Logan 
wrote:

> Hi all,
>
> I'm looking for some advice on MrBUMP. Is it possible to access MrBUMP via
> CCP4I2 with all the options it had in CCP4I? The options seem to have been
> drastically trimmed in CCP4I2. The reason I ask is that I have a tutorial
> that I've put a lot of work into over the years that involves the students
> solving the thaumatin structure using two different search models with
> higher and lower sequence identity, which involves specifying them
> individually. The advantage of using MrBUMP is that the students don't have
> to do a separate step with Chainsaw or Sculptor. What's more, we do one run
> with and one run without automated model building and refinement for each
> model to compare the final results. CCP4I2 doesn't seem to offer any of
> these options.
>
> Of course I can run the tutorial using CCP4I but I was trying to
> "modernise" it a bit.
>
> Any advice is welcome
> Derek
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Element type N+1

[Jon Cooper]

Hello Sam

thanks for the pictures. It looks like the guanidinium group of the first Arg 
is not very planar. I don't know the detailed nuts-and-bolts of how Coot and 
Refmac handle this but the problem may arise from the initial geometry at the 
affected nitrogen being off-target.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 16 Oct 2020, 06:57, Sam Tang wrote:

> Dear all
>
> I attach herewith the Arg concerned. I actually saw no issue in Coot when I 
> checked residue info. The issue was repeatable using both Refmac from Coot 
> and from CCP4i. I rectified the issue simply by changing "N+1" back to "N" 
> using a word editor, but would surely be glad to know more about the cause of 
> the problem.
>
> https://drive.google.com/file/d/137Q0CybNynOlI0R-b-3-OL2eWk7f6L2a/view?usp=sharing
>
> Best Regards
>
> Sam
>
> On Fri, 16 Oct 2020 at 00:51, Jon Cooper  wrote:
>
>> Hello, can you possibly show us a couple of screenshots with atom labels of 
>> the affected side chain and a normal one?
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>>  Original Message 
>> On 15 Oct 2020, 15:07, Sam Tang < samtys0...@gmail.com> wrote:
>>
>>> Dear colleagues
>>>
>>> I am trying to refine a structure with Refmac and the work completes 
>>> without any warning. However I am a bit puzzled for one single N atom on an 
>>> Arg residue the element type becomes N+1. This doesn't happen on my another 
>>> NCS chain and the input PDB seems fine. Could anyone kindly point me to the 
>>> possible cause?
>>>
>>> Thanks in advance!
>>>
>>> BRS
>>>
>>> Sam
>>>
>>> ---
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Windows binary for probe and reduce

[Reza Khayat]

?Hi,


Has anyone been able to compile a windows version (non cygwin) of probe and 
reduce? I'm asking for the windows version of coot.  Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Element type N+1

[Sam Tang]

Hello,

When I further refine my structure the N+1 is gone and it becomes a
normal N again. So it is very much possible this is related to geometry.
Thanks everyone (Esp. to Jon) for the input!

Sam


On Fri, 16 Oct 2020 at 19:31, Jon Cooper 
wrote:

> Hello Sam
>
> thanks for the pictures. It looks like the guanidinium group of the first
> Arg is not very planar. I don't know the detailed nuts-and-bolts of how
> Coot and Refmac handle this but the problem may arise from the initial
> geometry at the affected nitrogen being off-target.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
>
>
>
>
>  Original Message 
> On 16 Oct 2020, 06:57, Sam Tang < samtys0...@gmail.com> wrote:
>
>
> Dear all
>
> I attach herewith the Arg concerned. I actually saw no issue in Coot when
> I checked residue info. The issue was repeatable using both Refmac from
> Coot and from CCP4i. I rectified the issue simply by changing "N+1" back to
> "N" using a word editor, but would surely be glad to know more about the
> cause of the problem.
>
>
> https://drive.google.com/file/d/137Q0CybNynOlI0R-b-3-OL2eWk7f6L2a/view?usp=sharing
>
> Best Regards
>
> Sam
>
>
> On Fri, 16 Oct 2020 at 00:51, Jon Cooper 
> wrote:
>
>> Hello, can you possibly show us a couple of screenshots with atom labels
>> of the affected side chain and a normal one?
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>>
>>
>>
>>
>>  Original Message 
>> On 15 Oct 2020, 15:07, Sam Tang < samtys0...@gmail.com> wrote:
>>
>>
>> Dear colleagues
>>
>> I am trying to refine a structure with Refmac and the work completes
>> without any warning. However I am a bit puzzled for one single N atom on an
>> Arg residue the element type becomes N+1. This doesn't happen on my another
>> NCS chain and the input PDB seems fine. Could anyone kindly point me to the
>> possible cause?
>>
>> Thanks in advance!
>>
>> BRS
>>
>> Sam
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

Hi Christian,

Thanks for pointing out that option. I will definitely try it out. Perhaps my 
tutorial can be adapted to this way of making the models.

/Derek

On 16 Oct 2020, at 10:26, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:

HI Derek,
I don't know which options you need, but there is the interactive task of model 
preparation with mrbump and ccp4mg in the bioinformatic tasks, which might 
allow what you want to do.

Cheers
Christian

On Thu, Oct 15, 2020 at 11:02 PM Derek Logan 
mailto:derek.lo...@biochemistry.lu.se>> wrote:
Hi all,

I'm looking for some advice on MrBUMP. Is it possible to access MrBUMP via 
CCP4I2 with all the options it had in CCP4I? The options seem to have been 
drastically trimmed in CCP4I2. The reason I ask is that I have a tutorial that 
I've put a lot of work into over the years that involves the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of 
www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions 
are available at https://www.jiscmail.ac.uk/policyandsecurity/




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Looking for help to read 4mm data tape

[Xiong, Jian-Ping]

Sorry for an unrelated request.


One of my colleagues is trying to fill in the Table 1 from datasets collected 
~20 years ago. Unfortunately, the log files were saved on 4mm data tapes 
(2gb/4gb, I believe). We just couldn't find such old computer to read these 
tapes in our local areas, so would like to see whether someone in our community 
might still keep such old computer with 4mm tape drive and willing to help us 
out. The tapes are located in the United States. Thanks!
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Looking for help to read 4mm data tape

[Jon Cooper]

Hello, one of my favourite subjects. 4mm is DAT tape, I believe. You need to 
find out if they are VAX or unix tapes. There is a VAX DAT tape drive which I 
gave to Jeremy Cockcroft at UCL Chemistry last year - it definitely worked 
about 12 months ago and allowed an early 90's tape to be read. For unix, there 
is an SGI DAT tape drive in Jeremy's lab (also mine ;-) and there is an O2 in 
Medicine which still worked about 4 years ago. I think I'm not really allowed 
into UCL these days as visiting staff, etc, so I probably can't help much 
myself. I would recommend someone called Jim Cheoros who has a living room full 
of tape drives and does this sort of thing as a commercial service 
(dataconversion.co.uk, sorry Charles). You can plead academic poverty and he 
gives you about 50% discount which comes to about £50-£100 per tape. It sounds 
like a lot but it's very much less hassle than doing it yourself, esp. in 
current situation. You will find equivalent services in the US, etc.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 16 Oct 2020, 19:22, Xiong, Jian-Ping wrote:

> Sorry for an unrelated request.
>
> One of my colleagues is trying to fill in the Table 1 from datasets collected 
> ~20 years ago. Unfortunately, the log files were saved on 4mm data tapes 
> (2gb/4gb, I believe). We just couldn't find such old computer to read these 
> tapes in our local areas, so would like to see whether someone in our 
> community might still keep such old computer with 4mm tape drive and willing 
> to help us out. The tapes are located in the United States. Thanks!
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Mass General Brigham 
> Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
> the e-mail was sent to you in error but does not contain patient information, 
> please contact the sender and properly dispose of the e-mail.
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/