Re: [ccp4bb] Issue with CSO in Coot & Refmac

2023-05-29 Thread Keitaro Yamashita 
Dear Nick,

Sorry for this. Refmacat is a replacement for the refmac5 command, so
it is totally unfriendly to the people who never used Refmac as a
command. But it is great you managed to use it!

Best regards,
Keitaro

On Mon, 29 May 2023 at 22:11, Nicholas Clark  wrote:
>
> Keitaro,
>
> Please disregard my previous email. After informing myself on how Refmac is 
> executed from command line (via online websites & log files from GUI Refmac 
> runs) and many trial and error executions, I was able to execute refmac5 from 
> command line and was able to recycle the code for execution of refmacat.
>
> Best,
>
> Nick Clark
>
> On Mon, May 29, 2023 at 1:48 PM Nicholas Clark  wrote:
>>
>> Hi Keitaro,
>>
>> Thanks for the response. Is there documentation somewhere on how to run 
>> refmacat (like an example for Crystallographic data refinement, I found the 
>> one for CryoEM data but )? I have made multiple attempts to get this to run 
>> on my end but when I input the command I get "Waiting for input.." as a 
>> response and it just seems to hold here. I've tried this with multiple 
>> different iterations but even the simplest of just coordinates & reflections 
>> yields the same response. The command I'm running is, as a simplified 
>> example with only coordinates & reflections:
>>
>> refmacat XYXIN /location/for/coordinates.pdb HKLIN 
>> /location/for/reflections.mtz
>>
>> I've also tried passing a full list of the Refmac5 arguments but I still get 
>> a hold at "waiting for input". I'm sure I'm not passing something 
>> appropriately, but I'm not very familiar with running CCP4 programs on the 
>> command line. Any assistance would be appreciated!
>>
>> Interestingly, when I use the "LINK" and change the type to "peptide" in 
>> Coot only the linkage to the preceding residue is broken during refinement, 
>> the subsequent residue remains bonded. I can "circumvent" this issue by 
>> adding an alternate conformation to the preceding residue (i.e., both 
>> covalent linkages remain).
>>
>> Best,
>>
>> Nick Clark
>>
>> On Sat, May 27, 2023 at 4:03 PM Keitaro Yamashita 
>>  wrote:
>>>
>>> Because of non-standard atom names, group names of some monomers were
>>> changed to NON-POLYMER. In this case the hydrogen atom is only the
>>> problem, so changing group to peptide works unless you have hydrogen.
>>> Moreover, in CSO, the problematic hydrogen is removed when forming a
>>> peptide link. The details are described in the paper Paul mentioned.
>>>
>>> Refmac would work, if "refmacat" (explained in the paper) is used. The
>>> command is already available in the latest CCP4 update, but not from
>>> the interfaces at the moment.
>>>
>>> Best regards,
>>> Keitaro
>>>
>>> On Sat, 27 May 2023 at 04:02, Nicholas Clark  wrote:
>>> >
>>> > Hi Paul,
>>> >
>>> > Thank you for providing that information. Editing the restraints for CSO 
>>> > corrected the issue! Your assistance is greatly appreciated. I figured I 
>>> > was missing something :)
>>> >
>>> > Best,
>>> >
>>> > Nick Clark
>>> >
>>> > On Fri, May 26, 2023 at 10:55 PM Paul Emsley  
>>> > wrote:
>>> >>
>>> >>
>>> >> On 27/05/2023 03:46, Nicholas Clark wrote:
>>> >>
>>> >> Paul,
>>> >>
>>> >> Yes, it appears that the upper level group is "NON-POLYMER". However, 
>>> >> there is an alias at the bottom that does state polymer.
>>> >>
>>> >>
>>> >> Hi Nick,
>>> >>
>>> >>
>>> >> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to 
>>> >> "peptide" and press enter in the entry, then "Apply"
>>> >>
>>> >> Now you can refine your CSO in Coot.
>>> >>
>>> >> Paul.
>>> >>
>>> >>
>>> >>
>>> >> Best,
>>> >>
>>> >> Nick Clark
>>> >>
>>> >>
>>> >> On Fri, May 26, 2023 at 10:37 PM Paul Emsley  
>>> >> wrote:
>>> >>>
>>> >>>
>>> >>> On 27/05/2023 03:23, Nicholas Clark wrote:
>>> >>>
>>> >>> Hey Paul,
>>> >>>
>>> >>> I found the dictionary entry for CSO, it appears to be in the "peptide" 
>>> >>> group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
>>> >>>
>>> >>> "loop_
>>> >>> _chem_comp_alias.comp_id
>>> >>> _chem_comp_alias.group
>>> >>> _chem_comp_alias.atom_id
>>> >>> _chem_comp_alias.atom_id_standard
>>> >>> CSO peptide HN2 H2"
>>> >>>
>>> >>>  I've attached the file I have for your reference, as I may not be 
>>> >>> looking in the correct place. Also, if I'm looking in the wrong file 
>>> >>> location, please let me know.
>>> >>>
>>> >>>
>>> >>> Due to other priorities, Coot is not up to speed with the developments 
>>> >>> of my colleagues:
>>> >>>
>>> >>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=JXhA8CQjRF0V%2BMDfmIeegB%2Bc2rvKjT6dEofU7gcVjt4%3D=0
>>> >>>  (Section 2)
>>> >>>
>>> >>> What is the value of _chem_comp.group ? That

Re: [ccp4bb] Issue with CSO in Coot & Refmac

2023-05-29 Thread Nicholas Clark 
Keitaro,

Please disregard my previous email. After informing myself on how Refmac is
executed from command line (via online websites & log files from GUI Refmac
runs) and many trial and error executions, I was able to execute refmac5
from command line and was able to recycle the code for execution of
refmacat.

Best,

Nick Clark

On Mon, May 29, 2023 at 1:48 PM Nicholas Clark  wrote:

> Hi Keitaro,
>
> Thanks for the response. Is there documentation somewhere on how to run
> refmacat (like an example for Crystallographic data refinement, I found the
> one for CryoEM data but )? I have made multiple attempts to get this to run
> on my end but when I input the command I get "Waiting for input.." as a
> response and it just seems to hold here. I've tried this with multiple
> different iterations but even the simplest of just coordinates &
> reflections yields the same response. The command I'm running is, as a
> simplified example with only coordinates & reflections:
>
> refmacat XYXIN /location/for/coordinates.pdb HKLIN
> /location/for/reflections.mtz
>
> I've also tried passing a full list of the Refmac5 arguments but I still
> get a hold at "waiting for input". I'm sure I'm not passing something
> appropriately, but I'm not very familiar with running CCP4 programs on the
> command line. Any assistance would be appreciated!
>
> Interestingly, when I use the "LINK" and change the type to "peptide" in
> Coot only the linkage to the preceding residue is broken during refinement,
> the subsequent residue remains bonded. I can "circumvent" this issue by
> adding an alternate conformation to the preceding residue (i.e., both
> covalent linkages remain).
>
> Best,
>
> Nick Clark
>
> On Sat, May 27, 2023 at 4:03 PM Keitaro Yamashita <
> kyamash...@mrc-lmb.cam.ac.uk> wrote:
>
>> Because of non-standard atom names, group names of some monomers were
>> changed to NON-POLYMER. In this case the hydrogen atom is only the
>> problem, so changing group to peptide works unless you have hydrogen.
>> Moreover, in CSO, the problematic hydrogen is removed when forming a
>> peptide link. The details are described in the paper Paul mentioned.
>>
>> Refmac would work, if "refmacat" (explained in the paper) is used. The
>> command is already available in the latest CCP4 update, but not from
>> the interfaces at the moment.
>>
>> Best regards,
>> Keitaro
>>
>> On Sat, 27 May 2023 at 04:02, Nicholas Clark 
>> wrote:
>> >
>> > Hi Paul,
>> >
>> > Thank you for providing that information. Editing the restraints for
>> CSO corrected the issue! Your assistance is greatly appreciated. I figured
>> I was missing something :)
>> >
>> > Best,
>> >
>> > Nick Clark
>> >
>> > On Fri, May 26, 2023 at 10:55 PM Paul Emsley 
>> wrote:
>> >>
>> >>
>> >> On 27/05/2023 03:46, Nicholas Clark wrote:
>> >>
>> >> Paul,
>> >>
>> >> Yes, it appears that the upper level group is "NON-POLYMER". However,
>> there is an alias at the bottom that does state polymer.
>> >>
>> >>
>> >> Hi Nick,
>> >>
>> >>
>> >> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to
>> "peptide" and press enter in the entry, then "Apply"
>> >>
>> >> Now you can refine your CSO in Coot.
>> >>
>> >> Paul.
>> >>
>> >>
>> >>
>> >> Best,
>> >>
>> >> Nick Clark
>> >>
>> >>
>> >> On Fri, May 26, 2023 at 10:37 PM Paul Emsley <
>> pems...@mrc-lmb.cam.ac.uk> wrote:
>> >>>
>> >>>
>> >>> On 27/05/2023 03:23, Nicholas Clark wrote:
>> >>>
>> >>> Hey Paul,
>> >>>
>> >>> I found the dictionary entry for CSO, it appears to be in the
>> "peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
>> >>>
>> >>> "loop_
>> >>> _chem_comp_alias.comp_id
>> >>> _chem_comp_alias.group
>> >>> _chem_comp_alias.atom_id
>> >>> _chem_comp_alias.atom_id_standard
>> >>> CSO peptide HN2 H2"
>> >>>
>> >>>  I've attached the file I have for your reference, as I may not be
>> looking in the correct place. Also, if I'm looking in the wrong file
>> location, please let me know.
>> >>>
>> >>>
>> >>> Due to other priorities, Coot is not up to speed with the
>> developments of my colleagues:
>> >>>
>> >>>
>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=JXhA8CQjRF0V%2BMDfmIeegB%2Bc2rvKjT6dEofU7gcVjt4%3D=0
>> (Section 2)
>> >>>
>> >>> What is the value of _chem_comp.group ? That is (for the moment) what
>> Coot cares about.
>> >>>
>> >>>
>> >>> Paul.
>> >>>
>> >>>
>> >>
>> >>
>> >> --
>> >> Nicholas D. Clark (He/Him)
>> >> PhD Candidate
>> >> Malkowski Lab
>> >> University at Buffalo
>> >> Department of Structural Biology
>> >> Jacob's School of Medicine & Biomedical Sciences
>> >> 955 Main Street, RM 5130
>> >> Buffalo, NY 14203
>> >>
>> >> Cell: 716-830-1908
>> >>
>> >>

Re: [ccp4bb] Issue with CSO in Coot & Refmac

2023-05-29 Thread Nicholas Clark 
Hi Keitaro,

Thanks for the response. Is there documentation somewhere on how to run
refmacat (like an example for Crystallographic data refinement, I found the
one for CryoEM data but )? I have made multiple attempts to get this to run
on my end but when I input the command I get "Waiting for input.." as a
response and it just seems to hold here. I've tried this with multiple
different iterations but even the simplest of just coordinates &
reflections yields the same response. The command I'm running is, as a
simplified example with only coordinates & reflections:

refmacat XYXIN /location/for/coordinates.pdb HKLIN
/location/for/reflections.mtz

I've also tried passing a full list of the Refmac5 arguments but I still
get a hold at "waiting for input". I'm sure I'm not passing something
appropriately, but I'm not very familiar with running CCP4 programs on the
command line. Any assistance would be appreciated!

Interestingly, when I use the "LINK" and change the type to "peptide" in
Coot only the linkage to the preceding residue is broken during refinement,
the subsequent residue remains bonded. I can "circumvent" this issue by
adding an alternate conformation to the preceding residue (i.e., both
covalent linkages remain).

Best,

Nick Clark

On Sat, May 27, 2023 at 4:03 PM Keitaro Yamashita <
kyamash...@mrc-lmb.cam.ac.uk> wrote:

> Because of non-standard atom names, group names of some monomers were
> changed to NON-POLYMER. In this case the hydrogen atom is only the
> problem, so changing group to peptide works unless you have hydrogen.
> Moreover, in CSO, the problematic hydrogen is removed when forming a
> peptide link. The details are described in the paper Paul mentioned.
>
> Refmac would work, if "refmacat" (explained in the paper) is used. The
> command is already available in the latest CCP4 update, but not from
> the interfaces at the moment.
>
> Best regards,
> Keitaro
>
> On Sat, 27 May 2023 at 04:02, Nicholas Clark  wrote:
> >
> > Hi Paul,
> >
> > Thank you for providing that information. Editing the restraints for CSO
> corrected the issue! Your assistance is greatly appreciated. I figured I
> was missing something :)
> >
> > Best,
> >
> > Nick Clark
> >
> > On Fri, May 26, 2023 at 10:55 PM Paul Emsley 
> wrote:
> >>
> >>
> >> On 27/05/2023 03:46, Nicholas Clark wrote:
> >>
> >> Paul,
> >>
> >> Yes, it appears that the upper level group is "NON-POLYMER". However,
> there is an alias at the bottom that does state polymer.
> >>
> >>
> >> Hi Nick,
> >>
> >>
> >> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to
> "peptide" and press enter in the entry, then "Apply"
> >>
> >> Now you can refine your CSO in Coot.
> >>
> >> Paul.
> >>
> >>
> >>
> >> Best,
> >>
> >> Nick Clark
> >>
> >>
> >> On Fri, May 26, 2023 at 10:37 PM Paul Emsley 
> wrote:
> >>>
> >>>
> >>> On 27/05/2023 03:23, Nicholas Clark wrote:
> >>>
> >>> Hey Paul,
> >>>
> >>> I found the dictionary entry for CSO, it appears to be in the
> "peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
> >>>
> >>> "loop_
> >>> _chem_comp_alias.comp_id
> >>> _chem_comp_alias.group
> >>> _chem_comp_alias.atom_id
> >>> _chem_comp_alias.atom_id_standard
> >>> CSO peptide HN2 H2"
> >>>
> >>>  I've attached the file I have for your reference, as I may not be
> looking in the correct place. Also, if I'm looking in the wrong file
> location, please let me know.
> >>>
> >>>
> >>> Due to other priorities, Coot is not up to speed with the developments
> of my colleagues:
> >>>
> >>>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=JXhA8CQjRF0V%2BMDfmIeegB%2Bc2rvKjT6dEofU7gcVjt4%3D=0
> (Section 2)
> >>>
> >>> What is the value of _chem_comp.group ? That is (for the moment) what
> Coot cares about.
> >>>
> >>>
> >>> Paul.
> >>>
> >>>
> >>
> >>
> >> --
> >> Nicholas D. Clark (He/Him)
> >> PhD Candidate
> >> Malkowski Lab
> >> University at Buffalo
> >> Department of Structural Biology
> >> Jacob's School of Medicine & Biomedical Sciences
> >> 955 Main Street, RM 5130
> >> Buffalo, NY 14203
> >>
> >> Cell: 716-830-1908
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=muO6FI75NWneFDirpnv3BOUH3C%2Fat3VcNpUPKq0JIGI%3D=0
> >
> >
> >
> > --
> > Nicholas D. Clark (He/Him)

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2023-05-29 Thread Magnus Wolf-Watz 
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---
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Vice head of department (research strategies)
Chemistry Department
Linnaeusväg 10
Umeå University
90187 Umeå
Sweden

Cell-phone: 0768 262053
www.biostruct.umu.se/principal-investigators/magnus-wolf-watz/

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